Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:45 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 865/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
gmapR 1.47.0 (landing page) Michael Lawrence
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the gmapR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gmapR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: gmapR |
Version: 1.47.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gmapR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gmapR_1.47.0.tar.gz |
StartedAt: 2024-08-26 21:39:42 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 21:42:55 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 193.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: gmapR.Rcheck |
Warnings: 7 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gmapR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gmapR_1.47.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/gmapR.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘gmapR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘gmapR’ version ‘1.47.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... WARNING Found the following files with non-portable file names: src/gmap/config/lt~obsolete.m4 src/gstruct/config/lt~obsolete.m4 These are not fully portable file names. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for sufficient/correct file permissions ... OK * checking whether package ‘gmapR’ can be installed ... WARNING Found the following significant warnings: WARNING: You don't seem to have gsnap specified. iit-read.c:1611:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:1611:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:1638:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:1638:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:1650:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:1650:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:1672:21: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:1672:28: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:1693:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:1693:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:1742:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:1742:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:1779:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:1779:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:1834:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:1834:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2344:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2344:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2360:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2360:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2372:12: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2372:19: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2381:12: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2381:19: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2408:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2408:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2429:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2429:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2446:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2446:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2466:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2466:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2495:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2495:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2608:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2608:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2626:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2626:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2643:12: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2643:19: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2652:12: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2652:19: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2681:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2681:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2702:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2702:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2719:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2719:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2744:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2744:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2770:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2770:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2823:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:2823:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:3010:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:3010:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:3026:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:3026:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:3043:12: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:3043:19: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:3052:12: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:3052:19: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:3081:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:3081:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:3107:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:3107:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:3124:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:3124:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:3149:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:3149:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:3175:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:3175:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:3220:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read.c:3220:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-write.c:113:17: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] iit-write.c:113:53: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] univinterval.c:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] access.c:358:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] access.c:358:15: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] access.c:423:11: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] access.c:493:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] access.c:556:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] access.c:641:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] iit-read-univ.c:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] compress-write.c:73:80: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] compress-write.c:252:13: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] compress-write.c:300:13: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] genome.c:10292:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] genome.c:10292:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] genome.c:10392:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] genome.c:10392:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] genome-write.c:253:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] genome-write.c:253:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] genome-write.c:256:15: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] genome-write.c:256:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] genome-write.c:430:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] genome-write.c:430:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] genome-write.c:433:15: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] genome-write.c:433:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] genome-write.c:595:87: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] genome-write.c:595:104: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] genome-write.c:595:119: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] genome-write.c:595:137: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] genome-write.c:643:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] genome-write.c:643:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] genome-write.c:646:15: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] genome-write.c:646:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] genome-write.c:787:46: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] indexdb.c:1363:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] indexdb.c:1483:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] indexdb.c:1653:63: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] indexdb.c:1792:6: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] indexdb.c:1792:30: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] indexdb.c:1934:76: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] indexdb.c:2026:76: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] pair.c:2419:24: warning: taking the absolute value of unsigned type 'Chrpos_T' (aka 'unsigned int') has no effect [-Wabsolute-value] pair.c:4651:17: warning: taking the absolute value of unsigned type 'Chrpos_T' (aka 'unsigned int') has no effect [-Wabsolute-value] stage2.c:1329:19: warning: taking the absolute value of unsigned type 'Chrpos_T' (aka 'unsigned int') has no effect [-Wabsolute-value] stage2.c:1812:19: warning: taking the absolute value of unsigned type 'Chrpos_T' (aka 'unsigned int') has no effect [-Wabsolute-value] getopt.c:208:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt.c:291:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt.c:376:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt.c:389:28: warning: passing arguments to 'getenv' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt.c:498:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt.c:1179:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] ./getopt.h:147:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent definition [-Wdeprecated-non-prototype] getopt1.c:71:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt1.c:87:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] ./getopt.h:147:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a previous declaration [-Wdeprecated-non-prototype] gmap.c:3244:28: warning: incompatible pointer types passing 'Diagpool_T' (aka 'struct Diagpool_T *') to parameter of type 'Cellpool_T' (aka 'struct Cellpool_T *') [-Wincompatible-pointer-types] gmap.c:3244:37: warning: incompatible pointer types passing 'Cellpool_T' (aka 'struct Cellpool_T *') to parameter of type 'Diagpool_T' (aka 'struct Diagpool_T *') [-Wincompatible-pointer-types] univinterval.c:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] iit-read-univ.c:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] compress-write.c:73:80: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] compress-write.c:252:13: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] compress-write.c:300:13: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] genome.c:10292:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] genome.c:10292:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] genome.c:10392:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] genome.c:10392:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] genome_sites.c:24729:17: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] genome_sites.c:24744:19: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] genome_sites.c:24751:17: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] genome-write.c:253:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] genome-write.c:253:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] genome-write.c:256:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] genome-write.c:256:32: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] genome-write.c:430:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] genome-write.c:430:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] genome-write.c:433:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] genome-write.c:433:32: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] genome-write.c:595:87: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] genome-write.c:595:104: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] genome-write.c:595:119: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] genome-write.c:595:137: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] genome-write.c:643:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] genome-write.c:643:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] genome-write.c:646:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] genome-write.c:646:32: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] genome-write.c:787:46: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] indexdb_hr.c:1008:43: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] indexdb_hr.c:1232:45: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] segmentpos.c:90:41: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] pair.c:546:25: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] pair.c:573:25: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] pair.c:600:25: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] pair.c:607:25: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] pair.c:1273:3: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] pair.c:1278:3: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] pair.c:1790:25: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] pair.c:1790:52: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] pair.c:1799:27: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] pair.c:1799:54: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] pair.c:1913:26: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] pair.c:1913:53: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] pair.c:1922:28: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] pair.c:1922:55: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] pair.c:6986:24: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] pair.c:6986:51: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] splicetrie_build.c:132:31: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] splicetrie_build.c:146:33: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] parserange.c:187:8: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] parserange.c:187:35: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] parserange.c:187:40: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] get-genome.c:194:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] get-genome.c:194:40: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] get-genome.c:410:41: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] get-genome.c:410:78: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] get-genome.c:428:41: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] get-genome.c:428:67: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] iit-write-univ.c:93:17: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] iit-write-univ.c:93:53: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] bitpack64-write.c:4146:38: warning: passing 'const UINT4 *' (aka 'const unsigned int *') to parameter of type 'Positionsptr_T *' (aka 'unsigned int *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] indexdb-write.c:2495:3: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] indexdb-write.c:2495:10: warning: format specifies type 'int' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] indexdb-write.c:2495:12: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] indexdb-write.c:2727:8: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] indexdb-write.c:2738:8: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] indexdb-write.c:2761:3: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] indexdb-write.c:2788:6: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] indexdb-write.c:2799:6: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] indexdb-write.c:2888:59: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] indexdb-write.c:2895:101: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] indexdb-write.c:2972:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] indexdb-write.c:3094:79: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] indexdb-write.c:3127:101: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] indexdb-write.c:3171:102: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] indexdb-write.c:3234:85: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] indexdb-write.c:3246:85: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] indexdb-write.c:3371:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] indexdb-write.c:3601:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] indexdb-write.c:3796:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] indexdb-write.c:3823:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] indexdb-write.c:3838:45: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] indexdb-write.c:3865:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] indexdb-write.c:3892:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] indexdb-write.c:3907:45: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] table.c:283:18: warning: passing 'const void **' to parameter of type 'void **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers] gmapindex.c:305:64: warning: format specifies type 'unsigned long *' but the argument has type 'Univcoord_T *' (aka 'unsigned long long *') [-Wformat] gmapindex.c:510:19: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] gmapindex.c:510:31: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] gmapindex.c:521:17: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] gmapindex.c:521:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] gmapindex.c:696:22: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] gmapindex.c:696:39: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] gmapindex.c:701:22: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] gmapindex.c:701:39: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] gmapindex.c:1061:54: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] iit-write.c:92:17: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] iit-write.c:92:53: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] iit_store.c:371:51: warning: format specifies type 'unsigned long *' but the argument has type 'Univcoord_T *' (aka 'unsigned long long *') [-Wformat] iit_store.c:371:61: warning: format specifies type 'unsigned long *' but the argument has type 'Univcoord_T *' (aka 'unsigned long long *') [-Wformat] iit_store.c:596:46: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] iit_store.c:597:62: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] iit_store.c:598:67: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] iit_get.c:619:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] iit_get.c:619:50: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] uint8list.c:202:28: warning: format specifies type 'unsigned int' but the argument has type 'UINT8' (aka 'unsigned long long') [-Wformat] uint8list.c:205:25: warning: format specifies type 'unsigned int' but the argument has type 'UINT8' (aka 'unsigned long long') [-Wformat] uint8list.c:211:28: warning: format specifies type 'unsigned int' but the argument has type 'UINT8' (aka 'unsigned long long') [-Wformat] uint8list.c:214:25: warning: format specifies type 'unsigned int' but the argument has type 'UINT8' (aka 'unsigned long long') [-Wformat] substring.c:1005:33: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] substring.c:1005:50: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] substring.c:3536:35: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] substring.c:3537:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] substring.c:3539:35: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] substring.c:3540:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] substring.c:3544:35: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] substring.c:3545:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] substring.c:3547:35: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] substring.c:3548:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] sarray-read.c:302:15: warning: incompatible pointer types assigning to 'UINT4 *' (aka 'unsigned int *') from 'Univcoord_T *' (aka 'unsigned long long *') [-Wincompatible-pointer-types] sarray-read.c:368:15: warning: incompatible pointer types assigning to 'UINT4 *' (aka 'unsigned int *') from 'Univcoord_T *' (aka 'unsigned long long *') [-Wincompatible-pointer-types] sarray-read.c:434:15: warning: incompatible pointer types assigning to 'UINT4 *' (aka 'unsigned int *') from 'Univcoord_T *' (aka 'unsigned long long *') [-Wincompatible-pointer-types] sarray-read.c:526:15: warning: incompatible pointer types assigning to 'UINT4 *' (aka 'unsigned int *') from 'Univcoord_T *' (aka 'unsigned long long *') [-Wincompatible-pointer-types] sarray-read.c:653:15: warning: incompatible pointer types assigning to 'UINT4 *' (aka 'unsigned int *') from 'Univcoord_T *' (aka 'unsigned long long *') [-Wincompatible-pointer-types] sarray-read.c:1667:53: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] sarray-read.c:1682:56: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] sarray-read.c:2170:11: warning: incompatible pointer types assigning to 'Univcoord_T *' (aka 'unsigned long long *') from 'UINT4 *' (aka 'unsigned int *') [-Wincompatible-pointer-types] sarray-read.c:2442:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] sarray-read.c:2442:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] sarray-read.c:2456:34: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] sarray-read.c:2499:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] sarray-read.c:2499:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] sarray-read.c:2513:10: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] sarray-read.c:2643:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] sarray-read.c:2643:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] sarray-read.c:2656:36: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] sarray-read.c:2699:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] sarray-read.c:2699:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] sarray-read.c:2712:12: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] sarray-read.c:2752:11: warning: incompatible pointer types assigning to 'Univcoord_T *' (aka 'unsigned long long *') from 'UINT4 *' (aka 'unsigned int *') [-Wincompatible-pointer-types] sarray-read.c:3024:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] sarray-read.c:3024:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] sarray-read.c:3038:34: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] sarray-read.c:3082:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] sarray-read.c:3082:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] sarray-read.c:3096:10: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] sarray-read.c:3217:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] sarray-read.c:3217:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] sarray-read.c:3231:34: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] sarray-read.c:3274:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] sarray-read.c:3274:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] sarray-read.c:3288:10: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] stage1hr.c:6630:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] stage1hr.c:6630:40: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] stage1hr.c:6630:76: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] stage1hr.c:6769:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] stage1hr.c:6769:37: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] stage1hr.c:6770:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] stage1hr.c:6770:40: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] stage1hr.c:6771:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] stage1hr.c:7146:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] stage1hr.c:7146:40: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] stage1hr.c:7146:76: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] stage1hr.c:7285:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] stage1hr.c:7285:40: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] stage1hr.c:7285:76: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] snpindex.c:889:75: warning: format specifies type 'unsigned long' but the argument has type 'UINT8' (aka 'unsigned long long') [-Wformat] snpindex.c:1143:71: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] snpindex.c:1270:66: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] See ‘/Users/biocbuild/bbs-3.20-bioc/meat/gmapR.Rcheck/00install.out’ for details. * checking installed package size ... NOTE installed size is 73.4Mb sub-directories of 1Mb or more: R 1.4Mb extdata 5.5Mb usr 65.8Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: Initial release (start date: 12 September, 2012) * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘AnnotationDbi’ Unexported objects imported by ':::' calls: ‘BiocGenerics:::testPackage’ ‘S4Vectors:::labeledLine’ ‘S4Vectors:::new_SimpleList_from_list’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE checkTallyConsistency: no visible binding for global variable ‘count.plus’ checkTallyConsistency: no visible binding for global variable ‘count.minus’ checkTallyConsistency: no visible binding for global variable ‘count.plus.ref’ checkTallyConsistency: no visible binding for global variable ‘count.minus.ref’ fieldNames: no visible global function definition for ‘R_iit_fieldNames’ newGmapAlignerParam: ... may be used in an incorrect context: ‘list(...)’ open.IITFile: no visible binding for global variable ‘R_iit_read’ open.IITFile: no visible global function definition for ‘resource’ typeNames: no visible global function definition for ‘R_iit_typeNames’ variantSummary: no visible binding for global variable ‘count.total’ variantSummary: no visible binding for global variable ‘count.ref’ variantSummary: no visible binding for global variable ‘count’ import,IITFile-ANY-ANY: no visible global function definition for ‘checkArgFormat’ import,IITFile-ANY-ANY: no visible binding for global variable ‘R_iit_read’ snps<-,GmapSnpDirectory-character-VCF: no visible global function definition for ‘rowData’ Undefined global functions or variables: R_iit_fieldNames R_iit_read R_iit_typeNames checkArgFormat count count.minus count.minus.ref count.plus count.plus.ref count.ref count.total resource rowData * checking Rd files ... WARNING checkRd: (5) GmapGenome-class.Rd:30-56: \item in \describe must have non-empty label checkRd: (5) GmapGenome-class.Rd:62-67: \item in \describe must have non-empty label checkRd: (5) GmapGenome-class.Rd:73-77: \item in \describe must have non-empty label checkRd: (5) GmapGenome-class.Rd:83-85: \item in \describe must have non-empty label checkRd: (5) GmapGenome-class.Rd:86-89: \item in \describe must have non-empty label checkRd: (5) GmapGenome-class.Rd:90: \item in \describe must have non-empty label checkRd: (5) GmapGenome-class.Rd:91-93: \item in \describe must have non-empty label checkRd: (5) GmapGenomeDirectory-class.Rd:24-28: \item in \describe must have non-empty label checkRd: (5) GmapGenomeDirectory-class.Rd:33: \item in \describe must have non-empty label checkRd: (5) GmapGenomeDirectory-class.Rd:34-35: \item in \describe must have non-empty label checkRd: (5) GmapSnps-class.Rd:35: \item in \describe must have non-empty label checkRd: (5) GmapSnps-class.Rd:36-38: \item in \describe must have non-empty label checkRd: (5) GsnapOutput-class.Rd:24-30: \item in \describe must have non-empty label checkRd: (5) GsnapOutput-class.Rd:31-36: \item in \describe must have non-empty label * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘GmapParam’ ‘gmap’ Undocumented S4 classes: ‘GmapParam’ ‘GmapAlignerParam’ Undocumented S4 methods: generic 'as.character' and siglist 'GmapGenomeDirectory' generic 'bamPaths' and siglist 'GmapAlignerOutput' generic 'gmap' and siglist 'ANY,GmapParam' generic 'gmap' and siglist 'FastaFile,GmapParam' generic 'gmap' and siglist 'character,GmapParam' generic 'path' and siglist 'GmapAlignerOutput' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... WARNING Found the following file(s) containing GNU extensions: src/Makefile Portable Makefiles do not use GNU extensions such as +=, :=, $(shell), $(wildcard), ifeq ... endif, .NOTPARALLEL See section ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking include directives in Makefiles ... OK * checking compiled code ... WARNING Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/libs/gmapR.so’: Found ‘___sprintf_chk’, possibly from ‘sprintf’ (C) Found ‘___stderrp’, possibly from ‘stderr’ (C) Found ‘_abort’, possibly from ‘abort’ (C) Found ‘_exit’, possibly from ‘exit’ (C) Found ‘_printf’, possibly from ‘printf’ (C) Found ‘_putchar’, possibly from ‘putchar’ (C) Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C) Found ‘_sprintf’, possibly from ‘sprintf’ (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘gmapR_unit_tests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 7 WARNINGs, 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/gmapR.Rcheck/00check.log’ for details.
gmapR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gmapR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘gmapR’ ... ** using staged installation ** libs cd gstruct/; \ CFLAGS="-g -O3" \ ./configure --enable-static --disable-shared \ --prefix=/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr --includedir=/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/include/gstruct \ --libdir=/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/lib \ --with-samtools-lib=/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/samtools \ --disable-maintainer-mode \ --disable-binaries checking package version... 2017-01-01 checking whether to enable maintainer-specific portions of Makefiles... no loading default site script ./config.site checking CFLAGS... -g -O3 checking build system type... arm-apple-darwin22.6.0 checking host system type... arm-apple-darwin22.6.0 checking target system type... arm-apple-darwin22.6.0 checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... rm: conftest.dSYM: is a directory yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... config/install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking for style of include used by make... GNU checking whether make supports nested variables... yes checking dependency style of gcc... gcc3 checking bindir... /Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/bin checking whether to link statically... not specified so disabled by default checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 786432 checking how to convert arm-apple-darwin22.6.0 file names to arm-apple-darwin22.6.0 format... func_convert_file_noop checking how to convert arm-apple-darwin22.6.0 file names to toolchain format... func_convert_file_noop checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... no checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dsymutil... dsymutil checking for nmedit... nmedit checking for lipo... lipo checking for otool... otool checking for otool64... no checking for -single_module linker flag... ld: warning: -single_module is obsolete no checking for -exported_symbols_list linker flag... yes checking for -force_load linker flag... yes checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... yes checking for gcc option to produce PIC... -fno-common -DPIC checking if gcc PIC flag -fno-common -DPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin22.6.0 dyld checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking for X... libraries /usr/X11/lib, headers /usr/X11/include checking whether -R must be followed by a space... neither works checking for gethostbyname... yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... yes checking for qsub... no checking gmap program directory... checking for get-genome... false checking for iit_store... false checking for iit_get... false checking for gmap_build... false checking for gmap... false checking for gsnap... false checking for sam_sort... false checking for uniqscan... false checking for rint in -lm... yes checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... -D_THREAD_SAFE checking for cc_r... gcc checking for ANSI C header files... (cached) yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 8 checking size of unsigned long long... 8 checking size of off_t... 8 checking for _LARGEFILE_SOURCE value needed for large files... no checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... yes checking for sigaction... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... yes checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for builtin popcount/clz/ctz features... not specified so enabled by default ./configure: line 16919: ACX_BUILTIN_POPCOUNT: command not found checking for bsr instruction in assembly... no checking whether sse2 is enabled... not specified so enabled by default checking compiler is defective and requires an immediate in sse2 shift commands... yes checking whether ssse3 is enabled... not specified so enabled by default checking whether sse4.1 is enabled... not specified so enabled by default checking whether sse4.2 is enabled... not specified so enabled by default checking whether avx is enabled... not specified so enabled by default checking whether avx2 is enabled... not specified so enabled by default checking whether simd is enabled... not specified so enabled by default checking gmapdb... /Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share checking whether to make binaries... disabled checking for zlib support... enabled checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for gzopen in -lz... yes checking for gzeof in -lz... yes checking for gzgetc in -lz... yes checking for gzgets in -lz... yes checking for gzclose in -lz... yes checking if zlib package is complete... working checking for gzbuffer in -lz... yes checking for samtools program... checking for samtools library... provided by --with-samtools-lib checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating lib/gstruct-1.0.pc config.status: creating src/config.h config.status: executing depfiles commands config.status: executing libtool commands configure: WARNING: WARNING: You don't seem to have gsnap specified. checking Standard compiler and flags to be used... gcc -g -O3 checking Standard linker flags to be used... checking pthread compiler flags to be used... -D_THREAD_SAFE checking popcnt compiler flags to be used... checking SIMD features available on computer... checking SIMD compiler flags to be used... clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/include -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bgzf.c -o samtools/bgzf.o samtools/bgzf.c:412:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable] int i, tmp, stop = 0; ^ samtools/bgzf.c:592:11: warning: variable 'count' set but not used [-Wunused-but-set-variable] int ret, count, block_length; ^ samtools/bgzf.c:83:1: warning: unused function 'kh_clear_cache' [-Wunused-function] KHASH_MAP_INIT_INT64(cache, cache_t) ^ samtools/khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64' KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ <scratch space>:35:1: note: expanded from here kh_clear_cache ^ 3 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/include -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/kstring.c -o samtools/kstring.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/include -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_aux.c -o samtools/bam_aux.o samtools/bam_aux.c:5:1: warning: unused function 'kh_clear_s' [-Wunused-function] KHASH_MAP_INIT_STR(s, int) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ <scratch space>:85:1: note: expanded from here kh_clear_s ^ samtools/bam_aux.c:5:1: warning: unused function 'kh_del_s' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ <scratch space>:99:1: note: expanded from here kh_del_s ^ samtools/bam_aux.c:6:1: warning: unused function 'kh_init_r2l' [-Wunused-function] KHASH_MAP_INIT_STR(r2l, str_p) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:168:23: note: expanded from macro 'KHASH_INIT2' SCOPE kh_##name##_t *kh_init_##name() { \ ^ <scratch space>:106:1: note: expanded from here kh_init_r2l ^ samtools/bam_aux.c:6:1: warning: unused function 'kh_destroy_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:171:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_destroy_##name(kh_##name##_t *h) \ ^ <scratch space>:111:1: note: expanded from here kh_destroy_r2l ^ samtools/bam_aux.c:6:1: warning: unused function 'kh_clear_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ <scratch space>:114:1: note: expanded from here kh_clear_r2l ^ samtools/bam_aux.c:6:1: warning: unused function 'kh_get_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:186:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ <scratch space>:117:1: note: expanded from here kh_get_r2l ^ samtools/bam_aux.c:6:1: warning: unused function 'kh_put_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:260:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \ ^ <scratch space>:123:1: note: expanded from here kh_put_r2l ^ samtools/bam_aux.c:6:1: warning: unused function 'kh_del_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ <scratch space>:128:1: note: expanded from here kh_del_r2l ^ 8 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/include -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam.c -o samtools/bam.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/include -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_import.c -o samtools/bam_import.o samtools/bam_import.c:20:1: warning: unused function 'kh_clear_ref' [-Wunused-function] KHASH_MAP_INIT_STR(ref, uint64_t) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ <scratch space>:417:1: note: expanded from here kh_clear_ref ^ samtools/bam_import.c:20:1: warning: unused function 'kh_get_ref' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:186:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ <scratch space>:420:1: note: expanded from here kh_get_ref ^ samtools/bam_import.c:20:1: warning: unused function 'kh_del_ref' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ <scratch space>:431:1: note: expanded from here kh_del_ref ^ 3 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/include -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/sam.c -o samtools/sam.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/include -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_index.c -o samtools/bam_index.o samtools/bam_index.c:64:1: warning: unused function 'kh_clear_i' [-Wunused-function] KHASH_MAP_INIT_INT(i, bam_binlist_t) ^ samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ <scratch space>:105:1: note: expanded from here kh_clear_i ^ samtools/bam_index.c:64:1: warning: unused function 'kh_del_i' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ <scratch space>:119:1: note: expanded from here kh_del_i ^ 2 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/include -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_pileup.c -o samtools/bam_pileup.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/include -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/include -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_md.c -o samtools/bam_md.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/include -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/razf.c -o samtools/razf.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/include -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/faidx.c -o samtools/faidx.o samtools/faidx.c:14:1: warning: unused function 'kh_clear_s' [-Wunused-function] KHASH_MAP_INIT_STR(s, faidx1_t) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ <scratch space>:415:1: note: expanded from here kh_clear_s ^ samtools/faidx.c:14:1: warning: unused function 'kh_del_s' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ <scratch space>:429:1: note: expanded from here kh_del_s ^ 2 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/include -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/knetfile.c -o samtools/knetfile.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/include -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_sort.c -o samtools/bam_sort.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/include -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/sam_header.c -o samtools/sam_header.o samtools/sam_header.c:10:1: warning: unused function 'kh_clear_str' [-Wunused-function] KHASH_MAP_INIT_STR(str, const char *) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ <scratch space>:415:1: note: expanded from here kh_clear_str ^ samtools/sam_header.c:10:1: warning: unused function 'kh_del_str' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ <scratch space>:429:1: note: expanded from here kh_del_str ^ 2 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/include -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_reheader.c -o samtools/bam_reheader.o samtools/bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable] bam_header_t *old; ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/include -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/kprobaln.c -o samtools/kprobaln.o samtools/kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable] int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr; ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/include -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/samtools_patch.c -o samtools/samtools_patch.o ar -crus samtools/libbam.a samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o samtools/razf.o samtools/faidx.o samtools/knetfile.o samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o samtools/kprobaln.o samtools/samtools_patch.o cd gstruct; \ make install Making install in src /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-except.lo -MD -MP -MF .deps/libgstruct_1.0_la-except.Tpo -c -o libgstruct_1.0_la-except.lo `test -f 'except.c' || echo './'`except.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-except.lo -MD -MP -MF .deps/libgstruct_1.0_la-except.Tpo -c except.c -o libgstruct_1.0_la-except.o mv -f .deps/libgstruct_1.0_la-except.Tpo .deps/libgstruct_1.0_la-except.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-assert.lo -MD -MP -MF .deps/libgstruct_1.0_la-assert.Tpo -c -o libgstruct_1.0_la-assert.lo `test -f 'assert.c' || echo './'`assert.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-assert.lo -MD -MP -MF .deps/libgstruct_1.0_la-assert.Tpo -c assert.c -o libgstruct_1.0_la-assert.o mv -f .deps/libgstruct_1.0_la-assert.Tpo .deps/libgstruct_1.0_la-assert.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-mem.lo -MD -MP -MF .deps/libgstruct_1.0_la-mem.Tpo -c -o libgstruct_1.0_la-mem.lo `test -f 'mem.c' || echo './'`mem.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-mem.lo -MD -MP -MF .deps/libgstruct_1.0_la-mem.Tpo -c mem.c -o libgstruct_1.0_la-mem.o mv -f .deps/libgstruct_1.0_la-mem.Tpo .deps/libgstruct_1.0_la-mem.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-intlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-intlist.Tpo -c -o libgstruct_1.0_la-intlist.lo `test -f 'intlist.c' || echo './'`intlist.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-intlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-intlist.Tpo -c intlist.c -o libgstruct_1.0_la-intlist.o mv -f .deps/libgstruct_1.0_la-intlist.Tpo .deps/libgstruct_1.0_la-intlist.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-list.lo -MD -MP -MF .deps/libgstruct_1.0_la-list.Tpo -c -o libgstruct_1.0_la-list.lo `test -f 'list.c' || echo './'`list.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-list.lo -MD -MP -MF .deps/libgstruct_1.0_la-list.Tpo -c list.c -o libgstruct_1.0_la-list.o mv -f .deps/libgstruct_1.0_la-list.Tpo .deps/libgstruct_1.0_la-list.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-littleendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-littleendian.Tpo -c -o libgstruct_1.0_la-littleendian.lo `test -f 'littleendian.c' || echo './'`littleendian.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-littleendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-littleendian.Tpo -c littleendian.c -o libgstruct_1.0_la-littleendian.o mv -f .deps/libgstruct_1.0_la-littleendian.Tpo .deps/libgstruct_1.0_la-littleendian.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bigendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-bigendian.Tpo -c -o libgstruct_1.0_la-bigendian.lo `test -f 'bigendian.c' || echo './'`bigendian.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bigendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-bigendian.Tpo -c bigendian.c -o libgstruct_1.0_la-bigendian.o mv -f .deps/libgstruct_1.0_la-bigendian.Tpo .deps/libgstruct_1.0_la-bigendian.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-interval.lo -MD -MP -MF .deps/libgstruct_1.0_la-interval.Tpo -c -o libgstruct_1.0_la-interval.lo `test -f 'interval.c' || echo './'`interval.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-interval.lo -MD -MP -MF .deps/libgstruct_1.0_la-interval.Tpo -c interval.c -o libgstruct_1.0_la-interval.o mv -f .deps/libgstruct_1.0_la-interval.Tpo .deps/libgstruct_1.0_la-interval.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-uintlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-uintlist.Tpo -c -o libgstruct_1.0_la-uintlist.lo `test -f 'uintlist.c' || echo './'`uintlist.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-uintlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-uintlist.Tpo -c uintlist.c -o libgstruct_1.0_la-uintlist.o mv -f .deps/libgstruct_1.0_la-uintlist.Tpo .deps/libgstruct_1.0_la-uintlist.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-stopwatch.lo -MD -MP -MF .deps/libgstruct_1.0_la-stopwatch.Tpo -c -o libgstruct_1.0_la-stopwatch.lo `test -f 'stopwatch.c' || echo './'`stopwatch.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-stopwatch.lo -MD -MP -MF .deps/libgstruct_1.0_la-stopwatch.Tpo -c stopwatch.c -o libgstruct_1.0_la-stopwatch.o mv -f .deps/libgstruct_1.0_la-stopwatch.Tpo .deps/libgstruct_1.0_la-stopwatch.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-access.lo -MD -MP -MF .deps/libgstruct_1.0_la-access.Tpo -c -o libgstruct_1.0_la-access.lo `test -f 'access.c' || echo './'`access.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-access.lo -MD -MP -MF .deps/libgstruct_1.0_la-access.Tpo -c access.c -o libgstruct_1.0_la-access.o mv -f .deps/libgstruct_1.0_la-access.Tpo .deps/libgstruct_1.0_la-access.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-iit-read.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-read.Tpo -c -o libgstruct_1.0_la-iit-read.lo `test -f 'iit-read.c' || echo './'`iit-read.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-iit-read.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-read.Tpo -c iit-read.c -o libgstruct_1.0_la-iit-read.o iit-read.c:1611:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:1611:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:1638:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:1638:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:1650:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:1650:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:1672:21: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,divno,offset,filesize); ^~~~~~ iit-read.c:1672:28: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,divno,offset,filesize); ^~~~~~~~ iit-read.c:1693:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:1693:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:1742:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:1742:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:1779:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:1779:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:1834:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:1834:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2344:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2344:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2360:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2360:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2372:12: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2372:19: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2381:12: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2381:19: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2408:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2408:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2429:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2429:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2446:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2446:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2466:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2466:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2495:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2495:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2608:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2608:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2626:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2626:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2643:12: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2643:19: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2652:12: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2652:19: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2681:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2681:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2702:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2702:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2719:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2719:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2744:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2744:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2770:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2770:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2823:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2823:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:3010:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:3010:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:3026:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:3026:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:3043:12: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:3043:19: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:3052:12: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:3052:19: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:3081:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:3081:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:3107:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:3107:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:3124:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:3124:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:3149:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:3149:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:3175:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:3175:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:3220:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:3220:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ 74 warnings generated. mv -f .deps/libgstruct_1.0_la-iit-read.Tpo .deps/libgstruct_1.0_la-iit-read.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-chrom.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrom.Tpo -c -o libgstruct_1.0_la-chrom.lo `test -f 'chrom.c' || echo './'`chrom.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-chrom.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrom.Tpo -c chrom.c -o libgstruct_1.0_la-chrom.o chrom.c:108:15: warning: comparing a pointer to a null character constant; did you mean to compare to NULL? [-Wpointer-compare] while (p != '\0' && *p >= '0' && *p <= '9') { ^~~~ (void *)0 1 warning generated. mv -f .deps/libgstruct_1.0_la-chrom.Tpo .deps/libgstruct_1.0_la-chrom.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-genomicpos.lo -MD -MP -MF .deps/libgstruct_1.0_la-genomicpos.Tpo -c -o libgstruct_1.0_la-genomicpos.lo `test -f 'genomicpos.c' || echo './'`genomicpos.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-genomicpos.lo -MD -MP -MF .deps/libgstruct_1.0_la-genomicpos.Tpo -c genomicpos.c -o libgstruct_1.0_la-genomicpos.o mv -f .deps/libgstruct_1.0_la-genomicpos.Tpo .deps/libgstruct_1.0_la-genomicpos.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-md5.lo -MD -MP -MF .deps/libgstruct_1.0_la-md5.Tpo -c -o libgstruct_1.0_la-md5.lo `test -f 'md5.c' || echo './'`md5.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-md5.lo -MD -MP -MF .deps/libgstruct_1.0_la-md5.Tpo -c md5.c -o libgstruct_1.0_la-md5.o mv -f .deps/libgstruct_1.0_la-md5.Tpo .deps/libgstruct_1.0_la-md5.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-sequence.lo -MD -MP -MF .deps/libgstruct_1.0_la-sequence.Tpo -c -o libgstruct_1.0_la-sequence.lo `test -f 'sequence.c' || echo './'`sequence.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-sequence.lo -MD -MP -MF .deps/libgstruct_1.0_la-sequence.Tpo -c sequence.c -o libgstruct_1.0_la-sequence.o mv -f .deps/libgstruct_1.0_la-sequence.Tpo .deps/libgstruct_1.0_la-sequence.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-genome.lo -MD -MP -MF .deps/libgstruct_1.0_la-genome.Tpo -c -o libgstruct_1.0_la-genome.lo `test -f 'genome.c' || echo './'`genome.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-genome.lo -MD -MP -MF .deps/libgstruct_1.0_la-genome.Tpo -c genome.c -o libgstruct_1.0_la-genome.o mv -f .deps/libgstruct_1.0_la-genome.Tpo .deps/libgstruct_1.0_la-genome.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-uinttable.lo -MD -MP -MF .deps/libgstruct_1.0_la-uinttable.Tpo -c -o libgstruct_1.0_la-uinttable.lo `test -f 'uinttable.c' || echo './'`uinttable.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-uinttable.lo -MD -MP -MF .deps/libgstruct_1.0_la-uinttable.Tpo -c uinttable.c -o libgstruct_1.0_la-uinttable.o mv -f .deps/libgstruct_1.0_la-uinttable.Tpo .deps/libgstruct_1.0_la-uinttable.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-table.lo -MD -MP -MF .deps/libgstruct_1.0_la-table.Tpo -c -o libgstruct_1.0_la-table.lo `test -f 'table.c' || echo './'`table.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-table.lo -MD -MP -MF .deps/libgstruct_1.0_la-table.Tpo -c table.c -o libgstruct_1.0_la-table.o mv -f .deps/libgstruct_1.0_la-table.Tpo .deps/libgstruct_1.0_la-table.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-chrnum.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrnum.Tpo -c -o libgstruct_1.0_la-chrnum.lo `test -f 'chrnum.c' || echo './'`chrnum.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-chrnum.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrnum.Tpo -c chrnum.c -o libgstruct_1.0_la-chrnum.o mv -f .deps/libgstruct_1.0_la-chrnum.Tpo .deps/libgstruct_1.0_la-chrnum.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bamread.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamread.Tpo -c -o libgstruct_1.0_la-bamread.lo `test -f 'bamread.c' || echo './'`bamread.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bamread.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamread.Tpo -c bamread.c -o libgstruct_1.0_la-bamread.o mv -f .deps/libgstruct_1.0_la-bamread.Tpo .deps/libgstruct_1.0_la-bamread.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-samread.lo -MD -MP -MF .deps/libgstruct_1.0_la-samread.Tpo -c -o libgstruct_1.0_la-samread.lo `test -f 'samread.c' || echo './'`samread.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-samread.lo -MD -MP -MF .deps/libgstruct_1.0_la-samread.Tpo -c samread.c -o libgstruct_1.0_la-samread.o mv -f .deps/libgstruct_1.0_la-samread.Tpo .deps/libgstruct_1.0_la-samread.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-parserange.lo -MD -MP -MF .deps/libgstruct_1.0_la-parserange.Tpo -c -o libgstruct_1.0_la-parserange.lo `test -f 'parserange.c' || echo './'`parserange.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-parserange.lo -MD -MP -MF .deps/libgstruct_1.0_la-parserange.Tpo -c parserange.c -o libgstruct_1.0_la-parserange.o mv -f .deps/libgstruct_1.0_la-parserange.Tpo .deps/libgstruct_1.0_la-parserange.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-tableuint.lo -MD -MP -MF .deps/libgstruct_1.0_la-tableuint.Tpo -c -o libgstruct_1.0_la-tableuint.lo `test -f 'tableuint.c' || echo './'`tableuint.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-tableuint.lo -MD -MP -MF .deps/libgstruct_1.0_la-tableuint.Tpo -c tableuint.c -o libgstruct_1.0_la-tableuint.o mv -f .deps/libgstruct_1.0_la-tableuint.Tpo .deps/libgstruct_1.0_la-tableuint.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-iit-write.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-write.Tpo -c -o libgstruct_1.0_la-iit-write.lo `test -f 'iit-write.c' || echo './'`iit-write.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-iit-write.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-write.Tpo -c iit-write.c -o libgstruct_1.0_la-iit-write.o iit-write.c:113:17: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] if (endpoint(intervals,array[lambda]) > endpoint(intervals,array[lambda + 1])) { ^ iit-write.c:113:53: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] if (endpoint(intervals,array[lambda]) > endpoint(intervals,array[lambda + 1])) { ^ 2 warnings generated. mv -f 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-DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-matchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-matchpool.Tpo -c -o libgstruct_1.0_la-matchpool.lo `test -f 'matchpool.c' || echo './'`matchpool.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-matchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-matchpool.Tpo -c matchpool.c -o libgstruct_1.0_la-matchpool.o mv -f .deps/libgstruct_1.0_la-matchpool.Tpo .deps/libgstruct_1.0_la-matchpool.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-mismatchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-mismatchpool.Tpo -c -o libgstruct_1.0_la-mismatchpool.lo `test -f 'mismatchpool.c' || echo './'`mismatchpool.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-mismatchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-mismatchpool.Tpo -c mismatchpool.c -o libgstruct_1.0_la-mismatchpool.o mv -f .deps/libgstruct_1.0_la-mismatchpool.Tpo .deps/libgstruct_1.0_la-mismatchpool.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-tally.lo -MD -MP -MF .deps/libgstruct_1.0_la-tally.Tpo -c -o libgstruct_1.0_la-tally.lo `test -f 'tally.c' || echo './'`tally.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-tally.lo -MD -MP -MF .deps/libgstruct_1.0_la-tally.Tpo -c tally.c -o libgstruct_1.0_la-tally.o mv -f .deps/libgstruct_1.0_la-tally.Tpo .deps/libgstruct_1.0_la-tally.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-translation.lo -MD -MP -MF .deps/libgstruct_1.0_la-translation.Tpo -c -o libgstruct_1.0_la-translation.lo `test -f 'translation.c' || echo './'`translation.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-translation.lo -MD -MP -MF .deps/libgstruct_1.0_la-translation.Tpo -c translation.c -o libgstruct_1.0_la-translation.o mv -f 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-DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bamtally.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamtally.Tpo -c -o libgstruct_1.0_la-bamtally.lo `test -f 'bamtally.c' || echo './'`bamtally.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bamtally.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamtally.Tpo -c bamtally.c -o libgstruct_1.0_la-bamtally.o mv -f .deps/libgstruct_1.0_la-bamtally.Tpo .deps/libgstruct_1.0_la-bamtally.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-datadir.lo -MD -MP -MF .deps/libgstruct_1.0_la-datadir.Tpo -c -o libgstruct_1.0_la-datadir.lo `test -f 'datadir.c' || echo './'`datadir.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-datadir.lo -MD -MP -MF .deps/libgstruct_1.0_la-datadir.Tpo -c datadir.c -o libgstruct_1.0_la-datadir.o mv -f .deps/libgstruct_1.0_la-datadir.Tpo .deps/libgstruct_1.0_la-datadir.Plo /bin/sh ../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -D_THREAD_SAFE -version-info 1:0:0 -o libgstruct-1.0.la -rpath /Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/lib libgstruct_1.0_la-except.lo libgstruct_1.0_la-assert.lo libgstruct_1.0_la-mem.lo libgstruct_1.0_la-intlist.lo libgstruct_1.0_la-list.lo libgstruct_1.0_la-littleendian.lo libgstruct_1.0_la-bigendian.lo libgstruct_1.0_la-interval.lo libgstruct_1.0_la-uintlist.lo libgstruct_1.0_la-stopwatch.lo libgstruct_1.0_la-access.lo libgstruct_1.0_la-iit-read.lo libgstruct_1.0_la-chrom.lo libgstruct_1.0_la-genomicpos.lo libgstruct_1.0_la-md5.lo libgstruct_1.0_la-sequence.lo libgstruct_1.0_la-genome.lo libgstruct_1.0_la-uinttable.lo libgstruct_1.0_la-table.lo libgstruct_1.0_la-chrnum.lo libgstruct_1.0_la-bamread.lo libgstruct_1.0_la-samread.lo libgstruct_1.0_la-parserange.lo libgstruct_1.0_la-tableuint.lo libgstruct_1.0_la-iit-write.lo libgstruct_1.0_la-ucharlist.lo libgstruct_1.0_la-matchpool.lo libgstruct_1.0_la-mismatchpool.lo libgstruct_1.0_la-tally.lo libgstruct_1.0_la-translation.lo libgstruct_1.0_la-expr.lo libgstruct_1.0_la-bamtally.lo libgstruct_1.0_la-datadir.lo -lz -lm libtool: link: ar cru .libs/libgstruct-1.0.a libgstruct_1.0_la-except.o libgstruct_1.0_la-assert.o libgstruct_1.0_la-mem.o libgstruct_1.0_la-intlist.o libgstruct_1.0_la-list.o libgstruct_1.0_la-littleendian.o libgstruct_1.0_la-bigendian.o libgstruct_1.0_la-interval.o libgstruct_1.0_la-uintlist.o libgstruct_1.0_la-stopwatch.o libgstruct_1.0_la-access.o libgstruct_1.0_la-iit-read.o libgstruct_1.0_la-chrom.o libgstruct_1.0_la-genomicpos.o libgstruct_1.0_la-md5.o libgstruct_1.0_la-sequence.o libgstruct_1.0_la-genome.o libgstruct_1.0_la-uinttable.o libgstruct_1.0_la-table.o libgstruct_1.0_la-chrnum.o libgstruct_1.0_la-bamread.o libgstruct_1.0_la-samread.o libgstruct_1.0_la-parserange.o libgstruct_1.0_la-tableuint.o libgstruct_1.0_la-iit-write.o libgstruct_1.0_la-ucharlist.o libgstruct_1.0_la-matchpool.o libgstruct_1.0_la-mismatchpool.o libgstruct_1.0_la-tally.o libgstruct_1.0_la-translation.o libgstruct_1.0_la-expr.o libgstruct_1.0_la-bamtally.o libgstruct_1.0_la-datadir.o libtool: link: ranlib .libs/libgstruct-1.0.a libtool: link: ( cd ".libs" && rm -f "libgstruct-1.0.la" && ln -s "../libgstruct-1.0.la" "libgstruct-1.0.la" ) ../config/install-sh -c -d '/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/lib' /bin/sh ../libtool --mode=install /usr/bin/install -c libgstruct-1.0.la '/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/lib' libtool: install: /usr/bin/install -c .libs/libgstruct-1.0.lai /Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.la libtool: install: /usr/bin/install -c .libs/libgstruct-1.0.a /Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a libtool: install: chmod 644 /Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a libtool: install: ranlib /Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a ../config/install-sh -c -d '/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/include/gstruct' /usr/bin/install -c -m 644 config.h fopen.h bool.h types.h except.h assert.h mem.h intlistdef.h intlist.h listdef.h list.h littleendian.h bigendian.h interval.h uintlist.h stopwatch.h access.h iitdef.h iit-read.h chrom.h genomicpos.h md5.h complement.h sequence.h genome.h uinttable.h table.h chrnum.h bamread.h samread.h parserange.h dynprog.h dynprog_nogap.h dynprog_simd.h dynprog_cigar.h dynprog_single.h tableuint.h iit-write.h ucharlist.h matchdef.h '/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/include/gstruct' /usr/bin/install -c -m 644 matchpool.h mismatchdef.h mismatchpool.h tally.h translation.h bamtally.h datadir.h '/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/include/gstruct' ../config/install-sh -c -d '/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/lib/pkgconfig' /usr/bin/install -c -m 644 ../lib/gstruct-1.0.pc '/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/lib/pkgconfig' make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/include -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bamreader.c -o bamreader.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/include -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bamtally.c -o bamtally.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/include -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c iit.c -o iit.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/include -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c variantsummary.c -o variantsummary.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/include -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c genome.c -o genome.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/include -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_gmapR.c -o R_init_gmapR.o clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L"/Library/Frameworks/R.framework/Resources/lib" -L/opt/R/arm64/lib -o gmapR.so bamreader.o bamtally.o iit.o variantsummary.o genome.o R_init_gmapR.o /Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a samtools/libbam.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation cd gmap/; \ ./configure --with-gmapdb= --prefix=/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr \ --libdir=/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/lib --disable-maintainer-mode checking package version... 2013-11-01 checking whether to enable maintainer-specific portions of Makefiles... no checking CONFIG_SITE... 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(cached) yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 8 checking size of unsigned long long... 8 checking size of off_t... 8 checking for _LARGEFILE_SOURCE value needed for large files... no checking whether mmap is enabled... not specified so enabled by default checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... yes checking for sigaction... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... yes checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for popcnt feature... not specified so enabled by default checking for __builtin_popcount... yes checking for __builtin_clz... yes checking for __builtin_ctz... yes checking for bsr instruction in assembly... no checking whether sse2 is enabled... not specified so enabled by default checking whether user has declared a defective SSE2 compiler... no checking whether sse4.1 is enabled... not specified so enabled by default checking whether simd is enabled... not specified so enabled by default checking gmapdb... /Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share checking MAX_READLENGTH... 250 checking for zlib support... enabled checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for gzopen in -lz... yes checking for gzeof in -lz... yes checking for gzgetc in -lz... yes checking for gzgets in -lz... yes checking for gzclose in -lz... yes checking if zlib package is complete... working checking for gzbuffer in -lz... yes checking for bzlib support... enabled checking bzlib.h usability... yes checking bzlib.h presence... yes checking for bzlib.h... yes checking for BZ2_bzReadOpen in -lbz2... yes checking for BZ2_bzRead in -lbz2... yes checking for BZ2_bzReadClose in -lbz2... yes checking if bzlib package is complete... working checking for goby library... disabled checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating util/Makefile config.status: creating util/gmap_compress.pl config.status: creating util/gmap_uncompress.pl config.status: creating util/gmap_process.pl config.status: creating util/gmap_setup.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_reassemble.pl config.status: creating util/md_coords.pl config.status: creating util/fa_coords.pl config.status: creating util/psl_splicesites.pl config.status: creating util/psl_introns.pl config.status: creating util/psl_genes.pl config.status: creating util/gtf_splicesites.pl config.status: creating util/gtf_introns.pl config.status: creating util/gtf_genes.pl config.status: creating util/gff3_splicesites.pl config.status: creating util/gff3_introns.pl config.status: creating util/gff3_genes.pl config.status: creating util/dbsnp_iit.pl config.status: creating util/gvf_iit.pl config.status: creating util/vcf_iit.pl config.status: creating tests/Makefile config.status: creating tests/align.test config.status: creating tests/coords1.test config.status: creating tests/setup1.test config.status: creating tests/iit.test config.status: creating src/config.h config.status: executing depfiles commands config.status: executing libtool commands cd gmap; \ make install Making install in src gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-except.o -MD -MP -MF .deps/gmap-except.Tpo -c -o gmap-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/gmap-except.Tpo .deps/gmap-except.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-assert.o -MD -MP -MF .deps/gmap-assert.Tpo -c -o gmap-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/gmap-assert.Tpo .deps/gmap-assert.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-mem.o -MD -MP -MF .deps/gmap-mem.Tpo -c -o gmap-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/gmap-mem.Tpo .deps/gmap-mem.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-intlist.o -MD -MP -MF .deps/gmap-intlist.Tpo -c -o gmap-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/gmap-intlist.Tpo .deps/gmap-intlist.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-list.o -MD -MP -MF .deps/gmap-list.Tpo -c -o gmap-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/gmap-list.Tpo .deps/gmap-list.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-littleendian.o -MD -MP -MF .deps/gmap-littleendian.Tpo -c -o gmap-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c mv -f .deps/gmap-littleendian.Tpo .deps/gmap-littleendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-bigendian.o -MD -MP -MF .deps/gmap-bigendian.Tpo -c -o gmap-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c mv -f .deps/gmap-bigendian.Tpo .deps/gmap-bigendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-univinterval.o -MD -MP -MF .deps/gmap-univinterval.Tpo -c -o gmap-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~ %u univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~~ %u 2 warnings generated. mv -f .deps/gmap-univinterval.Tpo .deps/gmap-univinterval.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-interval.o -MD -MP -MF .deps/gmap-interval.Tpo -c -o gmap-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/gmap-interval.Tpo .deps/gmap-interval.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-uintlist.o -MD -MP -MF .deps/gmap-uintlist.Tpo -c -o gmap-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/gmap-uintlist.Tpo .deps/gmap-uintlist.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-stopwatch.o -MD -MP -MF .deps/gmap-stopwatch.Tpo -c -o gmap-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/gmap-stopwatch.Tpo .deps/gmap-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-access.o -MD -MP -MF .deps/gmap-access.Tpo -c -o gmap-access.o `test -f 'access.c' || echo './'`access.c access.c:358:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] length,length,errno,strerror(errno)); ^~~~~~ access.c:358:15: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] length,length,errno,strerror(errno)); ^~~~~~ access.c:423:11: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] fd,offset,length,errno,strerror(errno)); ^~~~~~ access.c:493:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] *len,length,errno,strerror(errno)); ^~~~~~ access.c:556:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] offset,length,errno,strerror(errno)); ^~~~~~ access.c:641:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] *len,length,errno,strerror(errno)); ^~~~~~ 6 warnings generated. mv -f .deps/gmap-access.Tpo .deps/gmap-access.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-iit-read-univ.o -MD -MP -MF .deps/gmap-iit-read-univ.Tpo -c -o gmap-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~~~ %u iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~ %u iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~~~ %u iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~ %u iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %u iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %u iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~ %u iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~~~ %u iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %u iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %u 10 warnings generated. mv -f .deps/gmap-iit-read-univ.Tpo .deps/gmap-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-iit-read.o -MD -MP -MF .deps/gmap-iit-read.Tpo -c -o gmap-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c mv -f .deps/gmap-iit-read.Tpo .deps/gmap-iit-read.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-md5.o -MD -MP -MF .deps/gmap-md5.Tpo -c -o gmap-md5.o `test -f 'md5.c' || echo './'`md5.c mv -f .deps/gmap-md5.Tpo .deps/gmap-md5.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-bzip2.o -MD -MP -MF .deps/gmap-bzip2.Tpo -c -o gmap-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c mv -f .deps/gmap-bzip2.Tpo .deps/gmap-bzip2.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-sequence.o -MD -MP -MF .deps/gmap-sequence.Tpo -c -o gmap-sequence.o `test -f 'sequence.c' || echo './'`sequence.c mv -f .deps/gmap-sequence.Tpo .deps/gmap-sequence.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-reader.o -MD -MP -MF .deps/gmap-reader.Tpo -c -o gmap-reader.o `test -f 'reader.c' || echo './'`reader.c mv -f .deps/gmap-reader.Tpo .deps/gmap-reader.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genomicpos.o -MD -MP -MF .deps/gmap-genomicpos.Tpo -c -o gmap-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/gmap-genomicpos.Tpo .deps/gmap-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-compress.o -MD -MP -MF .deps/gmap-compress.Tpo -c -o gmap-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/gmap-compress.Tpo .deps/gmap-compress.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-compress-write.o -MD -MP -MF .deps/gmap-compress-write.Tpo -c -o gmap-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c compress-write.c:73:80: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i); ~~~ ^~~~~~~~~~ %u compress-write.c:252:13: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] Buffer[i],position+i); ^~~~~~~~~~ compress-write.c:300:13: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] Buffer[i],position+i); ^~~~~~~~~~ 3 warnings generated. mv -f .deps/gmap-compress-write.Tpo .deps/gmap-compress-write.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-gbuffer.o -MD -MP -MF .deps/gmap-gbuffer.Tpo -c -o gmap-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c mv -f .deps/gmap-gbuffer.Tpo .deps/gmap-gbuffer.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genome.o -MD -MP -MF .deps/gmap-genome.Tpo -c -o gmap-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c:10292:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %u genome.c:10292:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %u genome.c:10392:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %u genome.c:10392:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %u 4 warnings generated. mv -f .deps/gmap-genome.Tpo .deps/gmap-genome.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genome_hr.o -MD -MP -MF .deps/gmap-genome_hr.Tpo -c -o gmap-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c mv -f .deps/gmap-genome_hr.Tpo .deps/gmap-genome_hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genome_sites.o -MD -MP -MF .deps/gmap-genome_sites.Tpo -c -o gmap-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c mv -f .deps/gmap-genome_sites.Tpo .deps/gmap-genome_sites.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genome-write.o -MD -MP -MF .deps/gmap-genome-write.Tpo -c -o gmap-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c genome-write.c:253:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~~~ genome-write.c:253:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~ genome-write.c:256:15: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~~~ genome-write.c:256:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~ genome-write.c:430:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~~~ genome-write.c:430:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~ genome-write.c:433:15: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~~~ genome-write.c:433:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~ genome-write.c:595:87: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] fprintf(stderr,"Chromosome %s is circular. Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U); ~~~ ^~~~~~~~~~~~~~~~ %u genome-write.c:595:104: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] fprintf(stderr,"Chromosome %s is circular. Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U); ~~~ ^~~~~~~~~~~~~~ %u genome-write.c:595:119: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] fprintf(stderr,"Chromosome %s is circular. Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U); ~~~ ^~~~~~~~~~~~~~~~~ %u genome-write.c:595:137: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] fprintf(stderr,"Chromosome %s is circular. Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U); ~~~ ^~~~~~~~~~~~~~~ %u genome-write.c:643:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~~~ genome-write.c:643:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~ genome-write.c:646:15: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~~~ genome-write.c:646:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~ genome-write.c:787:46: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] fprintf(stderr,"Genome length is %lu nt\n",genomelength); ~~~ ^~~~~~~~~~~~ %u 17 warnings generated. mv -f .deps/gmap-genome-write.Tpo .deps/gmap-genome-write.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-bitpack64-read.o -MD -MP -MF .deps/gmap-bitpack64-read.Tpo -c -o gmap-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c mv -f .deps/gmap-bitpack64-read.Tpo .deps/gmap-bitpack64-read.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-indexdb.o -MD -MP -MF .deps/gmap-indexdb.Tpo -c -o gmap-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c:1363:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1483:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1653:63: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1792:6: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] ptr,sizeof(Univcoord_T),offset); ^~~ indexdb.c:1792:30: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] ptr,sizeof(Univcoord_T),offset); ^~~~~~ indexdb.c:1934:76: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, ~~~ ^~~~~~~~~~~~~~ %llu indexdb.c:2026:76: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, ~~~ ^~~~~~~~~~~~~~ %llu 7 warnings generated. mv -f .deps/gmap-indexdb.Tpo .deps/gmap-indexdb.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-indexdb_hr.o -MD -MP -MF .deps/gmap-indexdb_hr.Tpo -c -o gmap-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c mv -f .deps/gmap-indexdb_hr.Tpo .deps/gmap-indexdb_hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-oligo.o -MD -MP -MF .deps/gmap-oligo.Tpo -c -o gmap-oligo.o `test -f 'oligo.c' || echo './'`oligo.c mv -f .deps/gmap-oligo.Tpo .deps/gmap-oligo.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-block.o -MD -MP -MF .deps/gmap-block.Tpo -c -o gmap-block.o `test -f 'block.c' || echo './'`block.c mv -f .deps/gmap-block.Tpo .deps/gmap-block.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-chrom.o -MD -MP -MF .deps/gmap-chrom.Tpo -c -o gmap-chrom.o `test -f 'chrom.c' || echo './'`chrom.c chrom.c:116:15: warning: comparing a pointer to a null character constant; did you mean to compare to NULL? [-Wpointer-compare] while (p != '\0' && *p >= '0' && *p <= '9') { ^~~~ (void *)0 1 warning generated. mv -f .deps/gmap-chrom.Tpo .deps/gmap-chrom.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-segmentpos.o -MD -MP -MF .deps/gmap-segmentpos.Tpo -c -o gmap-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c mv -f .deps/gmap-segmentpos.Tpo .deps/gmap-segmentpos.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-chrnum.o -MD -MP -MF .deps/gmap-chrnum.Tpo -c -o gmap-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c mv -f .deps/gmap-chrnum.Tpo .deps/gmap-chrnum.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-chrsubset.o -MD -MP -MF .deps/gmap-chrsubset.Tpo -c -o gmap-chrsubset.o `test -f 'chrsubset.c' || echo './'`chrsubset.c mv -f .deps/gmap-chrsubset.Tpo .deps/gmap-chrsubset.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-uinttable.o -MD -MP -MF .deps/gmap-uinttable.Tpo -c -o gmap-uinttable.o `test -f 'uinttable.c' || echo './'`uinttable.c mv -f .deps/gmap-uinttable.Tpo .deps/gmap-uinttable.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-gregion.o -MD -MP -MF .deps/gmap-gregion.Tpo -c -o gmap-gregion.o `test -f 'gregion.c' || echo './'`gregion.c mv -f .deps/gmap-gregion.Tpo .deps/gmap-gregion.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-match.o -MD -MP -MF .deps/gmap-match.Tpo -c -o gmap-match.o `test -f 'match.c' || echo './'`match.c mv -f .deps/gmap-match.Tpo .deps/gmap-match.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-matchpool.o -MD -MP -MF .deps/gmap-matchpool.Tpo -c -o gmap-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c mv -f .deps/gmap-matchpool.Tpo .deps/gmap-matchpool.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-diagnostic.o -MD -MP -MF .deps/gmap-diagnostic.Tpo -c -o gmap-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c mv -f .deps/gmap-diagnostic.Tpo .deps/gmap-diagnostic.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-stage1.o -MD -MP -MF .deps/gmap-stage1.Tpo -c -o gmap-stage1.o `test -f 'stage1.c' || echo './'`stage1.c mv -f .deps/gmap-stage1.Tpo .deps/gmap-stage1.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-diag.o -MD -MP -MF .deps/gmap-diag.Tpo -c -o gmap-diag.o `test -f 'diag.c' || echo './'`diag.c mv -f .deps/gmap-diag.Tpo .deps/gmap-diag.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-diagpool.o -MD -MP -MF .deps/gmap-diagpool.Tpo -c -o gmap-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c mv -f .deps/gmap-diagpool.Tpo .deps/gmap-diagpool.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-cmet.o -MD -MP -MF .deps/gmap-cmet.Tpo -c -o gmap-cmet.o `test -f 'cmet.c' || echo './'`cmet.c mv -f .deps/gmap-cmet.Tpo .deps/gmap-cmet.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-atoi.o -MD -MP -MF .deps/gmap-atoi.Tpo -c -o gmap-atoi.o `test -f 'atoi.c' || echo './'`atoi.c mv -f .deps/gmap-atoi.Tpo .deps/gmap-atoi.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-orderstat.o -MD -MP -MF .deps/gmap-orderstat.Tpo -c -o gmap-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c mv -f .deps/gmap-orderstat.Tpo .deps/gmap-orderstat.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-oligoindex_hr.o -MD -MP -MF .deps/gmap-oligoindex_hr.Tpo -c -o gmap-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c mv -f .deps/gmap-oligoindex_hr.Tpo .deps/gmap-oligoindex_hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-intron.o -MD -MP -MF .deps/gmap-intron.Tpo -c -o gmap-intron.o `test -f 'intron.c' || echo './'`intron.c mv -f .deps/gmap-intron.Tpo .deps/gmap-intron.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-maxent.o -MD -MP -MF .deps/gmap-maxent.Tpo -c -o gmap-maxent.o `test -f 'maxent.c' || echo './'`maxent.c mv -f .deps/gmap-maxent.Tpo .deps/gmap-maxent.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-maxent_hr.o -MD -MP -MF .deps/gmap-maxent_hr.Tpo -c -o gmap-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c mv -f .deps/gmap-maxent_hr.Tpo .deps/gmap-maxent_hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-pair.o -MD -MP -MF .deps/gmap-pair.Tpo -c -o gmap-pair.o `test -f 'pair.c' || echo './'`pair.c pair.c:2419:24: warning: taking the absolute value of unsigned type 'Chrpos_T' (aka 'unsigned int') has no effect [-Wabsolute-value] sprintf(token,"N%u",abs(intron_end - intron_start) + 1); ^ pair.c:2419:24: note: remove the call to 'abs' since unsigned values cannot be negative sprintf(token,"N%u",abs(intron_end - intron_start) + 1); ^~~ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ pair.c:4651:17: warning: taking the absolute value of unsigned type 'Chrpos_T' (aka 'unsigned int') has no effect [-Wabsolute-value] genome_gap = abs(intron_end - intron_start) + 1; ^ pair.c:4651:17: note: remove the call to 'abs' since unsigned values cannot be negative genome_gap = abs(intron_end - intron_start) + 1; ^~~ 2 warnings generated. mv -f .deps/gmap-pair.Tpo .deps/gmap-pair.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-pairpool.o -MD -MP -MF .deps/gmap-pairpool.Tpo -c -o gmap-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c mv -f .deps/gmap-pairpool.Tpo .deps/gmap-pairpool.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-cellpool.o -MD -MP -MF .deps/gmap-cellpool.Tpo -c -o gmap-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c mv -f .deps/gmap-cellpool.Tpo .deps/gmap-cellpool.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-stage2.o -MD -MP -MF .deps/gmap-stage2.Tpo -c -o gmap-stage2.o `test -f 'stage2.c' || echo './'`stage2.c stage2.c:1329:19: warning: taking the absolute value of unsigned type 'Chrpos_T' (aka 'unsigned int') has no effect [-Wabsolute-value] diffdistance = abs(gendistance - querydistance); ^ stage2.c:1329:19: note: remove the call to 'abs' since unsigned values cannot be negative diffdistance = abs(gendistance - querydistance); ^~~ stage2.c:1812:19: warning: taking the absolute value of unsigned type 'Chrpos_T' (aka 'unsigned int') has no effect [-Wabsolute-value] diffdistance = abs(gendistance - querydistance); ^ stage2.c:1812:19: note: remove the call to 'abs' since unsigned values cannot be negative diffdistance = abs(gendistance - querydistance); ^~~ 2 warnings generated. mv -f .deps/gmap-stage2.Tpo .deps/gmap-stage2.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-doublelist.o -MD -MP -MF .deps/gmap-doublelist.Tpo -c -o gmap-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c mv -f .deps/gmap-doublelist.Tpo .deps/gmap-doublelist.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-smooth.o -MD -MP -MF .deps/gmap-smooth.Tpo -c -o gmap-smooth.o `test -f 'smooth.c' || echo './'`smooth.c mv -f .deps/gmap-smooth.Tpo .deps/gmap-smooth.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-splicestringpool.o -MD -MP -MF .deps/gmap-splicestringpool.Tpo -c -o gmap-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c mv -f .deps/gmap-splicestringpool.Tpo .deps/gmap-splicestringpool.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-splicetrie_build.o -MD -MP -MF .deps/gmap-splicetrie_build.Tpo -c -o gmap-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c mv -f .deps/gmap-splicetrie_build.Tpo .deps/gmap-splicetrie_build.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-splicetrie.o -MD -MP -MF .deps/gmap-splicetrie.Tpo -c -o gmap-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c mv -f .deps/gmap-splicetrie.Tpo .deps/gmap-splicetrie.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-boyer-moore.o -MD -MP -MF .deps/gmap-boyer-moore.Tpo -c -o gmap-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c mv -f .deps/gmap-boyer-moore.Tpo .deps/gmap-boyer-moore.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-dynprog.o -MD -MP -MF .deps/gmap-dynprog.Tpo -c -o gmap-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c mv -f .deps/gmap-dynprog.Tpo .deps/gmap-dynprog.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-translation.o -MD -MP -MF .deps/gmap-translation.Tpo -c -o gmap-translation.o `test -f 'translation.c' || echo './'`translation.c mv -f .deps/gmap-translation.Tpo .deps/gmap-translation.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-pbinom.o -MD -MP -MF .deps/gmap-pbinom.Tpo -c -o gmap-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c mv -f .deps/gmap-pbinom.Tpo .deps/gmap-pbinom.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-changepoint.o -MD -MP -MF .deps/gmap-changepoint.Tpo -c -o gmap-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c mv -f .deps/gmap-changepoint.Tpo .deps/gmap-changepoint.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-stage3.o -MD -MP -MF .deps/gmap-stage3.Tpo -c -o gmap-stage3.o `test -f 'stage3.c' || echo './'`stage3.c mv -f .deps/gmap-stage3.Tpo .deps/gmap-stage3.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-request.o -MD -MP -MF .deps/gmap-request.Tpo -c -o gmap-request.o `test -f 'request.c' || echo './'`request.c mv -f .deps/gmap-request.Tpo .deps/gmap-request.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-result.o -MD -MP -MF .deps/gmap-result.Tpo -c -o gmap-result.o `test -f 'result.c' || echo './'`result.c mv -f .deps/gmap-result.Tpo .deps/gmap-result.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-inbuffer.o -MD -MP -MF .deps/gmap-inbuffer.Tpo -c -o gmap-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c mv -f .deps/gmap-inbuffer.Tpo .deps/gmap-inbuffer.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-samheader.o -MD -MP -MF .deps/gmap-samheader.Tpo -c -o gmap-samheader.o `test -f 'samheader.c' || echo './'`samheader.c mv -f .deps/gmap-samheader.Tpo .deps/gmap-samheader.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-outbuffer.o -MD -MP -MF .deps/gmap-outbuffer.Tpo -c -o gmap-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c mv -f .deps/gmap-outbuffer.Tpo .deps/gmap-outbuffer.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-chimera.o -MD -MP -MF .deps/gmap-chimera.Tpo -c -o gmap-chimera.o `test -f 'chimera.c' || echo './'`chimera.c mv -f .deps/gmap-chimera.Tpo .deps/gmap-chimera.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-datadir.o -MD -MP -MF .deps/gmap-datadir.Tpo -c -o gmap-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/gmap-datadir.Tpo .deps/gmap-datadir.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-getopt.o -MD -MP -MF .deps/gmap-getopt.Tpo -c -o gmap-getopt.o `test -f 'getopt.c' || echo './'`getopt.c getopt.c:208:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] my_index (str, chr) ^ getopt.c:291:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] exchange (argv) ^ getopt.c:376:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] _getopt_initialize (argc, argv, optstring) ^ getopt.c:389:28: warning: passing arguments to 'getenv' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] posixly_correct = getenv ("POSIXLY_CORRECT"); ^ getopt.c:498:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] _getopt_internal (argc, argv, optstring, longopts, longind, long_only) ^ getopt.c:1179:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt (argc, argv, optstring) ^ In file included from getopt.c:97: ./getopt.h:147:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent definition [-Wdeprecated-non-prototype] extern int getopt (); ^ 7 warnings generated. mv -f .deps/gmap-getopt.Tpo .deps/gmap-getopt.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-getopt1.o -MD -MP -MF .deps/gmap-getopt1.Tpo -c -o gmap-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c getopt1.c:71:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt_long (argc, argv, options, long_options, opt_index) ^ getopt1.c:87:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt_long_only (argc, argv, options, long_options, opt_index) ^ 2 warnings generated. mv -f .deps/gmap-getopt1.Tpo .deps/gmap-getopt1.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-gmap.o -MD -MP -MF .deps/gmap-gmap.Tpo -c -o gmap-gmap.o `test -f 'gmap.c' || echo './'`gmap.c In file included from gmap.c:74: ./getopt.h:147:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a previous declaration [-Wdeprecated-non-prototype] extern int getopt (); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/unistd.h:509:6: note: conflicting prototype is here int getopt(int, char * const [], const char *) __DARWIN_ALIAS(getopt); ^ gmap.c:3244:28: warning: incompatible pointer types passing 'Diagpool_T' (aka 'struct Diagpool_T *') to parameter of type 'Cellpool_T' (aka 'struct Cellpool_T *') [-Wincompatible-pointer-types] matchpool,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR); ^~~~~~~~ gmap.c:2672:61: note: passing argument to parameter 'cellpool' here Matchpool_T matchpool, Pairpool_T pairpool, Cellpool_T cellpool, ^ gmap.c:3244:37: warning: incompatible pointer types passing 'Cellpool_T' (aka 'struct Cellpool_T *') to parameter of type 'Diagpool_T' (aka 'struct Diagpool_T *') [-Wincompatible-pointer-types] matchpool,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR); ^~~~~~~~ gmap.c:2673:17: note: passing argument to parameter 'diagpool' here Diagpool_T diagpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR) { ^ 3 warnings generated. mv -f .deps/gmap-gmap.Tpo .deps/gmap-gmap.Po /bin/sh ../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -o gmap gmap-except.o gmap-assert.o gmap-mem.o gmap-intlist.o gmap-list.o gmap-littleendian.o gmap-bigendian.o gmap-univinterval.o gmap-interval.o gmap-uintlist.o gmap-stopwatch.o gmap-access.o gmap-iit-read-univ.o gmap-iit-read.o gmap-md5.o gmap-bzip2.o gmap-sequence.o gmap-reader.o gmap-genomicpos.o gmap-compress.o gmap-compress-write.o gmap-gbuffer.o gmap-genome.o gmap-genome_hr.o gmap-genome_sites.o gmap-genome-write.o gmap-bitpack64-read.o gmap-indexdb.o gmap-indexdb_hr.o gmap-oligo.o gmap-block.o gmap-chrom.o gmap-segmentpos.o gmap-chrnum.o gmap-chrsubset.o gmap-uinttable.o gmap-gregion.o gmap-match.o gmap-matchpool.o gmap-diagnostic.o gmap-stage1.o gmap-diag.o gmap-diagpool.o gmap-cmet.o gmap-atoi.o gmap-orderstat.o gmap-oligoindex_hr.o gmap-intron.o gmap-maxent.o gmap-maxent_hr.o gmap-pair.o gmap-pairpool.o gmap-cellpool.o gmap-stage2.o gmap-doublelist.o gmap-smooth.o gmap-splicestringpool.o gmap-splicetrie_build.o gmap-splicetrie.o gmap-boyer-moore.o gmap-dynprog.o gmap-translation.o gmap-pbinom.o gmap-changepoint.o gmap-stage3.o gmap-request.o gmap-result.o gmap-inbuffer.o gmap-samheader.o gmap-outbuffer.o gmap-chimera.o gmap-datadir.o gmap-getopt.o gmap-getopt1.o gmap-gmap.o -lz -lbz2 -lm libtool: link: gcc -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -o gmap gmap-except.o gmap-assert.o gmap-mem.o gmap-intlist.o gmap-list.o gmap-littleendian.o gmap-bigendian.o gmap-univinterval.o gmap-interval.o gmap-uintlist.o gmap-stopwatch.o gmap-access.o gmap-iit-read-univ.o gmap-iit-read.o gmap-md5.o gmap-bzip2.o gmap-sequence.o gmap-reader.o gmap-genomicpos.o gmap-compress.o gmap-compress-write.o gmap-gbuffer.o gmap-genome.o gmap-genome_hr.o gmap-genome_sites.o gmap-genome-write.o gmap-bitpack64-read.o gmap-indexdb.o gmap-indexdb_hr.o gmap-oligo.o gmap-block.o gmap-chrom.o gmap-segmentpos.o gmap-chrnum.o gmap-chrsubset.o gmap-uinttable.o gmap-gregion.o gmap-match.o gmap-matchpool.o gmap-diagnostic.o gmap-stage1.o gmap-diag.o gmap-diagpool.o gmap-cmet.o gmap-atoi.o gmap-orderstat.o gmap-oligoindex_hr.o gmap-intron.o gmap-maxent.o gmap-maxent_hr.o gmap-pair.o gmap-pairpool.o gmap-cellpool.o gmap-stage2.o gmap-doublelist.o gmap-smooth.o gmap-splicestringpool.o gmap-splicetrie_build.o gmap-splicetrie.o gmap-boyer-moore.o gmap-dynprog.o gmap-translation.o gmap-pbinom.o gmap-changepoint.o gmap-stage3.o gmap-request.o gmap-result.o gmap-inbuffer.o gmap-samheader.o gmap-outbuffer.o gmap-chimera.o gmap-datadir.o gmap-getopt.o gmap-getopt1.o gmap-gmap.o -lz -lbz2 -lm gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-except.o -MD -MP -MF .deps/gmapl-except.Tpo -c -o gmapl-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/gmapl-except.Tpo .deps/gmapl-except.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-assert.o -MD -MP -MF .deps/gmapl-assert.Tpo -c -o gmapl-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/gmapl-assert.Tpo .deps/gmapl-assert.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-mem.o -MD -MP -MF .deps/gmapl-mem.Tpo -c -o gmapl-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/gmapl-mem.Tpo .deps/gmapl-mem.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-intlist.o -MD -MP -MF .deps/gmapl-intlist.Tpo -c -o gmapl-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/gmapl-intlist.Tpo .deps/gmapl-intlist.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-list.o -MD -MP -MF .deps/gmapl-list.Tpo -c -o gmapl-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/gmapl-list.Tpo .deps/gmapl-list.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-littleendian.o -MD -MP -MF .deps/gmapl-littleendian.Tpo -c -o gmapl-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c mv -f .deps/gmapl-littleendian.Tpo .deps/gmapl-littleendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-bigendian.o -MD -MP -MF .deps/gmapl-bigendian.Tpo -c -o gmapl-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c mv -f .deps/gmapl-bigendian.Tpo .deps/gmapl-bigendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-univinterval.o -MD -MP -MF .deps/gmapl-univinterval.Tpo -c -o gmapl-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~ %llu univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~~ %llu 2 warnings generated. mv -f .deps/gmapl-univinterval.Tpo .deps/gmapl-univinterval.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-interval.o -MD -MP -MF .deps/gmapl-interval.Tpo -c -o gmapl-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/gmapl-interval.Tpo .deps/gmapl-interval.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-uintlist.o -MD -MP -MF .deps/gmapl-uintlist.Tpo -c -o gmapl-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/gmapl-uintlist.Tpo .deps/gmapl-uintlist.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-stopwatch.o -MD -MP -MF .deps/gmapl-stopwatch.Tpo -c -o gmapl-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/gmapl-stopwatch.Tpo .deps/gmapl-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-access.o -MD -MP -MF .deps/gmapl-access.Tpo -c -o gmapl-access.o `test -f 'access.c' || echo './'`access.c access.c:358:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] length,length,errno,strerror(errno)); ^~~~~~ access.c:358:15: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] length,length,errno,strerror(errno)); ^~~~~~ access.c:423:11: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] fd,offset,length,errno,strerror(errno)); ^~~~~~ access.c:493:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] *len,length,errno,strerror(errno)); ^~~~~~ access.c:556:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] offset,length,errno,strerror(errno)); ^~~~~~ access.c:641:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] *len,length,errno,strerror(errno)); ^~~~~~ 6 warnings generated. mv -f .deps/gmapl-access.Tpo .deps/gmapl-access.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-iit-read-univ.o -MD -MP -MF .deps/gmapl-iit-read-univ.Tpo -c -o gmapl-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~~~ %llu iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~ %llu iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~~~ %llu iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~ %llu iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %llu iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~ %llu iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %llu 10 warnings generated. mv -f .deps/gmapl-iit-read-univ.Tpo .deps/gmapl-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-iit-read.o -MD -MP -MF .deps/gmapl-iit-read.Tpo -c -o gmapl-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c mv -f .deps/gmapl-iit-read.Tpo .deps/gmapl-iit-read.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-md5.o -MD -MP -MF .deps/gmapl-md5.Tpo -c -o gmapl-md5.o `test -f 'md5.c' || echo './'`md5.c mv -f .deps/gmapl-md5.Tpo .deps/gmapl-md5.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-bzip2.o -MD -MP -MF .deps/gmapl-bzip2.Tpo -c -o gmapl-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c mv -f .deps/gmapl-bzip2.Tpo .deps/gmapl-bzip2.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-sequence.o -MD -MP -MF .deps/gmapl-sequence.Tpo -c -o gmapl-sequence.o `test -f 'sequence.c' || echo './'`sequence.c mv -f .deps/gmapl-sequence.Tpo .deps/gmapl-sequence.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-reader.o -MD -MP -MF .deps/gmapl-reader.Tpo -c -o gmapl-reader.o `test -f 'reader.c' || echo './'`reader.c mv -f .deps/gmapl-reader.Tpo .deps/gmapl-reader.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-genomicpos.o -MD -MP -MF .deps/gmapl-genomicpos.Tpo -c -o gmapl-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/gmapl-genomicpos.Tpo .deps/gmapl-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-compress.o -MD -MP -MF .deps/gmapl-compress.Tpo -c -o gmapl-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/gmapl-compress.Tpo .deps/gmapl-compress.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-compress-write.o -MD -MP -MF .deps/gmapl-compress-write.Tpo -c -o gmapl-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c compress-write.c:73:80: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i); ~~~ ^~~~~~~~~~ %llu compress-write.c:252:13: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Buffer[i],position+i); ^~~~~~~~~~ compress-write.c:300:13: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Buffer[i],position+i); ^~~~~~~~~~ 3 warnings generated. mv -f .deps/gmapl-compress-write.Tpo .deps/gmapl-compress-write.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-gbuffer.o -MD -MP -MF .deps/gmapl-gbuffer.Tpo -c -o gmapl-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c mv -f .deps/gmapl-gbuffer.Tpo .deps/gmapl-gbuffer.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-genome.o -MD -MP -MF .deps/gmapl-genome.Tpo -c -o gmapl-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c:10292:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu genome.c:10292:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu genome.c:10392:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu genome.c:10392:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu 4 warnings generated. mv -f .deps/gmapl-genome.Tpo .deps/gmapl-genome.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-genome_hr.o -MD -MP -MF .deps/gmapl-genome_hr.Tpo -c -o gmapl-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c mv -f .deps/gmapl-genome_hr.Tpo .deps/gmapl-genome_hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-genome_sites.o -MD -MP -MF .deps/gmapl-genome_sites.Tpo -c -o gmapl-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c genome_sites.c:24729:17: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%u\t",startblock/3*32U); ~~ ^~~~~~~~~~~~~~~~ %llu genome_sites.c:24744:19: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%u\t",ptr/3*32U); ~~ ^~~~~~~~~ %llu genome_sites.c:24751:17: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%u\t",(endblock+3)/3*32U); ~~ ^~~~~~~~~~~~~~~~~~ %llu 3 warnings generated. mv -f .deps/gmapl-genome_sites.Tpo .deps/gmapl-genome_sites.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-genome-write.o -MD -MP -MF .deps/gmapl-genome-write.Tpo -c -o gmapl-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c genome-write.c:253:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~~~ genome-write.c:253:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~ genome-write.c:256:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~~~ genome-write.c:256:32: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~ genome-write.c:430:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~~~ genome-write.c:430:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~ genome-write.c:433:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~~~ genome-write.c:433:32: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~ genome-write.c:595:87: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Chromosome %s is circular. Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U); ~~~ ^~~~~~~~~~~~~~~~ %llu genome-write.c:595:104: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Chromosome %s is circular. Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U); ~~~ ^~~~~~~~~~~~~~ %llu genome-write.c:595:119: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Chromosome %s is circular. Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U); ~~~ ^~~~~~~~~~~~~~~~~ %llu genome-write.c:595:137: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Chromosome %s is circular. Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U); ~~~ ^~~~~~~~~~~~~~~ %llu genome-write.c:643:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~~~ genome-write.c:643:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~ genome-write.c:646:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~~~ genome-write.c:646:32: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~ genome-write.c:787:46: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Genome length is %lu nt\n",genomelength); ~~~ ^~~~~~~~~~~~ %llu 17 warnings generated. mv -f .deps/gmapl-genome-write.Tpo .deps/gmapl-genome-write.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-bitpack64-read.o -MD -MP -MF .deps/gmapl-bitpack64-read.Tpo -c -o gmapl-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c mv -f .deps/gmapl-bitpack64-read.Tpo .deps/gmapl-bitpack64-read.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-indexdb.o -MD -MP -MF .deps/gmapl-indexdb.Tpo -c -o gmapl-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c:1363:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1483:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1653:63: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1792:6: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] ptr,sizeof(Univcoord_T),offset); ^~~ indexdb.c:1792:30: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] ptr,sizeof(Univcoord_T),offset); ^~~~~~ indexdb.c:1934:76: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, ~~~ ^~~~~~~~~~~~~~ %llu indexdb.c:2026:76: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, ~~~ ^~~~~~~~~~~~~~ %llu 7 warnings generated. mv -f .deps/gmapl-indexdb.Tpo .deps/gmapl-indexdb.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-indexdb_hr.o -MD -MP -MF .deps/gmapl-indexdb_hr.Tpo -c -o gmapl-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c indexdb_hr.c:1008:43: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" compound%d.%d:%u+%d\n",i,j,compoundpos->positions[i][j],diagterm); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ %llu indexdb_hr.c:1232:45: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("#%d--%d:%u ",i,batch->nentries,batch->position); ~~ ^~~~~~~~~~~~~~~ %llu 2 warnings generated. mv -f .deps/gmapl-indexdb_hr.Tpo .deps/gmapl-indexdb_hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-oligo.o -MD -MP -MF .deps/gmapl-oligo.Tpo -c -o gmapl-oligo.o `test -f 'oligo.c' || echo './'`oligo.c mv -f .deps/gmapl-oligo.Tpo .deps/gmapl-oligo.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-block.o -MD -MP -MF .deps/gmapl-block.Tpo -c -o gmapl-block.o `test -f 'block.c' || echo './'`block.c mv -f .deps/gmapl-block.Tpo .deps/gmapl-block.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-chrom.o -MD -MP -MF .deps/gmapl-chrom.Tpo -c -o gmapl-chrom.o `test -f 'chrom.c' || echo './'`chrom.c chrom.c:116:15: warning: comparing a pointer to a null character constant; did you mean to compare to NULL? [-Wpointer-compare] while (p != '\0' && *p >= '0' && *p <= '9') { ^~~~ (void *)0 1 warning generated. mv -f .deps/gmapl-chrom.Tpo .deps/gmapl-chrom.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-segmentpos.o -MD -MP -MF .deps/gmapl-segmentpos.Tpo -c -o gmapl-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c segmentpos.c:90:41: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"%s\t%u\t%s\t%u\t%u\n",acc,chroffset+this->chrpos1,Chrom_string(this->chrom),this->chrpos1,this->length); ~~ ^~~~~~~~~~~~~~~~~~~~~~~ %llu 1 warning generated. mv -f .deps/gmapl-segmentpos.Tpo .deps/gmapl-segmentpos.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-chrnum.o -MD -MP -MF .deps/gmapl-chrnum.Tpo -c -o gmapl-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c mv -f .deps/gmapl-chrnum.Tpo .deps/gmapl-chrnum.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-chrsubset.o -MD -MP -MF .deps/gmapl-chrsubset.Tpo -c -o gmapl-chrsubset.o `test -f 'chrsubset.c' || echo './'`chrsubset.c mv -f .deps/gmapl-chrsubset.Tpo .deps/gmapl-chrsubset.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-uinttable.o -MD -MP -MF .deps/gmapl-uinttable.Tpo -c -o gmapl-uinttable.o `test -f 'uinttable.c' || echo './'`uinttable.c mv -f .deps/gmapl-uinttable.Tpo .deps/gmapl-uinttable.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-gregion.o -MD -MP -MF .deps/gmapl-gregion.Tpo -c -o gmapl-gregion.o `test -f 'gregion.c' || echo './'`gregion.c mv -f .deps/gmapl-gregion.Tpo .deps/gmapl-gregion.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-match.o -MD -MP -MF .deps/gmapl-match.Tpo -c -o gmapl-match.o `test -f 'match.c' || echo './'`match.c mv -f .deps/gmapl-match.Tpo .deps/gmapl-match.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-matchpool.o -MD -MP -MF .deps/gmapl-matchpool.Tpo -c -o gmapl-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c mv -f .deps/gmapl-matchpool.Tpo .deps/gmapl-matchpool.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-diagnostic.o -MD -MP -MF .deps/gmapl-diagnostic.Tpo -c -o gmapl-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c mv -f .deps/gmapl-diagnostic.Tpo .deps/gmapl-diagnostic.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-stage1.o -MD -MP -MF .deps/gmapl-stage1.Tpo -c -o gmapl-stage1.o `test -f 'stage1.c' || echo './'`stage1.c mv -f .deps/gmapl-stage1.Tpo .deps/gmapl-stage1.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-diag.o -MD -MP -MF .deps/gmapl-diag.Tpo -c -o gmapl-diag.o `test -f 'diag.c' || echo './'`diag.c mv -f .deps/gmapl-diag.Tpo .deps/gmapl-diag.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-diagpool.o -MD -MP -MF .deps/gmapl-diagpool.Tpo -c -o gmapl-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c mv -f .deps/gmapl-diagpool.Tpo .deps/gmapl-diagpool.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-cmet.o -MD -MP -MF .deps/gmapl-cmet.Tpo -c -o gmapl-cmet.o `test -f 'cmet.c' || echo './'`cmet.c mv -f .deps/gmapl-cmet.Tpo .deps/gmapl-cmet.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-atoi.o -MD -MP -MF .deps/gmapl-atoi.Tpo -c -o gmapl-atoi.o `test -f 'atoi.c' || echo './'`atoi.c mv -f .deps/gmapl-atoi.Tpo .deps/gmapl-atoi.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-orderstat.o -MD -MP -MF .deps/gmapl-orderstat.Tpo -c -o gmapl-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c mv -f .deps/gmapl-orderstat.Tpo .deps/gmapl-orderstat.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-oligoindex_hr.o -MD -MP -MF .deps/gmapl-oligoindex_hr.Tpo -c -o gmapl-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c mv -f .deps/gmapl-oligoindex_hr.Tpo .deps/gmapl-oligoindex_hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-intron.o -MD -MP -MF .deps/gmapl-intron.Tpo -c -o gmapl-intron.o `test -f 'intron.c' || echo './'`intron.c mv -f .deps/gmapl-intron.Tpo .deps/gmapl-intron.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-maxent.o -MD -MP -MF .deps/gmapl-maxent.Tpo -c -o gmapl-maxent.o `test -f 'maxent.c' || echo './'`maxent.c mv -f .deps/gmapl-maxent.Tpo .deps/gmapl-maxent.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-maxent_hr.o -MD -MP -MF .deps/gmapl-maxent_hr.Tpo -c -o gmapl-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c mv -f .deps/gmapl-maxent_hr.Tpo .deps/gmapl-maxent_hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-pair.o -MD -MP -MF .deps/gmapl-pair.Tpo -c -o gmapl-pair.o `test -f 'pair.c' || echo './'`pair.c pair.c:546:25: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP); ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %llu /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^~~~~~~~~~~ pair.c:573:25: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP); ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %llu /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^~~~~~~~~~~ pair.c:600:25: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] sprintf(Buffer,"%u",chroffset + start->genomepos + ONEBASEDP); ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %llu /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^~~~~~~~~~~ pair.c:607:25: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] sprintf(Buffer,"%u",chroffset + end->genomepos + ONEBASEDP); ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %llu /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^~~~~~~~~~~ pair.c:1273:3: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] chroffset + this->genomepos + ONEBASEDP, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:1278:3: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] chroffset + this->genomepos + ONEBASEDP, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:1790:25: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~ %llu pair.c:1790:52: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~ %llu pair.c:1799:27: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~ %llu pair.c:1799:54: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~ %llu pair.c:1913:26: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~ %llu pair.c:1913:53: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~ %llu pair.c:1922:28: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~ %llu pair.c:1922:55: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~ %llu pair.c:2419:24: warning: taking the absolute value of unsigned type 'Chrpos_T' (aka 'unsigned int') has no effect [-Wabsolute-value] sprintf(token,"N%u",abs(intron_end - intron_start) + 1); ^ pair.c:2419:24: note: remove the call to 'abs' since unsigned values cannot be negative sprintf(token,"N%u",abs(intron_end - intron_start) + 1); ^~~ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ pair.c:4651:17: warning: taking the absolute value of unsigned type 'Chrpos_T' (aka 'unsigned int') has no effect [-Wabsolute-value] genome_gap = abs(intron_end - intron_start) + 1; ^ pair.c:4651:17: note: remove the call to 'abs' since unsigned values cannot be negative genome_gap = abs(intron_end - intron_start) + 1; ^~~ pair.c:6986:24: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp," %u%s%u",position1 + ONEBASEDP,"..",position2 + ONEBASEDP); ~~ ^~~~~~~~~~~~~~~~~~~~~ %llu pair.c:6986:51: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp," %u%s%u",position1 + ONEBASEDP,"..",position2 + ONEBASEDP); ~~ ^~~~~~~~~~~~~~~~~~~~~ %llu 18 warnings generated. mv -f .deps/gmapl-pair.Tpo .deps/gmapl-pair.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-pairpool.o -MD -MP -MF .deps/gmapl-pairpool.Tpo -c -o gmapl-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c mv -f .deps/gmapl-pairpool.Tpo .deps/gmapl-pairpool.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-cellpool.o -MD -MP -MF .deps/gmapl-cellpool.Tpo -c -o gmapl-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c mv -f .deps/gmapl-cellpool.Tpo .deps/gmapl-cellpool.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-stage2.o -MD -MP -MF .deps/gmapl-stage2.Tpo -c -o gmapl-stage2.o `test -f 'stage2.c' || echo './'`stage2.c stage2.c:1329:19: warning: taking the absolute value of unsigned type 'Chrpos_T' (aka 'unsigned int') has no effect [-Wabsolute-value] diffdistance = abs(gendistance - querydistance); ^ stage2.c:1329:19: note: remove the call to 'abs' since unsigned values cannot be negative diffdistance = abs(gendistance - querydistance); ^~~ stage2.c:1812:19: warning: taking the absolute value of unsigned type 'Chrpos_T' (aka 'unsigned int') has no effect [-Wabsolute-value] diffdistance = abs(gendistance - querydistance); ^ stage2.c:1812:19: note: remove the call to 'abs' since unsigned values cannot be negative diffdistance = abs(gendistance - querydistance); ^~~ 2 warnings generated. mv -f .deps/gmapl-stage2.Tpo .deps/gmapl-stage2.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-doublelist.o -MD -MP -MF .deps/gmapl-doublelist.Tpo -c -o gmapl-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c mv -f .deps/gmapl-doublelist.Tpo .deps/gmapl-doublelist.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-smooth.o -MD -MP -MF .deps/gmapl-smooth.Tpo -c -o gmapl-smooth.o `test -f 'smooth.c' || echo './'`smooth.c mv -f .deps/gmapl-smooth.Tpo .deps/gmapl-smooth.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-splicestringpool.o -MD -MP -MF .deps/gmapl-splicestringpool.Tpo -c -o gmapl-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c mv -f .deps/gmapl-splicestringpool.Tpo .deps/gmapl-splicestringpool.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-splicetrie_build.o -MD -MP -MF .deps/gmapl-splicetrie_build.Tpo -c -o gmapl-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c splicetrie_build.c:132:31: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%d %u",(int) leaf,position); ~~ ^~~~~~~~ %llu splicetrie_build.c:146:33: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%d %u",(int) leaf,position); ~~ ^~~~~~~~ %llu 2 warnings generated. mv -f .deps/gmapl-splicetrie_build.Tpo .deps/gmapl-splicetrie_build.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-splicetrie.o -MD -MP -MF .deps/gmapl-splicetrie.Tpo -c -o gmapl-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c mv -f .deps/gmapl-splicetrie.Tpo .deps/gmapl-splicetrie.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-boyer-moore.o -MD -MP -MF .deps/gmapl-boyer-moore.Tpo -c -o gmapl-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c mv -f .deps/gmapl-boyer-moore.Tpo .deps/gmapl-boyer-moore.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-dynprog.o -MD -MP -MF .deps/gmapl-dynprog.Tpo -c -o gmapl-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c mv -f .deps/gmapl-dynprog.Tpo .deps/gmapl-dynprog.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-translation.o -MD -MP -MF .deps/gmapl-translation.Tpo -c -o gmapl-translation.o `test -f 'translation.c' || echo './'`translation.c mv -f .deps/gmapl-translation.Tpo .deps/gmapl-translation.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-pbinom.o -MD -MP -MF .deps/gmapl-pbinom.Tpo -c -o gmapl-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c mv -f .deps/gmapl-pbinom.Tpo .deps/gmapl-pbinom.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-changepoint.o -MD -MP -MF .deps/gmapl-changepoint.Tpo -c -o gmapl-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c mv -f .deps/gmapl-changepoint.Tpo .deps/gmapl-changepoint.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-stage3.o -MD -MP -MF .deps/gmapl-stage3.Tpo -c -o gmapl-stage3.o `test -f 'stage3.c' || echo './'`stage3.c mv -f .deps/gmapl-stage3.Tpo .deps/gmapl-stage3.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-request.o -MD -MP -MF .deps/gmapl-request.Tpo -c -o gmapl-request.o `test -f 'request.c' || echo './'`request.c mv -f .deps/gmapl-request.Tpo .deps/gmapl-request.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-result.o -MD -MP -MF .deps/gmapl-result.Tpo -c -o gmapl-result.o `test -f 'result.c' || echo './'`result.c mv -f .deps/gmapl-result.Tpo .deps/gmapl-result.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-inbuffer.o -MD -MP -MF .deps/gmapl-inbuffer.Tpo -c -o gmapl-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c mv -f .deps/gmapl-inbuffer.Tpo .deps/gmapl-inbuffer.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-samheader.o -MD -MP -MF .deps/gmapl-samheader.Tpo -c -o gmapl-samheader.o `test -f 'samheader.c' || echo './'`samheader.c mv -f .deps/gmapl-samheader.Tpo .deps/gmapl-samheader.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-outbuffer.o -MD -MP -MF .deps/gmapl-outbuffer.Tpo -c -o gmapl-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c mv -f .deps/gmapl-outbuffer.Tpo .deps/gmapl-outbuffer.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-chimera.o -MD -MP -MF .deps/gmapl-chimera.Tpo -c -o gmapl-chimera.o `test -f 'chimera.c' || echo './'`chimera.c mv -f .deps/gmapl-chimera.Tpo .deps/gmapl-chimera.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-datadir.o -MD -MP -MF .deps/gmapl-datadir.Tpo -c -o gmapl-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/gmapl-datadir.Tpo .deps/gmapl-datadir.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-getopt.o -MD -MP -MF .deps/gmapl-getopt.Tpo -c -o gmapl-getopt.o `test -f 'getopt.c' || echo './'`getopt.c getopt.c:208:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] my_index (str, chr) ^ getopt.c:291:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] exchange (argv) ^ getopt.c:376:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] _getopt_initialize (argc, argv, optstring) ^ getopt.c:389:28: warning: passing arguments to 'getenv' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] posixly_correct = getenv ("POSIXLY_CORRECT"); ^ getopt.c:498:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] _getopt_internal (argc, argv, optstring, longopts, longind, long_only) ^ getopt.c:1179:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt (argc, argv, optstring) ^ In file included from getopt.c:97: ./getopt.h:147:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent definition [-Wdeprecated-non-prototype] extern int getopt (); ^ 7 warnings generated. mv -f .deps/gmapl-getopt.Tpo .deps/gmapl-getopt.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-getopt1.o -MD -MP -MF .deps/gmapl-getopt1.Tpo -c -o gmapl-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c getopt1.c:71:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt_long (argc, argv, options, long_options, opt_index) ^ getopt1.c:87:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt_long_only (argc, argv, options, long_options, opt_index) ^ 2 warnings generated. mv -f .deps/gmapl-getopt1.Tpo .deps/gmapl-getopt1.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-gmap.o -MD -MP -MF .deps/gmapl-gmap.Tpo -c -o gmapl-gmap.o `test -f 'gmap.c' || echo './'`gmap.c In file included from gmap.c:74: ./getopt.h:147:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a previous declaration [-Wdeprecated-non-prototype] extern int getopt (); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/unistd.h:509:6: note: conflicting prototype is here int getopt(int, char * const [], const char *) __DARWIN_ALIAS(getopt); ^ gmap.c:3244:28: warning: incompatible pointer types passing 'Diagpool_T' (aka 'struct Diagpool_T *') to parameter of type 'Cellpool_T' (aka 'struct Cellpool_T *') [-Wincompatible-pointer-types] matchpool,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR); ^~~~~~~~ gmap.c:2672:61: note: passing argument to parameter 'cellpool' here Matchpool_T matchpool, Pairpool_T pairpool, Cellpool_T cellpool, ^ gmap.c:3244:37: warning: incompatible pointer types passing 'Cellpool_T' (aka 'struct Cellpool_T *') to parameter of type 'Diagpool_T' (aka 'struct Diagpool_T *') [-Wincompatible-pointer-types] matchpool,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR); ^~~~~~~~ gmap.c:2673:17: note: passing argument to parameter 'diagpool' here Diagpool_T diagpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR) { ^ 3 warnings generated. mv -f .deps/gmapl-gmap.Tpo .deps/gmapl-gmap.Po /bin/sh ../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -o gmapl gmapl-except.o gmapl-assert.o gmapl-mem.o gmapl-intlist.o gmapl-list.o gmapl-littleendian.o gmapl-bigendian.o gmapl-univinterval.o gmapl-interval.o gmapl-uintlist.o gmapl-stopwatch.o gmapl-access.o gmapl-iit-read-univ.o gmapl-iit-read.o gmapl-md5.o gmapl-bzip2.o gmapl-sequence.o gmapl-reader.o gmapl-genomicpos.o gmapl-compress.o gmapl-compress-write.o gmapl-gbuffer.o gmapl-genome.o gmapl-genome_hr.o gmapl-genome_sites.o gmapl-genome-write.o gmapl-bitpack64-read.o gmapl-indexdb.o gmapl-indexdb_hr.o gmapl-oligo.o gmapl-block.o gmapl-chrom.o gmapl-segmentpos.o gmapl-chrnum.o gmapl-chrsubset.o gmapl-uinttable.o gmapl-gregion.o gmapl-match.o gmapl-matchpool.o gmapl-diagnostic.o gmapl-stage1.o gmapl-diag.o gmapl-diagpool.o gmapl-cmet.o gmapl-atoi.o gmapl-orderstat.o gmapl-oligoindex_hr.o gmapl-intron.o gmapl-maxent.o gmapl-maxent_hr.o gmapl-pair.o gmapl-pairpool.o gmapl-cellpool.o gmapl-stage2.o gmapl-doublelist.o gmapl-smooth.o gmapl-splicestringpool.o gmapl-splicetrie_build.o gmapl-splicetrie.o gmapl-boyer-moore.o gmapl-dynprog.o gmapl-translation.o gmapl-pbinom.o gmapl-changepoint.o gmapl-stage3.o gmapl-request.o gmapl-result.o gmapl-inbuffer.o gmapl-samheader.o gmapl-outbuffer.o gmapl-chimera.o gmapl-datadir.o gmapl-getopt.o gmapl-getopt1.o gmapl-gmap.o -lz -lbz2 -lm libtool: link: gcc -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -o gmapl gmapl-except.o gmapl-assert.o gmapl-mem.o gmapl-intlist.o gmapl-list.o gmapl-littleendian.o gmapl-bigendian.o gmapl-univinterval.o gmapl-interval.o gmapl-uintlist.o gmapl-stopwatch.o gmapl-access.o gmapl-iit-read-univ.o gmapl-iit-read.o gmapl-md5.o gmapl-bzip2.o gmapl-sequence.o gmapl-reader.o gmapl-genomicpos.o gmapl-compress.o gmapl-compress-write.o gmapl-gbuffer.o gmapl-genome.o gmapl-genome_hr.o gmapl-genome_sites.o gmapl-genome-write.o gmapl-bitpack64-read.o gmapl-indexdb.o gmapl-indexdb_hr.o gmapl-oligo.o gmapl-block.o gmapl-chrom.o gmapl-segmentpos.o gmapl-chrnum.o gmapl-chrsubset.o gmapl-uinttable.o gmapl-gregion.o gmapl-match.o gmapl-matchpool.o gmapl-diagnostic.o gmapl-stage1.o gmapl-diag.o gmapl-diagpool.o gmapl-cmet.o gmapl-atoi.o gmapl-orderstat.o gmapl-oligoindex_hr.o gmapl-intron.o gmapl-maxent.o gmapl-maxent_hr.o gmapl-pair.o gmapl-pairpool.o gmapl-cellpool.o gmapl-stage2.o gmapl-doublelist.o gmapl-smooth.o gmapl-splicestringpool.o gmapl-splicetrie_build.o gmapl-splicetrie.o gmapl-boyer-moore.o gmapl-dynprog.o gmapl-translation.o gmapl-pbinom.o gmapl-changepoint.o gmapl-stage3.o gmapl-request.o gmapl-result.o gmapl-inbuffer.o gmapl-samheader.o gmapl-outbuffer.o gmapl-chimera.o gmapl-datadir.o gmapl-getopt.o gmapl-getopt1.o gmapl-gmap.o -lz -lbz2 -lm gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-except.o -MD -MP -MF .deps/get_genome-except.Tpo -c -o get_genome-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/get_genome-except.Tpo .deps/get_genome-except.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-assert.o -MD -MP -MF .deps/get_genome-assert.Tpo -c -o get_genome-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/get_genome-assert.Tpo .deps/get_genome-assert.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-mem.o -MD -MP -MF .deps/get_genome-mem.Tpo -c -o get_genome-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/get_genome-mem.Tpo .deps/get_genome-mem.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-intlist.o -MD -MP -MF .deps/get_genome-intlist.Tpo -c -o get_genome-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/get_genome-intlist.Tpo .deps/get_genome-intlist.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-list.o -MD -MP -MF .deps/get_genome-list.Tpo -c -o get_genome-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/get_genome-list.Tpo .deps/get_genome-list.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-littleendian.o -MD -MP -MF .deps/get_genome-littleendian.Tpo -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c mv -f .deps/get_genome-littleendian.Tpo .deps/get_genome-littleendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-bigendian.o -MD -MP -MF .deps/get_genome-bigendian.Tpo -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c mv -f .deps/get_genome-bigendian.Tpo .deps/get_genome-bigendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-univinterval.o -MD -MP -MF .deps/get_genome-univinterval.Tpo -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~ %llu univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~~ %llu 2 warnings generated. mv -f .deps/get_genome-univinterval.Tpo .deps/get_genome-univinterval.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-interval.o -MD -MP -MF .deps/get_genome-interval.Tpo -c -o get_genome-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/get_genome-interval.Tpo .deps/get_genome-interval.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-uintlist.o -MD -MP -MF .deps/get_genome-uintlist.Tpo -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/get_genome-uintlist.Tpo .deps/get_genome-uintlist.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-stopwatch.o -MD -MP -MF .deps/get_genome-stopwatch.Tpo -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/get_genome-stopwatch.Tpo .deps/get_genome-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-access.o -MD -MP -MF .deps/get_genome-access.Tpo -c -o get_genome-access.o `test -f 'access.c' || echo './'`access.c access.c:358:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] length,length,errno,strerror(errno)); ^~~~~~ access.c:358:15: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] length,length,errno,strerror(errno)); ^~~~~~ access.c:423:11: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] fd,offset,length,errno,strerror(errno)); ^~~~~~ access.c:493:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] *len,length,errno,strerror(errno)); ^~~~~~ access.c:556:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] offset,length,errno,strerror(errno)); ^~~~~~ access.c:641:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] *len,length,errno,strerror(errno)); ^~~~~~ 6 warnings generated. mv -f .deps/get_genome-access.Tpo .deps/get_genome-access.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-iit-read-univ.o -MD -MP -MF .deps/get_genome-iit-read-univ.Tpo -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~~~ %llu iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~ %llu iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~~~ %llu iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~ %llu iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %llu iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~ %llu iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %llu 10 warnings generated. mv -f .deps/get_genome-iit-read-univ.Tpo .deps/get_genome-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-iit-read.o -MD -MP -MF .deps/get_genome-iit-read.Tpo -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c mv -f .deps/get_genome-iit-read.Tpo .deps/get_genome-iit-read.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-md5.o -MD -MP -MF .deps/get_genome-md5.Tpo -c -o get_genome-md5.o `test -f 'md5.c' || echo './'`md5.c mv -f .deps/get_genome-md5.Tpo .deps/get_genome-md5.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-bzip2.o -MD -MP -MF .deps/get_genome-bzip2.Tpo -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c mv -f .deps/get_genome-bzip2.Tpo .deps/get_genome-bzip2.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-sequence.o -MD -MP -MF .deps/get_genome-sequence.Tpo -c -o get_genome-sequence.o `test -f 'sequence.c' || echo './'`sequence.c mv -f .deps/get_genome-sequence.Tpo .deps/get_genome-sequence.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-genome.o -MD -MP -MF .deps/get_genome-genome.Tpo -c -o get_genome-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c:10292:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu genome.c:10292:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu genome.c:10392:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu genome.c:10392:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu 4 warnings generated. mv -f .deps/get_genome-genome.Tpo .deps/get_genome-genome.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-genomicpos.o -MD -MP -MF .deps/get_genome-genomicpos.Tpo -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/get_genome-genomicpos.Tpo .deps/get_genome-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-chrom.o -MD -MP -MF .deps/get_genome-chrom.Tpo -c -o get_genome-chrom.o `test -f 'chrom.c' || echo './'`chrom.c chrom.c:116:15: warning: comparing a pointer to a null character constant; did you mean to compare to NULL? [-Wpointer-compare] while (p != '\0' && *p >= '0' && *p <= '9') { ^~~~ (void *)0 1 warning generated. mv -f .deps/get_genome-chrom.Tpo .deps/get_genome-chrom.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-chrnum.o -MD -MP -MF .deps/get_genome-chrnum.Tpo -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c mv -f .deps/get_genome-chrnum.Tpo .deps/get_genome-chrnum.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-chrsubset.o -MD -MP -MF .deps/get_genome-chrsubset.Tpo -c -o get_genome-chrsubset.o `test -f 'chrsubset.c' || echo './'`chrsubset.c mv -f .deps/get_genome-chrsubset.Tpo .deps/get_genome-chrsubset.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-datadir.o -MD -MP -MF .deps/get_genome-datadir.Tpo -c -o get_genome-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/get_genome-datadir.Tpo .deps/get_genome-datadir.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-parserange.o -MD -MP -MF .deps/get_genome-parserange.Tpo -c -o get_genome-parserange.o `test -f 'parserange.c' || echo './'`parserange.c parserange.c:187:8: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Univinterval_low(interval),left,*genomicstart); ^~~~~~~~~~~~~~~~~~~~~~~~~~ parserange.c:187:35: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Univinterval_low(interval),left,*genomicstart); ^~~~ parserange.c:187:40: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Univinterval_low(interval),left,*genomicstart); ^~~~~~~~~~~~~ 3 warnings generated. mv -f .deps/get_genome-parserange.Tpo .deps/get_genome-parserange.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-getopt.o -MD -MP -MF .deps/get_genome-getopt.Tpo -c -o get_genome-getopt.o `test -f 'getopt.c' || echo './'`getopt.c getopt.c:208:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] my_index (str, chr) ^ getopt.c:291:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] exchange (argv) ^ getopt.c:376:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] _getopt_initialize (argc, argv, optstring) ^ getopt.c:389:28: warning: passing arguments to 'getenv' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] posixly_correct = getenv ("POSIXLY_CORRECT"); ^ getopt.c:498:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] _getopt_internal (argc, argv, optstring, longopts, longind, long_only) ^ getopt.c:1179:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt (argc, argv, optstring) ^ In file included from getopt.c:97: ./getopt.h:147:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent definition [-Wdeprecated-non-prototype] extern int getopt (); ^ 7 warnings generated. mv -f .deps/get_genome-getopt.Tpo .deps/get_genome-getopt.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-getopt1.o -MD -MP -MF .deps/get_genome-getopt1.Tpo -c -o get_genome-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c getopt1.c:71:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt_long (argc, argv, options, long_options, opt_index) ^ getopt1.c:87:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt_long_only (argc, argv, options, long_options, opt_index) ^ 2 warnings generated. mv -f .deps/get_genome-getopt1.Tpo .deps/get_genome-getopt1.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-get-genome.o -MD -MP -MF .deps/get_genome-get-genome.Tpo -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo './'`get-genome.c In file included from get-genome.c:25: ./getopt.h:147:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a previous declaration [-Wdeprecated-non-prototype] extern int getopt (); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/unistd.h:509:6: note: conflicting prototype is here int getopt(int, char * const [], const char *) __DARWIN_ALIAS(getopt); ^ get-genome.c:194:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu%s%lu\t",left+1,SEPARATOR,left+length); ~~~ ^~~~~~ %llu get-genome.c:194:40: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu%s%lu\t",left+1,SEPARATOR,left+length); ~~~ ^~~~~~~~~~~ %llu get-genome.c:410:41: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" %s:%lu%s%lu\n",dbversion,genomicstart+genomiclength,SEPARATOR,genomicstart+1U); ~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~ %llu get-genome.c:410:78: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" %s:%lu%s%lu\n",dbversion,genomicstart+genomiclength,SEPARATOR,genomicstart+1U); ~~~ ^~~~~~~~~~~~~~~ %llu get-genome.c:428:41: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" %s:%lu%s%lu\n",dbversion,genomicstart+1U,SEPARATOR,genomicstart+genomiclength); ~~~ ^~~~~~~~~~~~~~~ %llu get-genome.c:428:67: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" %s:%lu%s%lu\n",dbversion,genomicstart+1U,SEPARATOR,genomicstart+genomiclength); ~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~ %llu 7 warnings generated. mv -f .deps/get_genome-get-genome.Tpo .deps/get_genome-get-genome.Po /bin/sh ../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-access.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-chrsubset.o get_genome-datadir.o get_genome-parserange.o get_genome-getopt.o get_genome-getopt1.o get_genome-get-genome.o -lz -lbz2 -lm libtool: link: gcc -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-access.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-chrsubset.o get_genome-datadir.o get_genome-parserange.o get_genome-getopt.o get_genome-getopt1.o get_genome-get-genome.o -lz -lbz2 -lm gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-except.o -MD -MP -MF .deps/gmapindex-except.Tpo -c -o gmapindex-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/gmapindex-except.Tpo .deps/gmapindex-except.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-assert.o -MD -MP -MF .deps/gmapindex-assert.Tpo -c -o gmapindex-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/gmapindex-assert.Tpo .deps/gmapindex-assert.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-mem.o -MD -MP -MF .deps/gmapindex-mem.Tpo -c -o gmapindex-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/gmapindex-mem.Tpo .deps/gmapindex-mem.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-intlist.o -MD -MP -MF .deps/gmapindex-intlist.Tpo -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/gmapindex-intlist.Tpo .deps/gmapindex-intlist.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-list.o -MD -MP -MF .deps/gmapindex-list.Tpo -c -o gmapindex-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/gmapindex-list.Tpo .deps/gmapindex-list.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-littleendian.o -MD -MP -MF .deps/gmapindex-littleendian.Tpo -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c mv -f .deps/gmapindex-littleendian.Tpo .deps/gmapindex-littleendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-bigendian.o -MD -MP -MF .deps/gmapindex-bigendian.Tpo -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c mv -f .deps/gmapindex-bigendian.Tpo .deps/gmapindex-bigendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-univinterval.o -MD -MP -MF .deps/gmapindex-univinterval.Tpo -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~ %llu univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~~ %llu 2 warnings generated. mv -f .deps/gmapindex-univinterval.Tpo .deps/gmapindex-univinterval.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-interval.o -MD -MP -MF .deps/gmapindex-interval.Tpo -c -o gmapindex-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/gmapindex-interval.Tpo .deps/gmapindex-interval.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-uintlist.o -MD -MP -MF .deps/gmapindex-uintlist.Tpo -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/gmapindex-uintlist.Tpo .deps/gmapindex-uintlist.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-stopwatch.o -MD -MP -MF .deps/gmapindex-stopwatch.Tpo -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/gmapindex-stopwatch.Tpo .deps/gmapindex-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-access.o -MD -MP -MF .deps/gmapindex-access.Tpo -c -o gmapindex-access.o `test -f 'access.c' || echo './'`access.c access.c:358:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] length,length,errno,strerror(errno)); ^~~~~~ access.c:358:15: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] length,length,errno,strerror(errno)); ^~~~~~ access.c:423:11: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] fd,offset,length,errno,strerror(errno)); ^~~~~~ access.c:493:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] *len,length,errno,strerror(errno)); ^~~~~~ access.c:556:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] offset,length,errno,strerror(errno)); ^~~~~~ access.c:641:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] *len,length,errno,strerror(errno)); ^~~~~~ 6 warnings generated. mv -f .deps/gmapindex-access.Tpo .deps/gmapindex-access.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-iit-read-univ.o -MD -MP -MF .deps/gmapindex-iit-read-univ.Tpo -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~~~ %llu iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~ %llu iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~~~ %llu iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~ %llu iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %llu iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~ %llu iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %llu 10 warnings generated. mv -f .deps/gmapindex-iit-read-univ.Tpo .deps/gmapindex-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-iit-write-univ.o -MD -MP -MF .deps/gmapindex-iit-write-univ.Tpo -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo './'`iit-write-univ.c iit-write-univ.c:93:17: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] if (endpoint(intervals,array[lambda]) > endpoint(intervals,array[lambda + 1])) { ^ iit-write-univ.c:93:53: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] if (endpoint(intervals,array[lambda]) > endpoint(intervals,array[lambda + 1])) { ^ 2 warnings generated. mv -f .deps/gmapindex-iit-write-univ.Tpo .deps/gmapindex-iit-write-univ.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-iit-read.o -MD -MP -MF .deps/gmapindex-iit-read.Tpo -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c mv -f .deps/gmapindex-iit-read.Tpo .deps/gmapindex-iit-read.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-md5.o -MD -MP -MF .deps/gmapindex-md5.Tpo -c -o gmapindex-md5.o `test -f 'md5.c' || echo './'`md5.c mv -f .deps/gmapindex-md5.Tpo .deps/gmapindex-md5.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-bzip2.o -MD -MP -MF .deps/gmapindex-bzip2.Tpo -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c mv -f .deps/gmapindex-bzip2.Tpo .deps/gmapindex-bzip2.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-sequence.o -MD -MP -MF .deps/gmapindex-sequence.Tpo -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo './'`sequence.c mv -f .deps/gmapindex-sequence.Tpo .deps/gmapindex-sequence.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-genome.o -MD -MP -MF .deps/gmapindex-genome.Tpo -c -o gmapindex-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c:10292:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu genome.c:10292:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu genome.c:10392:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu genome.c:10392:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu 4 warnings generated. mv -f .deps/gmapindex-genome.Tpo .deps/gmapindex-genome.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-genomicpos.o -MD -MP -MF .deps/gmapindex-genomicpos.Tpo -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/gmapindex-genomicpos.Tpo .deps/gmapindex-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-compress-write.o -MD -MP -MF .deps/gmapindex-compress-write.Tpo -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c compress-write.c:73:80: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i); ~~~ ^~~~~~~~~~ %llu compress-write.c:252:13: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Buffer[i],position+i); ^~~~~~~~~~ compress-write.c:300:13: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Buffer[i],position+i); ^~~~~~~~~~ 3 warnings generated. mv -f .deps/gmapindex-compress-write.Tpo .deps/gmapindex-compress-write.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-genome-write.o -MD -MP -MF .deps/gmapindex-genome-write.Tpo -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c genome-write.c:253:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~~~ genome-write.c:253:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~ genome-write.c:256:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~~~ genome-write.c:256:32: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~ genome-write.c:430:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~~~ genome-write.c:430:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~ genome-write.c:433:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~~~ genome-write.c:433:32: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~ genome-write.c:595:87: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Chromosome %s is circular. Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U); ~~~ ^~~~~~~~~~~~~~~~ %llu genome-write.c:595:104: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Chromosome %s is circular. Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U); ~~~ ^~~~~~~~~~~~~~ %llu genome-write.c:595:119: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Chromosome %s is circular. Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U); ~~~ ^~~~~~~~~~~~~~~~~ %llu genome-write.c:595:137: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Chromosome %s is circular. Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U); ~~~ ^~~~~~~~~~~~~~~ %llu genome-write.c:643:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~~~ genome-write.c:643:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~ genome-write.c:646:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~~~ genome-write.c:646:32: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~ genome-write.c:787:46: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Genome length is %lu nt\n",genomelength); ~~~ ^~~~~~~~~~~~ %llu 17 warnings generated. mv -f .deps/gmapindex-genome-write.Tpo .deps/gmapindex-genome-write.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-compress.o -MD -MP -MF .deps/gmapindex-compress.Tpo -c -o gmapindex-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/gmapindex-compress.Tpo .deps/gmapindex-compress.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-genome_hr.o -MD -MP -MF .deps/gmapindex-genome_hr.Tpo -c -o gmapindex-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c mv -f .deps/gmapindex-genome_hr.Tpo .deps/gmapindex-genome_hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-bitpack64-read.o -MD -MP -MF .deps/gmapindex-bitpack64-read.Tpo -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c mv -f .deps/gmapindex-bitpack64-read.Tpo .deps/gmapindex-bitpack64-read.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-bitpack64-write.o -MD -MP -MF .deps/gmapindex-bitpack64-write.Tpo -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c bitpack64-write.c:4146:38: warning: passing 'const UINT4 *' (aka 'const unsigned int *') to parameter of type 'Positionsptr_T *' (aka 'unsigned int *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] reorder_values_vertically(vertical,horizontal); ^~~~~~~~~~ bitpack64-write.c:4091:70: note: passing argument to parameter 'horizontal' here reorder_values_vertically (Positionsptr_T *vertical, Positionsptr_T *horizontal) { ^ 1 warning generated. mv -f .deps/gmapindex-bitpack64-write.Tpo .deps/gmapindex-bitpack64-write.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-indexdb.o -MD -MP -MF .deps/gmapindex-indexdb.Tpo -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c:1363:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1483:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1653:63: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1792:6: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] ptr,sizeof(Univcoord_T),offset); ^~~ indexdb.c:1792:30: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] ptr,sizeof(Univcoord_T),offset); ^~~~~~ indexdb.c:1934:76: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, ~~~ ^~~~~~~~~~~~~~ %llu indexdb.c:2026:76: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, ~~~ ^~~~~~~~~~~~~~ %llu 7 warnings generated. mv -f .deps/gmapindex-indexdb.Tpo .deps/gmapindex-indexdb.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-indexdb-write.o -MD -MP -MF .deps/gmapindex-indexdb-write.Tpo -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c indexdb-write.c:2495:3: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]); ^~~~~~ indexdb-write.c:2495:10: warning: format specifies type 'int' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]); ^ indexdb-write.c:2495:12: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]); ^~~~~~~~ indexdb-write.c:2727:8: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligok,offsetscomp[gammaptrs[p-1]],cum); ^~~~~~ indexdb-write.c:2738:8: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligok-1UL,offsets[oligok-1],cum); ^~~~~~~~~~ indexdb-write.c:2761:3: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligok-1UL,offsets[oligok-1],cum); ^~~~~~~~~~ indexdb-write.c:2788:6: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligok,offsetscomp[gammaptrs[p-1]],cum); ^~~~~~ indexdb-write.c:2799:6: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligok,offsets[oligok],*ptr); ^~~~~~ indexdb-write.c:2888:59: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Allocating %lu*%lu bytes for offsets\n",oligospace+1UL,sizeof(Positionsptr_T)); ~~~ ^~~~~~~~~~~~~~ %llu indexdb-write.c:2895:101: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Unable to allocate %lu bytes of memory, needed to build offsets with %d-mers\n",oligospace+1UL,index1part); ~~~ ^~~~~~~~~~~~~~ %llu indexdb-write.c:2972:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Bad character %c at position %lu\n",c,position); ~~~ ^~~~~~~~ %llu indexdb-write.c:3094:79: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Writing %lu offsets to file with total of %u k-mers...",oligospace+1,offsets[oligospace]); ~~~ ^~~~~~~~~~~~ %llu indexdb-write.c:3127:101: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Writing %lu offsets compressed via gammas to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]); ~~~ ^~~~~~~~~~~~~~ %llu indexdb-write.c:3171:102: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Writing %lu offsets compressed via bitpack to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]); ~~~ ^~~~~~~~~~~~~~ %llu indexdb-write.c:3234:85: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] fprintf(stderr,"Attempted to do lseek on offset %u*%lu=%lu\n",ptr,sizeof(UINT4),offset); ~~~ ^~~~~~ %lld indexdb-write.c:3246:85: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] fprintf(stderr,"Attempted to do lseek on offset %u*%lu=%lu\n",ptr,sizeof(UINT8),offset); ~~~ ^~~~~~ %lld indexdb-write.c:3371:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Bad character %c at position %lu\n",c,position); ~~~ ^~~~~~~~ %llu indexdb-write.c:3601:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Bad character %c at position %lu\n",c,position); ~~~ ^~~~~~~~ %llu indexdb-write.c:3796:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] positionsfile,totalcounts*sizeof(UINT8),filesize); ^~~~~~~~ indexdb-write.c:3823:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] positionsfile,totalcounts*sizeof(UINT8),filesize); ^~~~~~~~ indexdb-write.c:3838:45: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] positionsfile,totalcounts*sizeof(UINT8),filesize); ^~~~~~~~ indexdb-write.c:3865:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] positionsfile,totalcounts*sizeof(UINT4),filesize); ^~~~~~~~ indexdb-write.c:3892:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] positionsfile,totalcounts*sizeof(UINT4),filesize); ^~~~~~~~ indexdb-write.c:3907:45: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] positionsfile,totalcounts*sizeof(UINT4),filesize); ^~~~~~~~ 24 warnings generated. mv -f .deps/gmapindex-indexdb-write.Tpo .deps/gmapindex-indexdb-write.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-table.o -MD -MP -MF .deps/gmapindex-table.Tpo -c -o gmapindex-table.o `test -f 'table.c' || echo './'`table.c table.c:283:18: warning: passing 'const void **' to parameter of type 'void **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers] (*keyfree)(&p->key); ^~~~~~~ 1 warning generated. mv -f .deps/gmapindex-table.Tpo .deps/gmapindex-table.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-tableuint.o -MD -MP -MF .deps/gmapindex-tableuint.Tpo -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo './'`tableuint.c mv -f .deps/gmapindex-tableuint.Tpo .deps/gmapindex-tableuint.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-tableuint8.o -MD -MP -MF .deps/gmapindex-tableuint8.Tpo -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo './'`tableuint8.c mv -f .deps/gmapindex-tableuint8.Tpo .deps/gmapindex-tableuint8.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-chrom.o -MD -MP -MF .deps/gmapindex-chrom.Tpo -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo './'`chrom.c chrom.c:116:15: warning: comparing a pointer to a null character constant; did you mean to compare to NULL? [-Wpointer-compare] while (p != '\0' && *p >= '0' && *p <= '9') { ^~~~ (void *)0 1 warning generated. mv -f .deps/gmapindex-chrom.Tpo .deps/gmapindex-chrom.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-segmentpos.o -MD -MP -MF .deps/gmapindex-segmentpos.Tpo -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c segmentpos.c:90:41: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"%s\t%u\t%s\t%u\t%u\n",acc,chroffset+this->chrpos1,Chrom_string(this->chrom),this->chrpos1,this->length); ~~ ^~~~~~~~~~~~~~~~~~~~~~~ %llu 1 warning generated. mv -f .deps/gmapindex-segmentpos.Tpo .deps/gmapindex-segmentpos.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-saca-k.o -MD -MP -MF .deps/gmapindex-saca-k.Tpo -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo './'`saca-k.c mv -f .deps/gmapindex-saca-k.Tpo .deps/gmapindex-saca-k.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-sarray-write.o -MD -MP -MF .deps/gmapindex-sarray-write.Tpo -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo './'`sarray-write.c mv -f .deps/gmapindex-sarray-write.Tpo .deps/gmapindex-sarray-write.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT gmapindex-gmapindex.o -MD -MP -MF .deps/gmapindex-gmapindex.Tpo -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo './'`gmapindex.c gmapindex.c:305:64: warning: format specifies type 'unsigned long *' but the argument has type 'Univcoord_T *' (aka 'unsigned long long *') [-Wformat] nitems = sscanf(Buffer,"%s %s %lu",accession_p,chrpos_string,&universal_coord); ~~~ ^~~~~~~~~~~~~~~~ %llu gmapindex.c:510:19: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] chr_string,chroffset+1,chroffset+1+chrlength-1); ^~~~~~~~~~~ gmapindex.c:510:31: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] chr_string,chroffset+1,chroffset+1+chrlength-1); ^~~~~~~~~~~~~~~~~~~~~~~ gmapindex.c:521:17: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] chr_string,chroffset+1,chroffset+chrlength,chrlength); ^~~~~~~~~~~ gmapindex.c:521:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] chr_string,chroffset+1,chroffset+chrlength,chrlength); ^~~~~~~~~~~~~~~~~~~ gmapindex.c:696:22: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accessions[i],universalpos2+1U,universalpos1, ^~~~~~~~~~~~~~~~ gmapindex.c:696:39: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accessions[i],universalpos2+1U,universalpos1, ^~~~~~~~~~~~~ gmapindex.c:701:22: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accessions[i],universalpos1+1U,universalpos2, ^~~~~~~~~~~~~~~~ gmapindex.c:701:39: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accessions[i],universalpos1+1U,universalpos2, ^~~~~~~~~~~~~ gmapindex.c:1061:54: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Total genomic length = %lu bp\n",totalnts); ~~~ ^~~~~~~~ %llu 10 warnings generated. mv -f .deps/gmapindex-gmapindex.Tpo .deps/gmapindex-gmapindex.Po /bin/sh ../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -DUTILITYP=1 -O3 -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-access.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-genome_hr.o gmapindex-bitpack64-read.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-saca-k.o gmapindex-sarray-write.o gmapindex-gmapindex.o -lz -lbz2 -lm libtool: link: gcc -D_THREAD_SAFE -DUTILITYP=1 -O3 -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-access.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-genome_hr.o gmapindex-bitpack64-read.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-saca-k.o gmapindex-sarray-write.o gmapindex-gmapindex.o -lz -lbz2 -lm gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_store-except.o -MD -MP -MF .deps/iit_store-except.Tpo -c -o iit_store-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/iit_store-except.Tpo .deps/iit_store-except.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_store-assert.o -MD -MP -MF .deps/iit_store-assert.Tpo -c -o iit_store-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/iit_store-assert.Tpo .deps/iit_store-assert.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_store-mem.o -MD -MP -MF .deps/iit_store-mem.Tpo -c -o iit_store-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/iit_store-mem.Tpo .deps/iit_store-mem.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_store-intlist.o -MD -MP -MF .deps/iit_store-intlist.Tpo -c -o iit_store-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/iit_store-intlist.Tpo .deps/iit_store-intlist.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_store-list.o -MD -MP -MF .deps/iit_store-list.Tpo -c -o iit_store-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/iit_store-list.Tpo .deps/iit_store-list.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_store-littleendian.o -MD -MP -MF .deps/iit_store-littleendian.Tpo -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c mv -f .deps/iit_store-littleendian.Tpo .deps/iit_store-littleendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_store-bigendian.o -MD -MP -MF .deps/iit_store-bigendian.Tpo -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c mv -f .deps/iit_store-bigendian.Tpo .deps/iit_store-bigendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_store-univinterval.o -MD -MP -MF .deps/iit_store-univinterval.Tpo -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~ %llu univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~~ %llu 2 warnings generated. mv -f .deps/iit_store-univinterval.Tpo .deps/iit_store-univinterval.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_store-interval.o -MD -MP -MF .deps/iit_store-interval.Tpo -c -o iit_store-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/iit_store-interval.Tpo .deps/iit_store-interval.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_store-uintlist.o -MD -MP -MF .deps/iit_store-uintlist.Tpo -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/iit_store-uintlist.Tpo .deps/iit_store-uintlist.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_store-stopwatch.o -MD -MP -MF .deps/iit_store-stopwatch.Tpo -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/iit_store-stopwatch.Tpo .deps/iit_store-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_store-access.o -MD -MP -MF .deps/iit_store-access.Tpo -c -o iit_store-access.o `test -f 'access.c' || echo './'`access.c access.c:358:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] length,length,errno,strerror(errno)); ^~~~~~ access.c:358:15: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] length,length,errno,strerror(errno)); ^~~~~~ access.c:423:11: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] fd,offset,length,errno,strerror(errno)); ^~~~~~ access.c:493:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] *len,length,errno,strerror(errno)); ^~~~~~ access.c:556:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] offset,length,errno,strerror(errno)); ^~~~~~ access.c:641:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] *len,length,errno,strerror(errno)); ^~~~~~ 6 warnings generated. mv -f .deps/iit_store-access.Tpo .deps/iit_store-access.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_store-iit-write-univ.o -MD -MP -MF .deps/iit_store-iit-write-univ.Tpo -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo './'`iit-write-univ.c iit-write-univ.c:93:17: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] if (endpoint(intervals,array[lambda]) > endpoint(intervals,array[lambda + 1])) { ^ iit-write-univ.c:93:53: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] if (endpoint(intervals,array[lambda]) > endpoint(intervals,array[lambda + 1])) { ^ 2 warnings generated. mv -f .deps/iit_store-iit-write-univ.Tpo .deps/iit_store-iit-write-univ.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_store-iit-write.o -MD -MP -MF .deps/iit_store-iit-write.Tpo -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo './'`iit-write.c iit-write.c:92:17: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] if (endpoint(intervals,array[lambda]) > endpoint(intervals,array[lambda + 1])) { ^ iit-write.c:92:53: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] if (endpoint(intervals,array[lambda]) > endpoint(intervals,array[lambda + 1])) { ^ 2 warnings generated. mv -f .deps/iit_store-iit-write.Tpo .deps/iit_store-iit-write.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_store-tableint.o -MD -MP -MF .deps/iit_store-tableint.Tpo -c -o iit_store-tableint.o `test -f 'tableint.c' || echo './'`tableint.c mv -f .deps/iit_store-tableint.Tpo .deps/iit_store-tableint.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_store-table.o -MD -MP -MF .deps/iit_store-table.Tpo -c -o iit_store-table.o `test -f 'table.c' || echo './'`table.c table.c:283:18: warning: passing 'const void **' to parameter of type 'void **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers] (*keyfree)(&p->key); ^~~~~~~ 1 warning generated. mv -f .deps/iit_store-table.Tpo .deps/iit_store-table.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_store-chrom.o -MD -MP -MF .deps/iit_store-chrom.Tpo -c -o iit_store-chrom.o `test -f 'chrom.c' || echo './'`chrom.c chrom.c:116:15: warning: comparing a pointer to a null character constant; did you mean to compare to NULL? [-Wpointer-compare] while (p != '\0' && *p >= '0' && *p <= '9') { ^~~~ (void *)0 1 warning generated. mv -f .deps/iit_store-chrom.Tpo .deps/iit_store-chrom.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_store-getopt.o -MD -MP -MF .deps/iit_store-getopt.Tpo -c -o iit_store-getopt.o `test -f 'getopt.c' || echo './'`getopt.c getopt.c:208:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] my_index (str, chr) ^ getopt.c:291:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] exchange (argv) ^ getopt.c:376:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] _getopt_initialize (argc, argv, optstring) ^ getopt.c:389:28: warning: passing arguments to 'getenv' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] posixly_correct = getenv ("POSIXLY_CORRECT"); ^ getopt.c:498:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] _getopt_internal (argc, argv, optstring, longopts, longind, long_only) ^ getopt.c:1179:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt (argc, argv, optstring) ^ In file included from getopt.c:97: ./getopt.h:147:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent definition [-Wdeprecated-non-prototype] extern int getopt (); ^ 7 warnings generated. mv -f .deps/iit_store-getopt.Tpo .deps/iit_store-getopt.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_store-getopt1.o -MD -MP -MF .deps/iit_store-getopt1.Tpo -c -o iit_store-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c getopt1.c:71:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt_long (argc, argv, options, long_options, opt_index) ^ getopt1.c:87:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt_long_only (argc, argv, options, long_options, opt_index) ^ 2 warnings generated. mv -f .deps/iit_store-getopt1.Tpo .deps/iit_store-getopt1.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_store-iit_store.o -MD -MP -MF .deps/iit_store-iit_store.Tpo -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo './'`iit_store.c In file included from iit_store.c:32: ./getopt.h:147:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a previous declaration [-Wdeprecated-non-prototype] extern int getopt (); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/unistd.h:509:6: note: conflicting prototype is here int getopt(int, char * const [], const char *) __DARWIN_ALIAS(getopt); ^ iit_store.c:371:51: warning: format specifies type 'unsigned long *' but the argument has type 'Univcoord_T *' (aka 'unsigned long long *') [-Wformat] nscanned = sscanf(header,">%s %lu %lu\n",Buffer,&(*start),&(*end)); ~~~ ^~~~~~~~~ %llu iit_store.c:371:61: warning: format specifies type 'unsigned long *' but the argument has type 'Univcoord_T *' (aka 'unsigned long long *') [-Wformat] nscanned = sscanf(header,">%s %lu %lu\n",Buffer,&(*start),&(*end)); ~~~ ^~~~~~~ %llu iit_store.c:596:46: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Maximum coordinate: %lu\n",*max_coordinate); ~~~ ^~~~~~~~~~~~~~~ %llu iit_store.c:597:62: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Total label length: %lu + %d separators\n",*label_totallength,nentries); ~~~ ^~~~~~~~~~~~~~~~~~ %llu iit_store.c:598:67: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Total annotation length: %lu + %d separators\n",*annot_totallength,nentries); ~~~ ^~~~~~~~~~~~~~~~~~ %llu 6 warnings generated. mv -f .deps/iit_store-iit_store.Tpo .deps/iit_store-iit_store.Po /bin/sh ../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -DUTILITYP=1 -O3 -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-access.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-getopt.o iit_store-getopt1.o iit_store-iit_store.o -lm libtool: link: gcc -D_THREAD_SAFE -DUTILITYP=1 -O3 -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-access.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-getopt.o iit_store-getopt1.o iit_store-iit_store.o -lm gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_get-except.o -MD -MP -MF .deps/iit_get-except.Tpo -c -o iit_get-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/iit_get-except.Tpo .deps/iit_get-except.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_get-assert.o -MD -MP -MF .deps/iit_get-assert.Tpo -c -o iit_get-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/iit_get-assert.Tpo .deps/iit_get-assert.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_get-mem.o -MD -MP -MF .deps/iit_get-mem.Tpo -c -o iit_get-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/iit_get-mem.Tpo .deps/iit_get-mem.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_get-intlist.o -MD -MP -MF .deps/iit_get-intlist.Tpo -c -o iit_get-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/iit_get-intlist.Tpo .deps/iit_get-intlist.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_get-list.o -MD -MP -MF .deps/iit_get-list.Tpo -c -o iit_get-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/iit_get-list.Tpo .deps/iit_get-list.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_get-littleendian.o -MD -MP -MF .deps/iit_get-littleendian.Tpo -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c mv -f .deps/iit_get-littleendian.Tpo .deps/iit_get-littleendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_get-bigendian.o -MD -MP -MF .deps/iit_get-bigendian.Tpo -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c mv -f .deps/iit_get-bigendian.Tpo .deps/iit_get-bigendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_get-univinterval.o -MD -MP -MF .deps/iit_get-univinterval.Tpo -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~ %llu univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~~ %llu 2 warnings generated. mv -f .deps/iit_get-univinterval.Tpo .deps/iit_get-univinterval.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_get-interval.o -MD -MP -MF .deps/iit_get-interval.Tpo -c -o iit_get-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/iit_get-interval.Tpo .deps/iit_get-interval.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_get-uintlist.o -MD -MP -MF .deps/iit_get-uintlist.Tpo -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/iit_get-uintlist.Tpo .deps/iit_get-uintlist.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_get-stopwatch.o -MD -MP -MF .deps/iit_get-stopwatch.Tpo -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/iit_get-stopwatch.Tpo .deps/iit_get-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_get-access.o -MD -MP -MF .deps/iit_get-access.Tpo -c -o iit_get-access.o `test -f 'access.c' || echo './'`access.c access.c:358:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] length,length,errno,strerror(errno)); ^~~~~~ access.c:358:15: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] length,length,errno,strerror(errno)); ^~~~~~ access.c:423:11: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] fd,offset,length,errno,strerror(errno)); ^~~~~~ access.c:493:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] *len,length,errno,strerror(errno)); ^~~~~~ access.c:556:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] offset,length,errno,strerror(errno)); ^~~~~~ access.c:641:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] *len,length,errno,strerror(errno)); ^~~~~~ 6 warnings generated. mv -f .deps/iit_get-access.Tpo .deps/iit_get-access.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_get-iit-read-univ.o -MD -MP -MF .deps/iit_get-iit-read-univ.Tpo -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~~~ %llu iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~ %llu iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~~~ %llu iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~ %llu iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %llu iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~ %llu iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %llu 10 warnings generated. mv -f .deps/iit_get-iit-read-univ.Tpo .deps/iit_get-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_get-iit-read.o -MD -MP -MF .deps/iit_get-iit-read.Tpo -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c mv -f .deps/iit_get-iit-read.Tpo .deps/iit_get-iit-read.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_get-parserange.o -MD -MP -MF .deps/iit_get-parserange.Tpo -c -o iit_get-parserange.o `test -f 'parserange.c' || echo './'`parserange.c parserange.c:187:8: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Univinterval_low(interval),left,*genomicstart); ^~~~~~~~~~~~~~~~~~~~~~~~~~ parserange.c:187:35: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Univinterval_low(interval),left,*genomicstart); ^~~~ parserange.c:187:40: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Univinterval_low(interval),left,*genomicstart); ^~~~~~~~~~~~~ 3 warnings generated. mv -f .deps/iit_get-parserange.Tpo .deps/iit_get-parserange.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_get-getopt.o -MD -MP -MF .deps/iit_get-getopt.Tpo -c -o iit_get-getopt.o `test -f 'getopt.c' || echo './'`getopt.c getopt.c:208:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] my_index (str, chr) ^ getopt.c:291:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] exchange (argv) ^ getopt.c:376:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] _getopt_initialize (argc, argv, optstring) ^ getopt.c:389:28: warning: passing arguments to 'getenv' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] posixly_correct = getenv ("POSIXLY_CORRECT"); ^ getopt.c:498:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] _getopt_internal (argc, argv, optstring, longopts, longind, long_only) ^ getopt.c:1179:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt (argc, argv, optstring) ^ In file included from getopt.c:97: ./getopt.h:147:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent definition [-Wdeprecated-non-prototype] extern int getopt (); ^ 7 warnings generated. mv -f .deps/iit_get-getopt.Tpo .deps/iit_get-getopt.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_get-getopt1.o -MD -MP -MF .deps/iit_get-getopt1.Tpo -c -o iit_get-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c getopt1.c:71:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt_long (argc, argv, options, long_options, opt_index) ^ getopt1.c:87:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt_long_only (argc, argv, options, long_options, opt_index) ^ 2 warnings generated. mv -f .deps/iit_get-getopt1.Tpo .deps/iit_get-getopt1.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_get-iit_get.o -MD -MP -MF .deps/iit_get-iit_get.Tpo -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo './'`iit_get.c In file included from iit_get.c:26: ./getopt.h:147:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a previous declaration [-Wdeprecated-non-prototype] extern int getopt (); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/unistd.h:509:6: note: conflicting prototype is here int getopt(int, char * const [], const char *) __DARWIN_ALIAS(getopt); ^ iit_get.c:619:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu",Univinterval_low(interval),Univinterval_high(interval)); ~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~ %llu iit_get.c:619:50: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu",Univinterval_low(interval),Univinterval_high(interval)); ~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~ %llu 3 warnings generated. mv -f .deps/iit_get-iit_get.Tpo .deps/iit_get-iit_get.Po /bin/sh ../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -DUTILITYP=1 -O3 -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-access.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-getopt.o iit_get-getopt1.o iit_get-iit_get.o -lm libtool: link: gcc -D_THREAD_SAFE -DUTILITYP=1 -O3 -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-access.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-getopt.o iit_get-getopt1.o iit_get-iit_get.o -lm gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_dump-except.o -MD -MP -MF .deps/iit_dump-except.Tpo -c -o iit_dump-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/iit_dump-except.Tpo .deps/iit_dump-except.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_dump-assert.o -MD -MP -MF .deps/iit_dump-assert.Tpo -c -o iit_dump-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/iit_dump-assert.Tpo .deps/iit_dump-assert.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_dump-mem.o -MD -MP -MF .deps/iit_dump-mem.Tpo -c -o iit_dump-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/iit_dump-mem.Tpo .deps/iit_dump-mem.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_dump-littleendian.o -MD -MP -MF .deps/iit_dump-littleendian.Tpo -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c mv -f .deps/iit_dump-littleendian.Tpo .deps/iit_dump-littleendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_dump-bigendian.o -MD -MP -MF .deps/iit_dump-bigendian.Tpo -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c mv -f .deps/iit_dump-bigendian.Tpo .deps/iit_dump-bigendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_dump-intlist.o -MD -MP -MF .deps/iit_dump-intlist.Tpo -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/iit_dump-intlist.Tpo .deps/iit_dump-intlist.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_dump-list.o -MD -MP -MF .deps/iit_dump-list.Tpo -c -o iit_dump-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/iit_dump-list.Tpo .deps/iit_dump-list.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_dump-univinterval.o -MD -MP -MF .deps/iit_dump-univinterval.Tpo -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~ %llu univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~~ %llu 2 warnings generated. mv -f .deps/iit_dump-univinterval.Tpo .deps/iit_dump-univinterval.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_dump-interval.o -MD -MP -MF .deps/iit_dump-interval.Tpo -c -o iit_dump-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/iit_dump-interval.Tpo .deps/iit_dump-interval.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_dump-uintlist.o -MD -MP -MF .deps/iit_dump-uintlist.Tpo -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/iit_dump-uintlist.Tpo .deps/iit_dump-uintlist.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_dump-stopwatch.o -MD -MP -MF .deps/iit_dump-stopwatch.Tpo -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/iit_dump-stopwatch.Tpo .deps/iit_dump-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_dump-access.o -MD -MP -MF .deps/iit_dump-access.Tpo -c -o iit_dump-access.o `test -f 'access.c' || echo './'`access.c access.c:358:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] length,length,errno,strerror(errno)); ^~~~~~ access.c:358:15: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] length,length,errno,strerror(errno)); ^~~~~~ access.c:423:11: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] fd,offset,length,errno,strerror(errno)); ^~~~~~ access.c:493:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] *len,length,errno,strerror(errno)); ^~~~~~ access.c:556:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] offset,length,errno,strerror(errno)); ^~~~~~ access.c:641:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] *len,length,errno,strerror(errno)); ^~~~~~ 6 warnings generated. mv -f .deps/iit_dump-access.Tpo .deps/iit_dump-access.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_dump-iit-read-univ.o -MD -MP -MF .deps/iit_dump-iit-read-univ.Tpo -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~~~ %llu iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~ %llu iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~~~ %llu iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~ %llu iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %llu iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~ %llu iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %llu 10 warnings generated. mv -f .deps/iit_dump-iit-read-univ.Tpo .deps/iit_dump-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_dump-iit-read.o -MD -MP -MF .deps/iit_dump-iit-read.Tpo -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c mv -f .deps/iit_dump-iit-read.Tpo .deps/iit_dump-iit-read.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_dump-getopt.o -MD -MP -MF .deps/iit_dump-getopt.Tpo -c -o iit_dump-getopt.o `test -f 'getopt.c' || echo './'`getopt.c getopt.c:208:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] my_index (str, chr) ^ getopt.c:291:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] exchange (argv) ^ getopt.c:376:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] _getopt_initialize (argc, argv, optstring) ^ getopt.c:389:28: warning: passing arguments to 'getenv' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] posixly_correct = getenv ("POSIXLY_CORRECT"); ^ getopt.c:498:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] _getopt_internal (argc, argv, optstring, longopts, longind, long_only) ^ getopt.c:1179:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt (argc, argv, optstring) ^ In file included from getopt.c:97: ./getopt.h:147:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent definition [-Wdeprecated-non-prototype] extern int getopt (); ^ 7 warnings generated. mv -f .deps/iit_dump-getopt.Tpo .deps/iit_dump-getopt.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_dump-getopt1.o -MD -MP -MF .deps/iit_dump-getopt1.Tpo -c -o iit_dump-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c getopt1.c:71:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt_long (argc, argv, options, long_options, opt_index) ^ getopt1.c:87:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt_long_only (argc, argv, options, long_options, opt_index) ^ 2 warnings generated. mv -f .deps/iit_dump-getopt1.Tpo .deps/iit_dump-getopt1.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -MT iit_dump-iit_dump.o -MD -MP -MF .deps/iit_dump-iit_dump.Tpo -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo './'`iit_dump.c In file included from iit_dump.c:18: ./getopt.h:147:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a previous declaration [-Wdeprecated-non-prototype] extern int getopt (); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/unistd.h:509:6: note: conflicting prototype is here int getopt(int, char * const [], const char *) __DARWIN_ALIAS(getopt); ^ 1 warning generated. mv -f .deps/iit_dump-iit_dump.Tpo .deps/iit_dump-iit_dump.Po /bin/sh ../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -DUTILITYP=1 -O3 -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-access.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-getopt.o iit_dump-getopt1.o iit_dump-iit_dump.o -lm libtool: link: gcc -D_THREAD_SAFE -DUTILITYP=1 -O3 -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-access.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-getopt.o iit_dump-getopt1.o iit_dump-iit_dump.o -lm gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-except.o -MD -MP -MF .deps/gsnap-except.Tpo -c -o gsnap-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/gsnap-except.Tpo .deps/gsnap-except.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-assert.o -MD -MP -MF .deps/gsnap-assert.Tpo -c -o gsnap-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/gsnap-assert.Tpo .deps/gsnap-assert.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-mem.o -MD -MP -MF .deps/gsnap-mem.Tpo -c -o gsnap-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/gsnap-mem.Tpo .deps/gsnap-mem.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-intlist.o -MD -MP -MF .deps/gsnap-intlist.Tpo -c -o gsnap-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/gsnap-intlist.Tpo .deps/gsnap-intlist.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-list.o -MD -MP -MF .deps/gsnap-list.Tpo -c -o gsnap-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/gsnap-list.Tpo .deps/gsnap-list.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-littleendian.o -MD -MP -MF .deps/gsnap-littleendian.Tpo -c -o gsnap-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c mv -f .deps/gsnap-littleendian.Tpo .deps/gsnap-littleendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-bigendian.o -MD -MP -MF .deps/gsnap-bigendian.Tpo -c -o gsnap-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c mv -f .deps/gsnap-bigendian.Tpo .deps/gsnap-bigendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-univinterval.o -MD -MP -MF .deps/gsnap-univinterval.Tpo -c -o gsnap-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~ %u univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~~ %u 2 warnings generated. mv -f .deps/gsnap-univinterval.Tpo .deps/gsnap-univinterval.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-interval.o -MD -MP -MF .deps/gsnap-interval.Tpo -c -o gsnap-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/gsnap-interval.Tpo .deps/gsnap-interval.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-uintlist.o -MD -MP -MF .deps/gsnap-uintlist.Tpo -c -o gsnap-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/gsnap-uintlist.Tpo .deps/gsnap-uintlist.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-stopwatch.o -MD -MP -MF .deps/gsnap-stopwatch.Tpo -c -o gsnap-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/gsnap-stopwatch.Tpo .deps/gsnap-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-access.o -MD -MP -MF .deps/gsnap-access.Tpo -c -o gsnap-access.o `test -f 'access.c' || echo './'`access.c access.c:358:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] length,length,errno,strerror(errno)); ^~~~~~ access.c:358:15: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] length,length,errno,strerror(errno)); ^~~~~~ access.c:423:11: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] fd,offset,length,errno,strerror(errno)); ^~~~~~ access.c:493:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] *len,length,errno,strerror(errno)); ^~~~~~ access.c:556:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] offset,length,errno,strerror(errno)); ^~~~~~ access.c:641:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] *len,length,errno,strerror(errno)); ^~~~~~ 6 warnings generated. mv -f .deps/gsnap-access.Tpo .deps/gsnap-access.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-iit-read-univ.o -MD -MP -MF .deps/gsnap-iit-read-univ.Tpo -c -o gsnap-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~~~ %u iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~ %u iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~~~ %u iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~ %u iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %u iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %u iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~ %u iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~~~ %u iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %u iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %u 10 warnings generated. mv -f .deps/gsnap-iit-read-univ.Tpo .deps/gsnap-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-iit-read.o -MD -MP -MF .deps/gsnap-iit-read.Tpo -c -o gsnap-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c mv -f .deps/gsnap-iit-read.Tpo .deps/gsnap-iit-read.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-md5.o -MD -MP -MF .deps/gsnap-md5.Tpo -c -o gsnap-md5.o `test -f 'md5.c' || echo './'`md5.c mv -f .deps/gsnap-md5.Tpo .deps/gsnap-md5.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-bzip2.o -MD -MP -MF .deps/gsnap-bzip2.Tpo -c -o gsnap-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c mv -f .deps/gsnap-bzip2.Tpo .deps/gsnap-bzip2.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-sequence.o -MD -MP -MF .deps/gsnap-sequence.Tpo -c -o gsnap-sequence.o `test -f 'sequence.c' || echo './'`sequence.c mv -f .deps/gsnap-sequence.Tpo .deps/gsnap-sequence.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-reader.o -MD -MP -MF .deps/gsnap-reader.Tpo -c -o gsnap-reader.o `test -f 'reader.c' || echo './'`reader.c mv -f .deps/gsnap-reader.Tpo .deps/gsnap-reader.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-genomicpos.o -MD -MP -MF .deps/gsnap-genomicpos.Tpo -c -o gsnap-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/gsnap-genomicpos.Tpo .deps/gsnap-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-compress.o -MD -MP -MF .deps/gsnap-compress.Tpo -c -o gsnap-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/gsnap-compress.Tpo .deps/gsnap-compress.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-genome.o -MD -MP -MF .deps/gsnap-genome.Tpo -c -o gsnap-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c:10292:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %u genome.c:10292:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %u genome.c:10392:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %u genome.c:10392:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %u 4 warnings generated. mv -f .deps/gsnap-genome.Tpo .deps/gsnap-genome.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-genome_hr.o -MD -MP -MF .deps/gsnap-genome_hr.Tpo -c -o gsnap-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c mv -f .deps/gsnap-genome_hr.Tpo .deps/gsnap-genome_hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-genome_sites.o -MD -MP -MF .deps/gsnap-genome_sites.Tpo -c -o gsnap-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c mv -f .deps/gsnap-genome_sites.Tpo .deps/gsnap-genome_sites.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-bitpack64-read.o -MD -MP -MF .deps/gsnap-bitpack64-read.Tpo -c -o gsnap-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c mv -f .deps/gsnap-bitpack64-read.Tpo .deps/gsnap-bitpack64-read.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-indexdb.o -MD -MP -MF .deps/gsnap-indexdb.Tpo -c -o gsnap-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c:1363:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1483:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1653:63: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1792:6: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] ptr,sizeof(Univcoord_T),offset); ^~~ indexdb.c:1792:30: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] ptr,sizeof(Univcoord_T),offset); ^~~~~~ indexdb.c:1934:76: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, ~~~ ^~~~~~~~~~~~~~ %llu indexdb.c:2026:76: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, ~~~ ^~~~~~~~~~~~~~ %llu 7 warnings generated. mv -f .deps/gsnap-indexdb.Tpo .deps/gsnap-indexdb.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-indexdb_hr.o -MD -MP -MF .deps/gsnap-indexdb_hr.Tpo -c -o gsnap-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c mv -f .deps/gsnap-indexdb_hr.Tpo .deps/gsnap-indexdb_hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-oligo.o -MD -MP -MF .deps/gsnap-oligo.Tpo -c -o gsnap-oligo.o `test -f 'oligo.c' || echo './'`oligo.c mv -f .deps/gsnap-oligo.Tpo .deps/gsnap-oligo.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-chrom.o -MD -MP -MF .deps/gsnap-chrom.Tpo -c -o gsnap-chrom.o `test -f 'chrom.c' || echo './'`chrom.c chrom.c:116:15: warning: comparing a pointer to a null character constant; did you mean to compare to NULL? [-Wpointer-compare] while (p != '\0' && *p >= '0' && *p <= '9') { ^~~~ (void *)0 1 warning generated. mv -f .deps/gsnap-chrom.Tpo .deps/gsnap-chrom.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-segmentpos.o -MD -MP -MF .deps/gsnap-segmentpos.Tpo -c -o gsnap-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c mv -f .deps/gsnap-segmentpos.Tpo .deps/gsnap-segmentpos.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-chrnum.o -MD -MP -MF .deps/gsnap-chrnum.Tpo -c -o gsnap-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c mv -f .deps/gsnap-chrnum.Tpo .deps/gsnap-chrnum.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-maxent_hr.o -MD -MP -MF .deps/gsnap-maxent_hr.Tpo -c -o gsnap-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c mv -f .deps/gsnap-maxent_hr.Tpo .deps/gsnap-maxent_hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-samprint.o -MD -MP -MF .deps/gsnap-samprint.Tpo -c -o gsnap-samprint.o `test -f 'samprint.c' || echo './'`samprint.c mv -f .deps/gsnap-samprint.Tpo .deps/gsnap-samprint.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-mapq.o -MD -MP -MF .deps/gsnap-mapq.Tpo -c -o gsnap-mapq.o `test -f 'mapq.c' || echo './'`mapq.c mv -f .deps/gsnap-mapq.Tpo .deps/gsnap-mapq.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-shortread.o -MD -MP -MF .deps/gsnap-shortread.Tpo -c -o gsnap-shortread.o `test -f 'shortread.c' || echo './'`shortread.c mv -f .deps/gsnap-shortread.Tpo .deps/gsnap-shortread.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-substring.o -MD -MP -MF .deps/gsnap-substring.Tpo -c -o gsnap-substring.o `test -f 'substring.c' || echo './'`substring.c mv -f .deps/gsnap-substring.Tpo .deps/gsnap-substring.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-stage3hr.o -MD -MP -MF .deps/gsnap-stage3hr.Tpo -c -o gsnap-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c mv -f .deps/gsnap-stage3hr.Tpo .deps/gsnap-stage3hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-goby.o -MD -MP -MF .deps/gsnap-goby.Tpo -c -o gsnap-goby.o `test -f 'goby.c' || echo './'`goby.c mv -f .deps/gsnap-goby.Tpo .deps/gsnap-goby.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-spanningelt.o -MD -MP -MF .deps/gsnap-spanningelt.Tpo -c -o gsnap-spanningelt.o `test -f 'spanningelt.c' || echo './'`spanningelt.c mv -f .deps/gsnap-spanningelt.Tpo .deps/gsnap-spanningelt.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-cmet.o -MD -MP -MF .deps/gsnap-cmet.Tpo -c -o gsnap-cmet.o `test -f 'cmet.c' || echo './'`cmet.c mv -f .deps/gsnap-cmet.Tpo .deps/gsnap-cmet.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-atoi.o -MD -MP -MF .deps/gsnap-atoi.Tpo -c -o gsnap-atoi.o `test -f 'atoi.c' || echo './'`atoi.c mv -f .deps/gsnap-atoi.Tpo .deps/gsnap-atoi.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-maxent.o -MD -MP -MF .deps/gsnap-maxent.Tpo -c -o gsnap-maxent.o `test -f 'maxent.c' || echo './'`maxent.c mv -f .deps/gsnap-maxent.Tpo .deps/gsnap-maxent.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-pair.o -MD -MP -MF .deps/gsnap-pair.Tpo -c -o gsnap-pair.o `test -f 'pair.c' || echo './'`pair.c pair.c:2419:24: warning: taking the absolute value of unsigned type 'Chrpos_T' (aka 'unsigned int') has no effect [-Wabsolute-value] sprintf(token,"N%u",abs(intron_end - intron_start) + 1); ^ pair.c:2419:24: note: remove the call to 'abs' since unsigned values cannot be negative sprintf(token,"N%u",abs(intron_end - intron_start) + 1); ^~~ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ pair.c:4651:17: warning: taking the absolute value of unsigned type 'Chrpos_T' (aka 'unsigned int') has no effect [-Wabsolute-value] genome_gap = abs(intron_end - intron_start) + 1; ^ pair.c:4651:17: note: remove the call to 'abs' since unsigned values cannot be negative genome_gap = abs(intron_end - intron_start) + 1; ^~~ 2 warnings generated. mv -f .deps/gsnap-pair.Tpo .deps/gsnap-pair.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-pairpool.o -MD -MP -MF .deps/gsnap-pairpool.Tpo -c -o gsnap-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c mv -f .deps/gsnap-pairpool.Tpo .deps/gsnap-pairpool.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-diag.o -MD -MP -MF .deps/gsnap-diag.Tpo -c -o gsnap-diag.o `test -f 'diag.c' || echo './'`diag.c mv -f .deps/gsnap-diag.Tpo .deps/gsnap-diag.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-diagpool.o -MD -MP -MF .deps/gsnap-diagpool.Tpo -c -o gsnap-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c mv -f .deps/gsnap-diagpool.Tpo .deps/gsnap-diagpool.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-orderstat.o -MD -MP -MF .deps/gsnap-orderstat.Tpo -c -o gsnap-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c mv -f .deps/gsnap-orderstat.Tpo .deps/gsnap-orderstat.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-oligoindex_hr.o -MD -MP -MF .deps/gsnap-oligoindex_hr.Tpo -c -o gsnap-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c mv -f .deps/gsnap-oligoindex_hr.Tpo .deps/gsnap-oligoindex_hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-cellpool.o -MD -MP -MF .deps/gsnap-cellpool.Tpo -c -o gsnap-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c mv -f .deps/gsnap-cellpool.Tpo .deps/gsnap-cellpool.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-stage2.o -MD -MP -MF .deps/gsnap-stage2.Tpo -c -o gsnap-stage2.o `test -f 'stage2.c' || echo './'`stage2.c stage2.c:1329:19: warning: taking the absolute value of unsigned type 'Chrpos_T' (aka 'unsigned int') has no effect [-Wabsolute-value] diffdistance = abs(gendistance - querydistance); ^ stage2.c:1329:19: note: remove the call to 'abs' since unsigned values cannot be negative diffdistance = abs(gendistance - querydistance); ^~~ stage2.c:1812:19: warning: taking the absolute value of unsigned type 'Chrpos_T' (aka 'unsigned int') has no effect [-Wabsolute-value] diffdistance = abs(gendistance - querydistance); ^ stage2.c:1812:19: note: remove the call to 'abs' since unsigned values cannot be negative diffdistance = abs(gendistance - querydistance); ^~~ 2 warnings generated. mv -f .deps/gsnap-stage2.Tpo .deps/gsnap-stage2.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-intron.o -MD -MP -MF .deps/gsnap-intron.Tpo -c -o gsnap-intron.o `test -f 'intron.c' || echo './'`intron.c mv -f .deps/gsnap-intron.Tpo .deps/gsnap-intron.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-boyer-moore.o -MD -MP -MF .deps/gsnap-boyer-moore.Tpo -c -o gsnap-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c mv -f .deps/gsnap-boyer-moore.Tpo .deps/gsnap-boyer-moore.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-changepoint.o -MD -MP -MF .deps/gsnap-changepoint.Tpo -c -o gsnap-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c mv -f .deps/gsnap-changepoint.Tpo .deps/gsnap-changepoint.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-pbinom.o -MD -MP -MF .deps/gsnap-pbinom.Tpo -c -o gsnap-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c mv -f .deps/gsnap-pbinom.Tpo .deps/gsnap-pbinom.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-dynprog.o -MD -MP -MF .deps/gsnap-dynprog.Tpo -c -o gsnap-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c mv -f .deps/gsnap-dynprog.Tpo .deps/gsnap-dynprog.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-gbuffer.o -MD -MP -MF .deps/gsnap-gbuffer.Tpo -c -o gsnap-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c mv -f .deps/gsnap-gbuffer.Tpo .deps/gsnap-gbuffer.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-translation.o -MD -MP -MF .deps/gsnap-translation.Tpo -c -o gsnap-translation.o `test -f 'translation.c' || echo './'`translation.c mv -f .deps/gsnap-translation.Tpo .deps/gsnap-translation.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-doublelist.o -MD -MP -MF .deps/gsnap-doublelist.Tpo -c -o gsnap-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c mv -f .deps/gsnap-doublelist.Tpo .deps/gsnap-doublelist.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-smooth.o -MD -MP -MF .deps/gsnap-smooth.Tpo -c -o gsnap-smooth.o `test -f 'smooth.c' || echo './'`smooth.c mv -f .deps/gsnap-smooth.Tpo .deps/gsnap-smooth.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-chimera.o -MD -MP -MF .deps/gsnap-chimera.Tpo -c -o gsnap-chimera.o `test -f 'chimera.c' || echo './'`chimera.c mv -f .deps/gsnap-chimera.Tpo .deps/gsnap-chimera.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-stage3.o -MD -MP -MF .deps/gsnap-stage3.Tpo -c -o gsnap-stage3.o `test -f 'stage3.c' || echo './'`stage3.c mv -f .deps/gsnap-stage3.Tpo .deps/gsnap-stage3.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-splicestringpool.o -MD -MP -MF .deps/gsnap-splicestringpool.Tpo -c -o gsnap-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c mv -f .deps/gsnap-splicestringpool.Tpo .deps/gsnap-splicestringpool.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-splicetrie_build.o -MD -MP -MF .deps/gsnap-splicetrie_build.Tpo -c -o gsnap-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c mv -f .deps/gsnap-splicetrie_build.Tpo .deps/gsnap-splicetrie_build.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-splicetrie.o -MD -MP -MF .deps/gsnap-splicetrie.Tpo -c -o gsnap-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c mv -f .deps/gsnap-splicetrie.Tpo .deps/gsnap-splicetrie.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-splice.o -MD -MP -MF .deps/gsnap-splice.Tpo -c -o gsnap-splice.o `test -f 'splice.c' || echo './'`splice.c mv -f .deps/gsnap-splice.Tpo .deps/gsnap-splice.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-indel.o -MD -MP -MF .deps/gsnap-indel.Tpo -c -o gsnap-indel.o `test -f 'indel.c' || echo './'`indel.c mv -f .deps/gsnap-indel.Tpo .deps/gsnap-indel.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-bitpack64-access.o -MD -MP -MF .deps/gsnap-bitpack64-access.Tpo -c -o gsnap-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c mv -f .deps/gsnap-bitpack64-access.Tpo .deps/gsnap-bitpack64-access.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-sarray-read.o -MD -MP -MF .deps/gsnap-sarray-read.Tpo -c -o gsnap-sarray-read.o `test -f 'sarray-read.c' || echo './'`sarray-read.c mv -f .deps/gsnap-sarray-read.Tpo .deps/gsnap-sarray-read.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-stage1hr.o -MD -MP -MF .deps/gsnap-stage1hr.Tpo -c -o gsnap-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c mv -f .deps/gsnap-stage1hr.Tpo .deps/gsnap-stage1hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-request.o -MD -MP -MF .deps/gsnap-request.Tpo -c -o gsnap-request.o `test -f 'request.c' || echo './'`request.c mv -f .deps/gsnap-request.Tpo .deps/gsnap-request.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-resulthr.o -MD -MP -MF .deps/gsnap-resulthr.Tpo -c -o gsnap-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c mv -f .deps/gsnap-resulthr.Tpo .deps/gsnap-resulthr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-inbuffer.o -MD -MP -MF .deps/gsnap-inbuffer.Tpo -c -o gsnap-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c mv -f .deps/gsnap-inbuffer.Tpo .deps/gsnap-inbuffer.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-samheader.o -MD -MP -MF .deps/gsnap-samheader.Tpo -c -o gsnap-samheader.o `test -f 'samheader.c' || echo './'`samheader.c mv -f .deps/gsnap-samheader.Tpo .deps/gsnap-samheader.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-outbuffer.o -MD -MP -MF .deps/gsnap-outbuffer.Tpo -c -o gsnap-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c mv -f .deps/gsnap-outbuffer.Tpo .deps/gsnap-outbuffer.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-datadir.o -MD -MP -MF .deps/gsnap-datadir.Tpo -c -o gsnap-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/gsnap-datadir.Tpo .deps/gsnap-datadir.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-getopt.o -MD -MP -MF .deps/gsnap-getopt.Tpo -c -o gsnap-getopt.o `test -f 'getopt.c' || echo './'`getopt.c getopt.c:208:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] my_index (str, chr) ^ getopt.c:291:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] exchange (argv) ^ getopt.c:376:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] _getopt_initialize (argc, argv, optstring) ^ getopt.c:389:28: warning: passing arguments to 'getenv' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] posixly_correct = getenv ("POSIXLY_CORRECT"); ^ getopt.c:498:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] _getopt_internal (argc, argv, optstring, longopts, longind, long_only) ^ getopt.c:1179:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt (argc, argv, optstring) ^ In file included from getopt.c:97: ./getopt.h:147:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent definition [-Wdeprecated-non-prototype] extern int getopt (); ^ 7 warnings generated. mv -f .deps/gsnap-getopt.Tpo .deps/gsnap-getopt.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-getopt1.o -MD -MP -MF .deps/gsnap-getopt1.Tpo -c -o gsnap-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c getopt1.c:71:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt_long (argc, argv, options, long_options, opt_index) ^ getopt1.c:87:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt_long_only (argc, argv, options, long_options, opt_index) ^ 2 warnings generated. mv -f .deps/gsnap-getopt1.Tpo .deps/gsnap-getopt1.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-gsnap.o -MD -MP -MF .deps/gsnap-gsnap.Tpo -c -o gsnap-gsnap.o `test -f 'gsnap.c' || echo './'`gsnap.c In file included from gsnap.c:84: ./getopt.h:147:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a previous declaration [-Wdeprecated-non-prototype] extern int getopt (); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/unistd.h:509:6: note: conflicting prototype is here int getopt(int, char * const [], const char *) __DARWIN_ALIAS(getopt); ^ 1 warning generated. mv -f .deps/gsnap-gsnap.Tpo .deps/gsnap-gsnap.Po /bin/sh ../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -o gsnap gsnap-except.o gsnap-assert.o gsnap-mem.o gsnap-intlist.o gsnap-list.o gsnap-littleendian.o gsnap-bigendian.o gsnap-univinterval.o gsnap-interval.o gsnap-uintlist.o gsnap-stopwatch.o gsnap-access.o gsnap-iit-read-univ.o gsnap-iit-read.o gsnap-md5.o gsnap-bzip2.o gsnap-sequence.o gsnap-reader.o gsnap-genomicpos.o gsnap-compress.o gsnap-genome.o gsnap-genome_hr.o gsnap-genome_sites.o gsnap-bitpack64-read.o gsnap-indexdb.o gsnap-indexdb_hr.o gsnap-oligo.o gsnap-chrom.o gsnap-segmentpos.o gsnap-chrnum.o gsnap-maxent_hr.o gsnap-samprint.o gsnap-mapq.o gsnap-shortread.o gsnap-substring.o gsnap-stage3hr.o gsnap-goby.o gsnap-spanningelt.o gsnap-cmet.o gsnap-atoi.o gsnap-maxent.o gsnap-pair.o gsnap-pairpool.o gsnap-diag.o gsnap-diagpool.o gsnap-orderstat.o gsnap-oligoindex_hr.o gsnap-cellpool.o gsnap-stage2.o gsnap-intron.o gsnap-boyer-moore.o gsnap-changepoint.o gsnap-pbinom.o gsnap-dynprog.o gsnap-gbuffer.o gsnap-translation.o gsnap-doublelist.o gsnap-smooth.o gsnap-chimera.o gsnap-stage3.o gsnap-splicestringpool.o gsnap-splicetrie_build.o gsnap-splicetrie.o gsnap-splice.o gsnap-indel.o gsnap-bitpack64-access.o gsnap-sarray-read.o gsnap-stage1hr.o gsnap-request.o gsnap-resulthr.o gsnap-inbuffer.o gsnap-samheader.o gsnap-outbuffer.o gsnap-datadir.o gsnap-getopt.o gsnap-getopt1.o gsnap-gsnap.o -lz -lbz2 -lm libtool: link: gcc -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -o gsnap gsnap-except.o gsnap-assert.o gsnap-mem.o gsnap-intlist.o gsnap-list.o gsnap-littleendian.o gsnap-bigendian.o gsnap-univinterval.o gsnap-interval.o gsnap-uintlist.o gsnap-stopwatch.o gsnap-access.o gsnap-iit-read-univ.o gsnap-iit-read.o gsnap-md5.o gsnap-bzip2.o gsnap-sequence.o gsnap-reader.o gsnap-genomicpos.o gsnap-compress.o gsnap-genome.o gsnap-genome_hr.o gsnap-genome_sites.o gsnap-bitpack64-read.o gsnap-indexdb.o gsnap-indexdb_hr.o gsnap-oligo.o gsnap-chrom.o gsnap-segmentpos.o gsnap-chrnum.o gsnap-maxent_hr.o gsnap-samprint.o gsnap-mapq.o gsnap-shortread.o gsnap-substring.o gsnap-stage3hr.o gsnap-goby.o gsnap-spanningelt.o gsnap-cmet.o gsnap-atoi.o gsnap-maxent.o gsnap-pair.o gsnap-pairpool.o gsnap-diag.o gsnap-diagpool.o gsnap-orderstat.o gsnap-oligoindex_hr.o gsnap-cellpool.o gsnap-stage2.o gsnap-intron.o gsnap-boyer-moore.o gsnap-changepoint.o gsnap-pbinom.o gsnap-dynprog.o gsnap-gbuffer.o gsnap-translation.o gsnap-doublelist.o gsnap-smooth.o gsnap-chimera.o gsnap-stage3.o gsnap-splicestringpool.o gsnap-splicetrie_build.o gsnap-splicetrie.o gsnap-splice.o gsnap-indel.o gsnap-bitpack64-access.o gsnap-sarray-read.o gsnap-stage1hr.o gsnap-request.o gsnap-resulthr.o gsnap-inbuffer.o gsnap-samheader.o gsnap-outbuffer.o gsnap-datadir.o gsnap-getopt.o gsnap-getopt1.o gsnap-gsnap.o -lz -lbz2 -lm gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-except.o -MD -MP -MF .deps/gsnapl-except.Tpo -c -o gsnapl-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/gsnapl-except.Tpo .deps/gsnapl-except.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-assert.o -MD -MP -MF .deps/gsnapl-assert.Tpo -c -o gsnapl-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/gsnapl-assert.Tpo .deps/gsnapl-assert.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-mem.o -MD -MP -MF .deps/gsnapl-mem.Tpo -c -o gsnapl-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/gsnapl-mem.Tpo .deps/gsnapl-mem.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-intlist.o -MD -MP -MF .deps/gsnapl-intlist.Tpo -c -o gsnapl-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/gsnapl-intlist.Tpo .deps/gsnapl-intlist.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-list.o -MD -MP -MF .deps/gsnapl-list.Tpo -c -o gsnapl-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/gsnapl-list.Tpo .deps/gsnapl-list.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-littleendian.o -MD -MP -MF .deps/gsnapl-littleendian.Tpo -c -o gsnapl-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c mv -f .deps/gsnapl-littleendian.Tpo .deps/gsnapl-littleendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-bigendian.o -MD -MP -MF .deps/gsnapl-bigendian.Tpo -c -o gsnapl-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c mv -f .deps/gsnapl-bigendian.Tpo .deps/gsnapl-bigendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-univinterval.o -MD -MP -MF .deps/gsnapl-univinterval.Tpo -c -o gsnapl-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~ %llu univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~~ %llu 2 warnings generated. mv -f .deps/gsnapl-univinterval.Tpo .deps/gsnapl-univinterval.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-interval.o -MD -MP -MF .deps/gsnapl-interval.Tpo -c -o gsnapl-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/gsnapl-interval.Tpo .deps/gsnapl-interval.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-uintlist.o -MD -MP -MF .deps/gsnapl-uintlist.Tpo -c -o gsnapl-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/gsnapl-uintlist.Tpo .deps/gsnapl-uintlist.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-uint8list.o -MD -MP -MF .deps/gsnapl-uint8list.Tpo -c -o gsnapl-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c uint8list.c:202:28: warning: format specifies type 'unsigned int' but the argument has type 'UINT8' (aka 'unsigned long long') [-Wformat] sprintf(Buffer,"%u,",Uint8list_head(p)); ~~ ^~~~~~~~~~~~~~~~~ %llu /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^~~~~~~~~~~ uint8list.c:205:25: warning: format specifies type 'unsigned int' but the argument has type 'UINT8' (aka 'unsigned long long') [-Wformat] sprintf(Buffer,"%u",Uint8list_head(p)); ~~ ^~~~~~~~~~~~~~~~~ %llu /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^~~~~~~~~~~ uint8list.c:211:28: warning: format specifies type 'unsigned int' but the argument has type 'UINT8' (aka 'unsigned long long') [-Wformat] sprintf(Buffer,"%u,",Uint8list_head(p)); ~~ ^~~~~~~~~~~~~~~~~ %llu /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^~~~~~~~~~~ uint8list.c:214:25: warning: format specifies type 'unsigned int' but the argument has type 'UINT8' (aka 'unsigned long long') [-Wformat] sprintf(Buffer,"%u",Uint8list_head(p)); ~~ ^~~~~~~~~~~~~~~~~ %llu /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^~~~~~~~~~~ 4 warnings generated. mv -f .deps/gsnapl-uint8list.Tpo .deps/gsnapl-uint8list.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-stopwatch.o -MD -MP -MF .deps/gsnapl-stopwatch.Tpo -c -o gsnapl-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/gsnapl-stopwatch.Tpo .deps/gsnapl-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-access.o -MD -MP -MF .deps/gsnapl-access.Tpo -c -o gsnapl-access.o `test -f 'access.c' || echo './'`access.c access.c:358:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] length,length,errno,strerror(errno)); ^~~~~~ access.c:358:15: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] length,length,errno,strerror(errno)); ^~~~~~ access.c:423:11: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] fd,offset,length,errno,strerror(errno)); ^~~~~~ access.c:493:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] *len,length,errno,strerror(errno)); ^~~~~~ access.c:556:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] offset,length,errno,strerror(errno)); ^~~~~~ access.c:641:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] *len,length,errno,strerror(errno)); ^~~~~~ 6 warnings generated. mv -f .deps/gsnapl-access.Tpo .deps/gsnapl-access.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-iit-read-univ.o -MD -MP -MF .deps/gsnapl-iit-read-univ.Tpo -c -o gsnapl-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~~~ %llu iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~ %llu iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~~~ %llu iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~ %llu iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %llu iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~ %llu iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %llu 10 warnings generated. mv -f .deps/gsnapl-iit-read-univ.Tpo .deps/gsnapl-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-iit-read.o -MD -MP -MF .deps/gsnapl-iit-read.Tpo -c -o gsnapl-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c mv -f .deps/gsnapl-iit-read.Tpo .deps/gsnapl-iit-read.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-md5.o -MD -MP -MF .deps/gsnapl-md5.Tpo -c -o gsnapl-md5.o `test -f 'md5.c' || echo './'`md5.c mv -f .deps/gsnapl-md5.Tpo .deps/gsnapl-md5.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-bzip2.o -MD -MP -MF .deps/gsnapl-bzip2.Tpo -c -o gsnapl-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c mv -f .deps/gsnapl-bzip2.Tpo .deps/gsnapl-bzip2.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-sequence.o -MD -MP -MF .deps/gsnapl-sequence.Tpo -c -o gsnapl-sequence.o `test -f 'sequence.c' || echo './'`sequence.c mv -f .deps/gsnapl-sequence.Tpo .deps/gsnapl-sequence.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-reader.o -MD -MP -MF .deps/gsnapl-reader.Tpo -c -o gsnapl-reader.o `test -f 'reader.c' || echo './'`reader.c mv -f .deps/gsnapl-reader.Tpo .deps/gsnapl-reader.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-genomicpos.o -MD -MP -MF .deps/gsnapl-genomicpos.Tpo -c -o gsnapl-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/gsnapl-genomicpos.Tpo .deps/gsnapl-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-compress.o -MD -MP -MF .deps/gsnapl-compress.Tpo -c -o gsnapl-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/gsnapl-compress.Tpo .deps/gsnapl-compress.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-genome.o -MD -MP -MF .deps/gsnapl-genome.Tpo -c -o gsnapl-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c:10292:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu genome.c:10292:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu genome.c:10392:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu genome.c:10392:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu 4 warnings generated. mv -f .deps/gsnapl-genome.Tpo .deps/gsnapl-genome.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-genome_hr.o -MD -MP -MF .deps/gsnapl-genome_hr.Tpo -c -o gsnapl-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c mv -f .deps/gsnapl-genome_hr.Tpo .deps/gsnapl-genome_hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-genome_sites.o -MD -MP -MF .deps/gsnapl-genome_sites.Tpo -c -o gsnapl-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c genome_sites.c:24729:17: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%u\t",startblock/3*32U); ~~ ^~~~~~~~~~~~~~~~ %llu genome_sites.c:24744:19: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%u\t",ptr/3*32U); ~~ ^~~~~~~~~ %llu genome_sites.c:24751:17: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%u\t",(endblock+3)/3*32U); ~~ ^~~~~~~~~~~~~~~~~~ %llu 3 warnings generated. mv -f .deps/gsnapl-genome_sites.Tpo .deps/gsnapl-genome_sites.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-bitpack64-read.o -MD -MP -MF .deps/gsnapl-bitpack64-read.Tpo -c -o gsnapl-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c mv -f .deps/gsnapl-bitpack64-read.Tpo .deps/gsnapl-bitpack64-read.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-indexdb.o -MD -MP -MF .deps/gsnapl-indexdb.Tpo -c -o gsnapl-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c:1363:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1483:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1653:63: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1792:6: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] ptr,sizeof(Univcoord_T),offset); ^~~ indexdb.c:1792:30: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] ptr,sizeof(Univcoord_T),offset); ^~~~~~ indexdb.c:1934:76: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, ~~~ ^~~~~~~~~~~~~~ %llu indexdb.c:2026:76: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, ~~~ ^~~~~~~~~~~~~~ %llu 7 warnings generated. mv -f .deps/gsnapl-indexdb.Tpo .deps/gsnapl-indexdb.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-indexdb_hr.o -MD -MP -MF .deps/gsnapl-indexdb_hr.Tpo -c -o gsnapl-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c indexdb_hr.c:1008:43: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" compound%d.%d:%u+%d\n",i,j,compoundpos->positions[i][j],diagterm); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ %llu indexdb_hr.c:1232:45: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("#%d--%d:%u ",i,batch->nentries,batch->position); ~~ ^~~~~~~~~~~~~~~ %llu 2 warnings generated. mv -f .deps/gsnapl-indexdb_hr.Tpo .deps/gsnapl-indexdb_hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-oligo.o -MD -MP -MF .deps/gsnapl-oligo.Tpo -c -o gsnapl-oligo.o `test -f 'oligo.c' || echo './'`oligo.c mv -f .deps/gsnapl-oligo.Tpo .deps/gsnapl-oligo.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-chrom.o -MD -MP -MF .deps/gsnapl-chrom.Tpo -c -o gsnapl-chrom.o `test -f 'chrom.c' || echo './'`chrom.c chrom.c:116:15: warning: comparing a pointer to a null character constant; did you mean to compare to NULL? [-Wpointer-compare] while (p != '\0' && *p >= '0' && *p <= '9') { ^~~~ (void *)0 1 warning generated. mv -f .deps/gsnapl-chrom.Tpo .deps/gsnapl-chrom.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-segmentpos.o -MD -MP -MF .deps/gsnapl-segmentpos.Tpo -c -o gsnapl-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c segmentpos.c:90:41: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"%s\t%u\t%s\t%u\t%u\n",acc,chroffset+this->chrpos1,Chrom_string(this->chrom),this->chrpos1,this->length); ~~ ^~~~~~~~~~~~~~~~~~~~~~~ %llu 1 warning generated. mv -f .deps/gsnapl-segmentpos.Tpo .deps/gsnapl-segmentpos.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-chrnum.o -MD -MP -MF .deps/gsnapl-chrnum.Tpo -c -o gsnapl-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c mv -f .deps/gsnapl-chrnum.Tpo .deps/gsnapl-chrnum.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-maxent_hr.o -MD -MP -MF .deps/gsnapl-maxent_hr.Tpo -c -o gsnapl-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c mv -f .deps/gsnapl-maxent_hr.Tpo .deps/gsnapl-maxent_hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-samprint.o -MD -MP -MF .deps/gsnapl-samprint.Tpo -c -o gsnapl-samprint.o `test -f 'samprint.c' || echo './'`samprint.c mv -f .deps/gsnapl-samprint.Tpo .deps/gsnapl-samprint.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-mapq.o -MD -MP -MF .deps/gsnapl-mapq.Tpo -c -o gsnapl-mapq.o `test -f 'mapq.c' || echo './'`mapq.c mv -f .deps/gsnapl-mapq.Tpo .deps/gsnapl-mapq.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-shortread.o -MD -MP -MF .deps/gsnapl-shortread.Tpo -c -o gsnapl-shortread.o `test -f 'shortread.c' || echo './'`shortread.c mv -f .deps/gsnapl-shortread.Tpo .deps/gsnapl-shortread.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-substring.o -MD -MP -MF .deps/gsnapl-substring.Tpo -c -o gsnapl-substring.o `test -f 'substring.c' || echo './'`substring.c substring.c:1005:33: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("#%d:%u..%u ",chrnum,this->alignstart,this->alignend); ~~ ^~~~~~~~~~~~~~~~ %llu substring.c:1005:50: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("#%d:%u..%u ",chrnum,this->alignstart,this->alignend); ~~ ^~~~~~~~~~~~~~ %llu substring.c:3536:35: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"+%s:%u..%u",chr,substring->alignstart_trim - substring->chroffset + 1U, ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %llu substring.c:3537:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] substring->alignend_trim - substring->chroffset); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ substring.c:3539:35: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"-%s:%u..%u",chr,substring->alignend_trim - substring->chroffset, ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %llu substring.c:3540:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] substring->alignstart_trim - substring->chroffset + 1U); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ substring.c:3544:35: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"-%s:%u..%u",chr,substring->alignstart_trim - substring->chroffset, ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %llu substring.c:3545:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] substring->alignend_trim - substring->chroffset + 1U); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ substring.c:3547:35: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"+%s:%u..%u",chr,substring->alignend_trim - substring->chroffset + 1U, ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %llu substring.c:3548:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] substring->alignstart_trim - substring->chroffset); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 10 warnings generated. mv -f .deps/gsnapl-substring.Tpo .deps/gsnapl-substring.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-stage3hr.o -MD -MP -MF .deps/gsnapl-stage3hr.Tpo -c -o gsnapl-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c mv -f .deps/gsnapl-stage3hr.Tpo .deps/gsnapl-stage3hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-goby.o -MD -MP -MF .deps/gsnapl-goby.Tpo -c -o gsnapl-goby.o `test -f 'goby.c' || echo './'`goby.c mv -f .deps/gsnapl-goby.Tpo .deps/gsnapl-goby.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-spanningelt.o -MD -MP -MF .deps/gsnapl-spanningelt.Tpo -c -o gsnapl-spanningelt.o `test -f 'spanningelt.c' || echo './'`spanningelt.c mv -f .deps/gsnapl-spanningelt.Tpo .deps/gsnapl-spanningelt.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-cmet.o -MD -MP -MF .deps/gsnapl-cmet.Tpo -c -o gsnapl-cmet.o `test -f 'cmet.c' || echo './'`cmet.c mv -f .deps/gsnapl-cmet.Tpo .deps/gsnapl-cmet.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-atoi.o -MD -MP -MF .deps/gsnapl-atoi.Tpo -c -o gsnapl-atoi.o `test -f 'atoi.c' || echo './'`atoi.c mv -f .deps/gsnapl-atoi.Tpo .deps/gsnapl-atoi.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-maxent.o -MD -MP -MF .deps/gsnapl-maxent.Tpo -c -o gsnapl-maxent.o `test -f 'maxent.c' || echo './'`maxent.c mv -f .deps/gsnapl-maxent.Tpo .deps/gsnapl-maxent.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-pair.o -MD -MP -MF .deps/gsnapl-pair.Tpo -c -o gsnapl-pair.o `test -f 'pair.c' || echo './'`pair.c pair.c:546:25: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP); ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %llu /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^~~~~~~~~~~ pair.c:573:25: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP); ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %llu /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^~~~~~~~~~~ pair.c:600:25: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] sprintf(Buffer,"%u",chroffset + start->genomepos + ONEBASEDP); ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %llu /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^~~~~~~~~~~ pair.c:607:25: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] sprintf(Buffer,"%u",chroffset + end->genomepos + ONEBASEDP); ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %llu /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^~~~~~~~~~~ pair.c:1273:3: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] chroffset + this->genomepos + ONEBASEDP, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:1278:3: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] chroffset + this->genomepos + ONEBASEDP, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:1790:25: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~ %llu pair.c:1790:52: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~ %llu pair.c:1799:27: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~ %llu pair.c:1799:54: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~ %llu pair.c:1913:26: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~ %llu pair.c:1913:53: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~ %llu pair.c:1922:28: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~ %llu pair.c:1922:55: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~ %llu pair.c:2419:24: warning: taking the absolute value of unsigned type 'Chrpos_T' (aka 'unsigned int') has no effect [-Wabsolute-value] sprintf(token,"N%u",abs(intron_end - intron_start) + 1); ^ pair.c:2419:24: note: remove the call to 'abs' since unsigned values cannot be negative sprintf(token,"N%u",abs(intron_end - intron_start) + 1); ^~~ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ pair.c:4651:17: warning: taking the absolute value of unsigned type 'Chrpos_T' (aka 'unsigned int') has no effect [-Wabsolute-value] genome_gap = abs(intron_end - intron_start) + 1; ^ pair.c:4651:17: note: remove the call to 'abs' since unsigned values cannot be negative genome_gap = abs(intron_end - intron_start) + 1; ^~~ pair.c:6986:24: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp," %u%s%u",position1 + ONEBASEDP,"..",position2 + ONEBASEDP); ~~ ^~~~~~~~~~~~~~~~~~~~~ %llu pair.c:6986:51: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp," %u%s%u",position1 + ONEBASEDP,"..",position2 + ONEBASEDP); ~~ ^~~~~~~~~~~~~~~~~~~~~ %llu 18 warnings generated. mv -f .deps/gsnapl-pair.Tpo .deps/gsnapl-pair.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-pairpool.o -MD -MP -MF .deps/gsnapl-pairpool.Tpo -c -o gsnapl-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c mv -f .deps/gsnapl-pairpool.Tpo .deps/gsnapl-pairpool.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-diag.o -MD -MP -MF .deps/gsnapl-diag.Tpo -c -o gsnapl-diag.o `test -f 'diag.c' || echo './'`diag.c mv -f .deps/gsnapl-diag.Tpo .deps/gsnapl-diag.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-diagpool.o -MD -MP -MF .deps/gsnapl-diagpool.Tpo -c -o gsnapl-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c mv -f .deps/gsnapl-diagpool.Tpo .deps/gsnapl-diagpool.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-orderstat.o -MD -MP -MF .deps/gsnapl-orderstat.Tpo -c -o gsnapl-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c mv -f .deps/gsnapl-orderstat.Tpo .deps/gsnapl-orderstat.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-oligoindex_hr.o -MD -MP -MF .deps/gsnapl-oligoindex_hr.Tpo -c -o gsnapl-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c mv -f .deps/gsnapl-oligoindex_hr.Tpo .deps/gsnapl-oligoindex_hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-cellpool.o -MD -MP -MF .deps/gsnapl-cellpool.Tpo -c -o gsnapl-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c mv -f .deps/gsnapl-cellpool.Tpo .deps/gsnapl-cellpool.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-stage2.o -MD -MP -MF .deps/gsnapl-stage2.Tpo -c -o gsnapl-stage2.o `test -f 'stage2.c' || echo './'`stage2.c stage2.c:1329:19: warning: taking the absolute value of unsigned type 'Chrpos_T' (aka 'unsigned int') has no effect [-Wabsolute-value] diffdistance = abs(gendistance - querydistance); ^ stage2.c:1329:19: note: remove the call to 'abs' since unsigned values cannot be negative diffdistance = abs(gendistance - querydistance); ^~~ stage2.c:1812:19: warning: taking the absolute value of unsigned type 'Chrpos_T' (aka 'unsigned int') has no effect [-Wabsolute-value] diffdistance = abs(gendistance - querydistance); ^ stage2.c:1812:19: note: remove the call to 'abs' since unsigned values cannot be negative diffdistance = abs(gendistance - querydistance); ^~~ 2 warnings generated. mv -f .deps/gsnapl-stage2.Tpo .deps/gsnapl-stage2.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-intron.o -MD -MP -MF .deps/gsnapl-intron.Tpo -c -o gsnapl-intron.o `test -f 'intron.c' || echo './'`intron.c mv -f .deps/gsnapl-intron.Tpo .deps/gsnapl-intron.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-boyer-moore.o -MD -MP -MF .deps/gsnapl-boyer-moore.Tpo -c -o gsnapl-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c mv -f .deps/gsnapl-boyer-moore.Tpo .deps/gsnapl-boyer-moore.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-changepoint.o -MD -MP -MF .deps/gsnapl-changepoint.Tpo -c -o gsnapl-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c mv -f .deps/gsnapl-changepoint.Tpo .deps/gsnapl-changepoint.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-pbinom.o -MD -MP -MF .deps/gsnapl-pbinom.Tpo -c -o gsnapl-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c mv -f .deps/gsnapl-pbinom.Tpo .deps/gsnapl-pbinom.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-dynprog.o -MD -MP -MF .deps/gsnapl-dynprog.Tpo -c -o gsnapl-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c mv -f .deps/gsnapl-dynprog.Tpo .deps/gsnapl-dynprog.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-gbuffer.o -MD -MP -MF .deps/gsnapl-gbuffer.Tpo -c -o gsnapl-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c mv -f .deps/gsnapl-gbuffer.Tpo .deps/gsnapl-gbuffer.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-translation.o -MD -MP -MF .deps/gsnapl-translation.Tpo -c -o gsnapl-translation.o `test -f 'translation.c' || echo './'`translation.c mv -f .deps/gsnapl-translation.Tpo .deps/gsnapl-translation.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-doublelist.o -MD -MP -MF .deps/gsnapl-doublelist.Tpo -c -o gsnapl-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c mv -f .deps/gsnapl-doublelist.Tpo .deps/gsnapl-doublelist.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-smooth.o -MD -MP -MF .deps/gsnapl-smooth.Tpo -c -o gsnapl-smooth.o `test -f 'smooth.c' || echo './'`smooth.c mv -f .deps/gsnapl-smooth.Tpo .deps/gsnapl-smooth.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-chimera.o -MD -MP -MF .deps/gsnapl-chimera.Tpo -c -o gsnapl-chimera.o `test -f 'chimera.c' || echo './'`chimera.c mv -f .deps/gsnapl-chimera.Tpo .deps/gsnapl-chimera.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-stage3.o -MD -MP -MF .deps/gsnapl-stage3.Tpo -c -o gsnapl-stage3.o `test -f 'stage3.c' || echo './'`stage3.c mv -f .deps/gsnapl-stage3.Tpo .deps/gsnapl-stage3.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-splicestringpool.o -MD -MP -MF .deps/gsnapl-splicestringpool.Tpo -c -o gsnapl-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c mv -f .deps/gsnapl-splicestringpool.Tpo .deps/gsnapl-splicestringpool.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-splicetrie_build.o -MD -MP -MF .deps/gsnapl-splicetrie_build.Tpo -c -o gsnapl-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c splicetrie_build.c:132:31: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%d %u",(int) leaf,position); ~~ ^~~~~~~~ %llu splicetrie_build.c:146:33: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%d %u",(int) leaf,position); ~~ ^~~~~~~~ %llu 2 warnings generated. mv -f .deps/gsnapl-splicetrie_build.Tpo .deps/gsnapl-splicetrie_build.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-splicetrie.o -MD -MP -MF .deps/gsnapl-splicetrie.Tpo -c -o gsnapl-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c mv -f .deps/gsnapl-splicetrie.Tpo .deps/gsnapl-splicetrie.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-splice.o -MD -MP -MF .deps/gsnapl-splice.Tpo -c -o gsnapl-splice.o `test -f 'splice.c' || echo './'`splice.c mv -f .deps/gsnapl-splice.Tpo .deps/gsnapl-splice.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-indel.o -MD -MP -MF .deps/gsnapl-indel.Tpo -c -o gsnapl-indel.o `test -f 'indel.c' || echo './'`indel.c mv -f .deps/gsnapl-indel.Tpo .deps/gsnapl-indel.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-bitpack64-access.o -MD -MP -MF .deps/gsnapl-bitpack64-access.Tpo -c -o gsnapl-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c mv -f .deps/gsnapl-bitpack64-access.Tpo .deps/gsnapl-bitpack64-access.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-sarray-read.o -MD -MP -MF .deps/gsnapl-sarray-read.Tpo -c -o gsnapl-sarray-read.o `test -f 'sarray-read.c' || echo './'`sarray-read.c sarray-read.c:302:15: warning: incompatible pointer types assigning to 'UINT4 *' (aka 'unsigned int *') from 'Univcoord_T *' (aka 'unsigned long long *') [-Wincompatible-pointer-types] new->lcpcomp = (Univcoord_T *) Access_allocated(&new->lcpcomp_len,&seconds2,filename,sizeof(Univcoord_T)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sarray-read.c:368:15: warning: incompatible pointer types assigning to 'UINT4 *' (aka 'unsigned int *') from 'Univcoord_T *' (aka 'unsigned long long *') [-Wincompatible-pointer-types] new->lcpcomp = (Univcoord_T *) Access_mmap_and_preload(&new->lcpcomp_fd,&new->lcpcomp_len,&npages,&seconds2, ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sarray-read.c:434:15: warning: incompatible pointer types assigning to 'UINT4 *' (aka 'unsigned int *') from 'Univcoord_T *' (aka 'unsigned long long *') [-Wincompatible-pointer-types] new->lcpcomp = (Univcoord_T *) Access_mmap(&new->lcpcomp_fd,&new->lcpcomp_len,filename,sizeof(Univcoord_T), ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sarray-read.c:526:15: warning: incompatible pointer types assigning to 'UINT4 *' (aka 'unsigned int *') from 'Univcoord_T *' (aka 'unsigned long long *') [-Wincompatible-pointer-types] new->lcpcomp = (Univcoord_T *) Access_allocated(&new->lcpcomp_len,&seconds2,filename,sizeof(Univcoord_T)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sarray-read.c:653:15: warning: incompatible pointer types assigning to 'UINT4 *' (aka 'unsigned int *') from 'Univcoord_T *' (aka 'unsigned long long *') [-Wincompatible-pointer-types] new->lcpcomp = (Univcoord_T *) Access_mmap(&new->lcpcomp_fd,&new->lcpcomp_len, ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sarray-read.c:1667:53: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%d..%d:%u\t",elt->querystart,elt->queryend,elt->positions[k]); ~~ ^~~~~~~~~~~~~~~~~ %llu sarray-read.c:1682:56: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%d..%d:%u\n",elt->querystart,elt->queryend,elt->positions[k]); ~~ ^~~~~~~~~~~~~~~~~ %llu sarray-read.c:2170:11: warning: incompatible pointer types assigning to 'Univcoord_T *' (aka 'unsigned long long *') from 'UINT4 *' (aka 'unsigned int *') [-Wincompatible-pointer-types] array = Uintlist_to_array(&n,difflist); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sarray-read.c:2442:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); ^~~~~~~~~ ./uint8list.h:11:19: note: passing argument to parameter 'list' here Uint8list_push (T list, UINT8 x); ^ sarray-read.c:2442:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sarray-read.c:2456:34: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] /*ambcoords_donor*/NULL,ambcoords, ^~~~~~~~~ ./stage3hr.h:296:50: note: passing argument to parameter 'ambcoords_acceptor' here Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, ^ sarray-read.c:2499:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); ^~~~~~~~~ ./uint8list.h:11:19: note: passing argument to parameter 'list' here Uint8list_push (T list, UINT8 x); ^ sarray-read.c:2499:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sarray-read.c:2513:10: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords,/*ambcoords_acceptor*/NULL, ^~~~~~~~~ ./stage3hr.h:296:21: note: passing argument to parameter 'ambcoords_donor' here Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, ^ sarray-read.c:2643:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); ^~~~~~~~~ ./uint8list.h:11:19: note: passing argument to parameter 'list' here Uint8list_push (T list, UINT8 x); ^ sarray-read.c:2643:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sarray-read.c:2656:36: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] /*ambcoords_donor*/NULL,ambcoords, ^~~~~~~~~ ./stage3hr.h:296:50: note: passing argument to parameter 'ambcoords_acceptor' here Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, ^ sarray-read.c:2699:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); ^~~~~~~~~ ./uint8list.h:11:19: note: passing argument to parameter 'list' here Uint8list_push (T list, UINT8 x); ^ sarray-read.c:2699:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sarray-read.c:2712:12: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords,/*ambcoords_acceptor*/NULL, ^~~~~~~~~ ./stage3hr.h:296:21: note: passing argument to parameter 'ambcoords_donor' here Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, ^ sarray-read.c:2752:11: warning: incompatible pointer types assigning to 'Univcoord_T *' (aka 'unsigned long long *') from 'UINT4 *' (aka 'unsigned int *') [-Wincompatible-pointer-types] array = Uintlist_to_array(&n,difflist); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sarray-read.c:3024:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); ^~~~~~~~~ ./uint8list.h:11:19: note: passing argument to parameter 'list' here Uint8list_push (T list, UINT8 x); ^ sarray-read.c:3024:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sarray-read.c:3038:34: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] /*ambcoords_donor*/NULL,ambcoords, ^~~~~~~~~ ./stage3hr.h:296:50: note: passing argument to parameter 'ambcoords_acceptor' here Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, ^ sarray-read.c:3082:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); ^~~~~~~~~ ./uint8list.h:11:19: note: passing argument to parameter 'list' here Uint8list_push (T list, UINT8 x); ^ sarray-read.c:3082:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sarray-read.c:3096:10: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords,/*ambcoords_acceptor*/NULL, ^~~~~~~~~ ./stage3hr.h:296:21: note: passing argument to parameter 'ambcoords_donor' here Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, ^ sarray-read.c:3217:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); ^~~~~~~~~ ./uint8list.h:11:19: note: passing argument to parameter 'list' here Uint8list_push (T list, UINT8 x); ^ sarray-read.c:3217:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sarray-read.c:3231:34: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] /*ambcoords_donor*/NULL,ambcoords, ^~~~~~~~~ ./stage3hr.h:296:50: note: passing argument to parameter 'ambcoords_acceptor' here Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, ^ sarray-read.c:3274:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); ^~~~~~~~~ ./uint8list.h:11:19: note: passing argument to parameter 'list' here Uint8list_push (T list, UINT8 x); ^ sarray-read.c:3274:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sarray-read.c:3288:10: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords,/*ambcoords_acceptor*/NULL, ^~~~~~~~~ ./stage3hr.h:296:21: note: passing argument to parameter 'ambcoords_donor' here Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, ^ 33 warnings generated. mv -f .deps/gsnapl-sarray-read.Tpo .deps/gsnapl-sarray-read.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-stage1hr.o -MD -MP -MF .deps/gsnapl-stage1hr.Tpo -c -o gsnapl-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c stage1hr.c:6630:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stage1hr.c:6630:40: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stage1hr.c:6630:76: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stage1hr.c:6769:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Substring_genomicstart(donor),Substring_genomicend(donor),Substring_plusp(donor), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stage1hr.c:6769:37: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Substring_genomicstart(donor),Substring_genomicend(donor),Substring_plusp(donor), ^~~~~~~~~~~~~~~~~~~~~~~~~~~ stage1hr.c:6770:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Substring_genomicstart(acceptor),Substring_genomicend(acceptor),Substring_plusp(acceptor), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stage1hr.c:6770:40: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Substring_genomicstart(acceptor),Substring_genomicend(acceptor),Substring_plusp(acceptor), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stage1hr.c:6771:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] segmenti->diagonal - querylength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stage1hr.c:7146:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stage1hr.c:7146:40: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stage1hr.c:7146:76: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stage1hr.c:7285:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stage1hr.c:7285:40: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stage1hr.c:7285:76: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 14 warnings generated. mv -f .deps/gsnapl-stage1hr.Tpo .deps/gsnapl-stage1hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-request.o -MD -MP -MF .deps/gsnapl-request.Tpo -c -o gsnapl-request.o `test -f 'request.c' || echo './'`request.c mv -f .deps/gsnapl-request.Tpo .deps/gsnapl-request.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-resulthr.o -MD -MP -MF .deps/gsnapl-resulthr.Tpo -c -o gsnapl-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c mv -f .deps/gsnapl-resulthr.Tpo .deps/gsnapl-resulthr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-inbuffer.o -MD -MP -MF .deps/gsnapl-inbuffer.Tpo -c -o gsnapl-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c mv -f .deps/gsnapl-inbuffer.Tpo .deps/gsnapl-inbuffer.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-samheader.o -MD -MP -MF .deps/gsnapl-samheader.Tpo -c -o gsnapl-samheader.o `test -f 'samheader.c' || echo './'`samheader.c mv -f .deps/gsnapl-samheader.Tpo .deps/gsnapl-samheader.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-outbuffer.o -MD -MP -MF .deps/gsnapl-outbuffer.Tpo -c -o gsnapl-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c mv -f .deps/gsnapl-outbuffer.Tpo .deps/gsnapl-outbuffer.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-datadir.o -MD -MP -MF .deps/gsnapl-datadir.Tpo -c -o gsnapl-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/gsnapl-datadir.Tpo .deps/gsnapl-datadir.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-getopt.o -MD -MP -MF .deps/gsnapl-getopt.Tpo -c -o gsnapl-getopt.o `test -f 'getopt.c' || echo './'`getopt.c getopt.c:208:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] my_index (str, chr) ^ getopt.c:291:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] exchange (argv) ^ getopt.c:376:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] _getopt_initialize (argc, argv, optstring) ^ getopt.c:389:28: warning: passing arguments to 'getenv' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] posixly_correct = getenv ("POSIXLY_CORRECT"); ^ getopt.c:498:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] _getopt_internal (argc, argv, optstring, longopts, longind, long_only) ^ getopt.c:1179:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt (argc, argv, optstring) ^ In file included from getopt.c:97: ./getopt.h:147:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent definition [-Wdeprecated-non-prototype] extern int getopt (); ^ 7 warnings generated. mv -f .deps/gsnapl-getopt.Tpo .deps/gsnapl-getopt.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-getopt1.o -MD -MP -MF .deps/gsnapl-getopt1.Tpo -c -o gsnapl-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c getopt1.c:71:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt_long (argc, argv, options, long_options, opt_index) ^ getopt1.c:87:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt_long_only (argc, argv, options, long_options, opt_index) ^ 2 warnings generated. mv -f .deps/gsnapl-getopt1.Tpo .deps/gsnapl-getopt1.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-gsnap.o -MD -MP -MF .deps/gsnapl-gsnap.Tpo -c -o gsnapl-gsnap.o `test -f 'gsnap.c' || echo './'`gsnap.c In file included from gsnap.c:84: ./getopt.h:147:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a previous declaration [-Wdeprecated-non-prototype] extern int getopt (); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/unistd.h:509:6: note: conflicting prototype is here int getopt(int, char * const [], const char *) __DARWIN_ALIAS(getopt); ^ 1 warning generated. mv -f .deps/gsnapl-gsnap.Tpo .deps/gsnapl-gsnap.Po /bin/sh ../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -o gsnapl gsnapl-except.o gsnapl-assert.o gsnapl-mem.o gsnapl-intlist.o gsnapl-list.o gsnapl-littleendian.o gsnapl-bigendian.o gsnapl-univinterval.o gsnapl-interval.o gsnapl-uintlist.o gsnapl-uint8list.o gsnapl-stopwatch.o gsnapl-access.o gsnapl-iit-read-univ.o gsnapl-iit-read.o gsnapl-md5.o gsnapl-bzip2.o gsnapl-sequence.o gsnapl-reader.o gsnapl-genomicpos.o gsnapl-compress.o gsnapl-genome.o gsnapl-genome_hr.o gsnapl-genome_sites.o gsnapl-bitpack64-read.o gsnapl-indexdb.o gsnapl-indexdb_hr.o gsnapl-oligo.o gsnapl-chrom.o gsnapl-segmentpos.o gsnapl-chrnum.o gsnapl-maxent_hr.o gsnapl-samprint.o gsnapl-mapq.o gsnapl-shortread.o gsnapl-substring.o gsnapl-stage3hr.o gsnapl-goby.o gsnapl-spanningelt.o gsnapl-cmet.o gsnapl-atoi.o gsnapl-maxent.o gsnapl-pair.o gsnapl-pairpool.o gsnapl-diag.o gsnapl-diagpool.o gsnapl-orderstat.o gsnapl-oligoindex_hr.o gsnapl-cellpool.o gsnapl-stage2.o gsnapl-intron.o gsnapl-boyer-moore.o gsnapl-changepoint.o gsnapl-pbinom.o gsnapl-dynprog.o gsnapl-gbuffer.o gsnapl-translation.o gsnapl-doublelist.o gsnapl-smooth.o gsnapl-chimera.o gsnapl-stage3.o gsnapl-splicestringpool.o gsnapl-splicetrie_build.o gsnapl-splicetrie.o gsnapl-splice.o gsnapl-indel.o gsnapl-bitpack64-access.o gsnapl-sarray-read.o gsnapl-stage1hr.o gsnapl-request.o gsnapl-resulthr.o gsnapl-inbuffer.o gsnapl-samheader.o gsnapl-outbuffer.o gsnapl-datadir.o gsnapl-getopt.o gsnapl-getopt1.o gsnapl-gsnap.o -lz -lbz2 -lm libtool: link: gcc -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -o gsnapl gsnapl-except.o gsnapl-assert.o gsnapl-mem.o gsnapl-intlist.o gsnapl-list.o gsnapl-littleendian.o gsnapl-bigendian.o gsnapl-univinterval.o gsnapl-interval.o gsnapl-uintlist.o gsnapl-uint8list.o gsnapl-stopwatch.o gsnapl-access.o gsnapl-iit-read-univ.o gsnapl-iit-read.o gsnapl-md5.o gsnapl-bzip2.o gsnapl-sequence.o gsnapl-reader.o gsnapl-genomicpos.o gsnapl-compress.o gsnapl-genome.o gsnapl-genome_hr.o gsnapl-genome_sites.o gsnapl-bitpack64-read.o gsnapl-indexdb.o gsnapl-indexdb_hr.o gsnapl-oligo.o gsnapl-chrom.o gsnapl-segmentpos.o gsnapl-chrnum.o gsnapl-maxent_hr.o gsnapl-samprint.o gsnapl-mapq.o gsnapl-shortread.o gsnapl-substring.o gsnapl-stage3hr.o gsnapl-goby.o gsnapl-spanningelt.o gsnapl-cmet.o gsnapl-atoi.o gsnapl-maxent.o gsnapl-pair.o gsnapl-pairpool.o gsnapl-diag.o gsnapl-diagpool.o gsnapl-orderstat.o gsnapl-oligoindex_hr.o gsnapl-cellpool.o gsnapl-stage2.o gsnapl-intron.o gsnapl-boyer-moore.o gsnapl-changepoint.o gsnapl-pbinom.o gsnapl-dynprog.o gsnapl-gbuffer.o gsnapl-translation.o gsnapl-doublelist.o gsnapl-smooth.o gsnapl-chimera.o gsnapl-stage3.o gsnapl-splicestringpool.o gsnapl-splicetrie_build.o gsnapl-splicetrie.o gsnapl-splice.o gsnapl-indel.o gsnapl-bitpack64-access.o gsnapl-sarray-read.o gsnapl-stage1hr.o gsnapl-request.o gsnapl-resulthr.o gsnapl-inbuffer.o gsnapl-samheader.o gsnapl-outbuffer.o gsnapl-datadir.o gsnapl-getopt.o gsnapl-getopt1.o gsnapl-gsnap.o -lz -lbz2 -lm gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-except.o -MD -MP -MF .deps/uniqscan-except.Tpo -c -o uniqscan-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/uniqscan-except.Tpo .deps/uniqscan-except.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-assert.o -MD -MP -MF .deps/uniqscan-assert.Tpo -c -o uniqscan-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/uniqscan-assert.Tpo .deps/uniqscan-assert.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-mem.o -MD -MP -MF .deps/uniqscan-mem.Tpo -c -o uniqscan-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/uniqscan-mem.Tpo .deps/uniqscan-mem.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-intlist.o -MD -MP -MF .deps/uniqscan-intlist.Tpo -c -o uniqscan-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/uniqscan-intlist.Tpo .deps/uniqscan-intlist.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-list.o -MD -MP -MF .deps/uniqscan-list.Tpo -c -o uniqscan-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/uniqscan-list.Tpo .deps/uniqscan-list.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-littleendian.o -MD -MP -MF .deps/uniqscan-littleendian.Tpo -c -o uniqscan-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c mv -f .deps/uniqscan-littleendian.Tpo .deps/uniqscan-littleendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-bigendian.o -MD -MP -MF .deps/uniqscan-bigendian.Tpo -c -o uniqscan-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c mv -f .deps/uniqscan-bigendian.Tpo .deps/uniqscan-bigendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-univinterval.o -MD -MP -MF .deps/uniqscan-univinterval.Tpo -c -o uniqscan-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~ %u univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~~ %u 2 warnings generated. mv -f .deps/uniqscan-univinterval.Tpo .deps/uniqscan-univinterval.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-interval.o -MD -MP -MF .deps/uniqscan-interval.Tpo -c -o uniqscan-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/uniqscan-interval.Tpo .deps/uniqscan-interval.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-uintlist.o -MD -MP -MF .deps/uniqscan-uintlist.Tpo -c -o uniqscan-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/uniqscan-uintlist.Tpo .deps/uniqscan-uintlist.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-stopwatch.o -MD -MP -MF .deps/uniqscan-stopwatch.Tpo -c -o uniqscan-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/uniqscan-stopwatch.Tpo .deps/uniqscan-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-access.o -MD -MP -MF .deps/uniqscan-access.Tpo -c -o uniqscan-access.o `test -f 'access.c' || echo './'`access.c access.c:358:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] length,length,errno,strerror(errno)); ^~~~~~ access.c:358:15: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] length,length,errno,strerror(errno)); ^~~~~~ access.c:423:11: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] fd,offset,length,errno,strerror(errno)); ^~~~~~ access.c:493:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] *len,length,errno,strerror(errno)); ^~~~~~ access.c:556:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] offset,length,errno,strerror(errno)); ^~~~~~ access.c:641:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] *len,length,errno,strerror(errno)); ^~~~~~ 6 warnings generated. mv -f .deps/uniqscan-access.Tpo .deps/uniqscan-access.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-iit-read-univ.o -MD -MP -MF .deps/uniqscan-iit-read-univ.Tpo -c -o uniqscan-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~~~ %u iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~ %u iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~~~ %u iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~ %u iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %u iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %u iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~ %u iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~~~ %u iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %u iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %u 10 warnings generated. mv -f .deps/uniqscan-iit-read-univ.Tpo .deps/uniqscan-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-iit-read.o -MD -MP -MF .deps/uniqscan-iit-read.Tpo -c -o uniqscan-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c mv -f .deps/uniqscan-iit-read.Tpo .deps/uniqscan-iit-read.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-md5.o -MD -MP -MF .deps/uniqscan-md5.Tpo -c -o uniqscan-md5.o `test -f 'md5.c' || echo './'`md5.c mv -f .deps/uniqscan-md5.Tpo .deps/uniqscan-md5.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-bzip2.o -MD -MP -MF .deps/uniqscan-bzip2.Tpo -c -o uniqscan-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c mv -f .deps/uniqscan-bzip2.Tpo .deps/uniqscan-bzip2.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-sequence.o -MD -MP -MF .deps/uniqscan-sequence.Tpo -c -o uniqscan-sequence.o `test -f 'sequence.c' || echo './'`sequence.c mv -f .deps/uniqscan-sequence.Tpo .deps/uniqscan-sequence.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-reader.o -MD -MP -MF .deps/uniqscan-reader.Tpo -c -o uniqscan-reader.o `test -f 'reader.c' || echo './'`reader.c mv -f .deps/uniqscan-reader.Tpo .deps/uniqscan-reader.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-genomicpos.o -MD -MP -MF .deps/uniqscan-genomicpos.Tpo -c -o uniqscan-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/uniqscan-genomicpos.Tpo .deps/uniqscan-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-compress.o -MD -MP -MF .deps/uniqscan-compress.Tpo -c -o uniqscan-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/uniqscan-compress.Tpo .deps/uniqscan-compress.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-genome.o -MD -MP -MF .deps/uniqscan-genome.Tpo -c -o uniqscan-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c:10292:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %u genome.c:10292:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %u genome.c:10392:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %u genome.c:10392:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %u 4 warnings generated. mv -f .deps/uniqscan-genome.Tpo .deps/uniqscan-genome.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-genome_hr.o -MD -MP -MF .deps/uniqscan-genome_hr.Tpo -c -o uniqscan-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c mv -f .deps/uniqscan-genome_hr.Tpo .deps/uniqscan-genome_hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-genome_sites.o -MD -MP -MF .deps/uniqscan-genome_sites.Tpo -c -o uniqscan-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c mv -f .deps/uniqscan-genome_sites.Tpo .deps/uniqscan-genome_sites.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-bitpack64-read.o -MD -MP -MF .deps/uniqscan-bitpack64-read.Tpo -c -o uniqscan-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c mv -f .deps/uniqscan-bitpack64-read.Tpo .deps/uniqscan-bitpack64-read.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-indexdb.o -MD -MP -MF .deps/uniqscan-indexdb.Tpo -c -o uniqscan-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c:1363:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1483:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1653:63: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1792:6: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] ptr,sizeof(Univcoord_T),offset); ^~~ indexdb.c:1792:30: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] ptr,sizeof(Univcoord_T),offset); ^~~~~~ indexdb.c:1934:76: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, ~~~ ^~~~~~~~~~~~~~ %llu indexdb.c:2026:76: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, ~~~ ^~~~~~~~~~~~~~ %llu 7 warnings generated. mv -f .deps/uniqscan-indexdb.Tpo .deps/uniqscan-indexdb.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-indexdb_hr.o -MD -MP -MF .deps/uniqscan-indexdb_hr.Tpo -c -o uniqscan-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c mv -f .deps/uniqscan-indexdb_hr.Tpo .deps/uniqscan-indexdb_hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-oligo.o -MD -MP -MF .deps/uniqscan-oligo.Tpo -c -o uniqscan-oligo.o `test -f 'oligo.c' || echo './'`oligo.c mv -f .deps/uniqscan-oligo.Tpo .deps/uniqscan-oligo.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-chrom.o -MD -MP -MF .deps/uniqscan-chrom.Tpo -c -o uniqscan-chrom.o `test -f 'chrom.c' || echo './'`chrom.c chrom.c:116:15: warning: comparing a pointer to a null character constant; did you mean to compare to NULL? [-Wpointer-compare] while (p != '\0' && *p >= '0' && *p <= '9') { ^~~~ (void *)0 1 warning generated. mv -f .deps/uniqscan-chrom.Tpo .deps/uniqscan-chrom.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-segmentpos.o -MD -MP -MF .deps/uniqscan-segmentpos.Tpo -c -o uniqscan-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c mv -f .deps/uniqscan-segmentpos.Tpo .deps/uniqscan-segmentpos.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-chrnum.o -MD -MP -MF .deps/uniqscan-chrnum.Tpo -c -o uniqscan-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c mv -f .deps/uniqscan-chrnum.Tpo .deps/uniqscan-chrnum.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-maxent_hr.o -MD -MP -MF .deps/uniqscan-maxent_hr.Tpo -c -o uniqscan-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c mv -f .deps/uniqscan-maxent_hr.Tpo .deps/uniqscan-maxent_hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-mapq.o -MD -MP -MF .deps/uniqscan-mapq.Tpo -c -o uniqscan-mapq.o `test -f 'mapq.c' || echo './'`mapq.c mv -f .deps/uniqscan-mapq.Tpo .deps/uniqscan-mapq.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-shortread.o -MD -MP -MF .deps/uniqscan-shortread.Tpo -c -o uniqscan-shortread.o `test -f 'shortread.c' || echo './'`shortread.c mv -f .deps/uniqscan-shortread.Tpo .deps/uniqscan-shortread.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-substring.o -MD -MP -MF .deps/uniqscan-substring.Tpo -c -o uniqscan-substring.o `test -f 'substring.c' || echo './'`substring.c mv -f .deps/uniqscan-substring.Tpo .deps/uniqscan-substring.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-stage3hr.o -MD -MP -MF .deps/uniqscan-stage3hr.Tpo -c -o uniqscan-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c mv -f .deps/uniqscan-stage3hr.Tpo .deps/uniqscan-stage3hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-spanningelt.o -MD -MP -MF .deps/uniqscan-spanningelt.Tpo -c -o uniqscan-spanningelt.o `test -f 'spanningelt.c' || echo './'`spanningelt.c mv -f .deps/uniqscan-spanningelt.Tpo .deps/uniqscan-spanningelt.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-cmet.o -MD -MP -MF .deps/uniqscan-cmet.Tpo -c -o uniqscan-cmet.o `test -f 'cmet.c' || echo './'`cmet.c mv -f .deps/uniqscan-cmet.Tpo .deps/uniqscan-cmet.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-atoi.o -MD -MP -MF .deps/uniqscan-atoi.Tpo -c -o uniqscan-atoi.o `test -f 'atoi.c' || echo './'`atoi.c mv -f .deps/uniqscan-atoi.Tpo .deps/uniqscan-atoi.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-maxent.o -MD -MP -MF .deps/uniqscan-maxent.Tpo -c -o uniqscan-maxent.o `test -f 'maxent.c' || echo './'`maxent.c mv -f .deps/uniqscan-maxent.Tpo .deps/uniqscan-maxent.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-pair.o -MD -MP -MF .deps/uniqscan-pair.Tpo -c -o uniqscan-pair.o `test -f 'pair.c' || echo './'`pair.c pair.c:2419:24: warning: taking the absolute value of unsigned type 'Chrpos_T' (aka 'unsigned int') has no effect [-Wabsolute-value] sprintf(token,"N%u",abs(intron_end - intron_start) + 1); ^ pair.c:2419:24: note: remove the call to 'abs' since unsigned values cannot be negative sprintf(token,"N%u",abs(intron_end - intron_start) + 1); ^~~ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ pair.c:4651:17: warning: taking the absolute value of unsigned type 'Chrpos_T' (aka 'unsigned int') has no effect [-Wabsolute-value] genome_gap = abs(intron_end - intron_start) + 1; ^ pair.c:4651:17: note: remove the call to 'abs' since unsigned values cannot be negative genome_gap = abs(intron_end - intron_start) + 1; ^~~ 2 warnings generated. mv -f .deps/uniqscan-pair.Tpo .deps/uniqscan-pair.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-pairpool.o -MD -MP -MF .deps/uniqscan-pairpool.Tpo -c -o uniqscan-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c mv -f .deps/uniqscan-pairpool.Tpo .deps/uniqscan-pairpool.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-diag.o -MD -MP -MF .deps/uniqscan-diag.Tpo -c -o uniqscan-diag.o `test -f 'diag.c' || echo './'`diag.c mv -f .deps/uniqscan-diag.Tpo .deps/uniqscan-diag.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-diagpool.o -MD -MP -MF .deps/uniqscan-diagpool.Tpo -c -o uniqscan-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c mv -f .deps/uniqscan-diagpool.Tpo .deps/uniqscan-diagpool.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-orderstat.o -MD -MP -MF .deps/uniqscan-orderstat.Tpo -c -o uniqscan-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c mv -f .deps/uniqscan-orderstat.Tpo .deps/uniqscan-orderstat.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-oligoindex_hr.o -MD -MP -MF .deps/uniqscan-oligoindex_hr.Tpo -c -o uniqscan-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c mv -f .deps/uniqscan-oligoindex_hr.Tpo .deps/uniqscan-oligoindex_hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-cellpool.o -MD -MP -MF .deps/uniqscan-cellpool.Tpo -c -o uniqscan-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c mv -f .deps/uniqscan-cellpool.Tpo .deps/uniqscan-cellpool.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-stage2.o -MD -MP -MF .deps/uniqscan-stage2.Tpo -c -o uniqscan-stage2.o `test -f 'stage2.c' || echo './'`stage2.c stage2.c:1329:19: warning: taking the absolute value of unsigned type 'Chrpos_T' (aka 'unsigned int') has no effect [-Wabsolute-value] diffdistance = abs(gendistance - querydistance); ^ stage2.c:1329:19: note: remove the call to 'abs' since unsigned values cannot be negative diffdistance = abs(gendistance - querydistance); ^~~ stage2.c:1812:19: warning: taking the absolute value of unsigned type 'Chrpos_T' (aka 'unsigned int') has no effect [-Wabsolute-value] diffdistance = abs(gendistance - querydistance); ^ stage2.c:1812:19: note: remove the call to 'abs' since unsigned values cannot be negative diffdistance = abs(gendistance - querydistance); ^~~ 2 warnings generated. mv -f .deps/uniqscan-stage2.Tpo .deps/uniqscan-stage2.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-intron.o -MD -MP -MF .deps/uniqscan-intron.Tpo -c -o uniqscan-intron.o `test -f 'intron.c' || echo './'`intron.c mv -f .deps/uniqscan-intron.Tpo .deps/uniqscan-intron.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-boyer-moore.o -MD -MP -MF .deps/uniqscan-boyer-moore.Tpo -c -o uniqscan-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c mv -f .deps/uniqscan-boyer-moore.Tpo .deps/uniqscan-boyer-moore.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-changepoint.o -MD -MP -MF .deps/uniqscan-changepoint.Tpo -c -o uniqscan-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c mv -f .deps/uniqscan-changepoint.Tpo .deps/uniqscan-changepoint.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-pbinom.o -MD -MP -MF .deps/uniqscan-pbinom.Tpo -c -o uniqscan-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c mv -f .deps/uniqscan-pbinom.Tpo .deps/uniqscan-pbinom.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-dynprog.o -MD -MP -MF .deps/uniqscan-dynprog.Tpo -c -o uniqscan-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c mv -f .deps/uniqscan-dynprog.Tpo .deps/uniqscan-dynprog.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-translation.o -MD -MP -MF .deps/uniqscan-translation.Tpo -c -o uniqscan-translation.o `test -f 'translation.c' || echo './'`translation.c mv -f .deps/uniqscan-translation.Tpo .deps/uniqscan-translation.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-doublelist.o -MD -MP -MF .deps/uniqscan-doublelist.Tpo -c -o uniqscan-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c mv -f .deps/uniqscan-doublelist.Tpo .deps/uniqscan-doublelist.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-smooth.o -MD -MP -MF .deps/uniqscan-smooth.Tpo -c -o uniqscan-smooth.o `test -f 'smooth.c' || echo './'`smooth.c mv -f .deps/uniqscan-smooth.Tpo .deps/uniqscan-smooth.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-chimera.o -MD -MP -MF .deps/uniqscan-chimera.Tpo -c -o uniqscan-chimera.o `test -f 'chimera.c' || echo './'`chimera.c mv -f .deps/uniqscan-chimera.Tpo .deps/uniqscan-chimera.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-stage3.o -MD -MP -MF .deps/uniqscan-stage3.Tpo -c -o uniqscan-stage3.o `test -f 'stage3.c' || echo './'`stage3.c mv -f .deps/uniqscan-stage3.Tpo .deps/uniqscan-stage3.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-splicestringpool.o -MD -MP -MF .deps/uniqscan-splicestringpool.Tpo -c -o uniqscan-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c mv -f .deps/uniqscan-splicestringpool.Tpo .deps/uniqscan-splicestringpool.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-splicetrie_build.o -MD -MP -MF .deps/uniqscan-splicetrie_build.Tpo -c -o uniqscan-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c mv -f .deps/uniqscan-splicetrie_build.Tpo .deps/uniqscan-splicetrie_build.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-splicetrie.o -MD -MP -MF .deps/uniqscan-splicetrie.Tpo -c -o uniqscan-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c mv -f .deps/uniqscan-splicetrie.Tpo .deps/uniqscan-splicetrie.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-splice.o -MD -MP -MF .deps/uniqscan-splice.Tpo -c -o uniqscan-splice.o `test -f 'splice.c' || echo './'`splice.c mv -f .deps/uniqscan-splice.Tpo .deps/uniqscan-splice.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-indel.o -MD -MP -MF .deps/uniqscan-indel.Tpo -c -o uniqscan-indel.o `test -f 'indel.c' || echo './'`indel.c mv -f .deps/uniqscan-indel.Tpo .deps/uniqscan-indel.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-bitpack64-access.o -MD -MP -MF .deps/uniqscan-bitpack64-access.Tpo -c -o uniqscan-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c mv -f .deps/uniqscan-bitpack64-access.Tpo .deps/uniqscan-bitpack64-access.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-sarray-read.o -MD -MP -MF .deps/uniqscan-sarray-read.Tpo -c -o uniqscan-sarray-read.o `test -f 'sarray-read.c' || echo './'`sarray-read.c mv -f .deps/uniqscan-sarray-read.Tpo .deps/uniqscan-sarray-read.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-stage1hr.o -MD -MP -MF .deps/uniqscan-stage1hr.Tpo -c -o uniqscan-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c mv -f .deps/uniqscan-stage1hr.Tpo .deps/uniqscan-stage1hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-resulthr.o -MD -MP -MF .deps/uniqscan-resulthr.Tpo -c -o uniqscan-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c mv -f .deps/uniqscan-resulthr.Tpo .deps/uniqscan-resulthr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-datadir.o -MD -MP -MF .deps/uniqscan-datadir.Tpo -c -o uniqscan-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/uniqscan-datadir.Tpo .deps/uniqscan-datadir.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-getopt.o -MD -MP -MF .deps/uniqscan-getopt.Tpo -c -o uniqscan-getopt.o `test -f 'getopt.c' || echo './'`getopt.c getopt.c:208:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] my_index (str, chr) ^ getopt.c:291:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] exchange (argv) ^ getopt.c:376:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] _getopt_initialize (argc, argv, optstring) ^ getopt.c:389:28: warning: passing arguments to 'getenv' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] posixly_correct = getenv ("POSIXLY_CORRECT"); ^ getopt.c:498:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] _getopt_internal (argc, argv, optstring, longopts, longind, long_only) ^ getopt.c:1179:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt (argc, argv, optstring) ^ In file included from getopt.c:97: ./getopt.h:147:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent definition [-Wdeprecated-non-prototype] extern int getopt (); ^ 7 warnings generated. mv -f .deps/uniqscan-getopt.Tpo .deps/uniqscan-getopt.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-getopt1.o -MD -MP -MF .deps/uniqscan-getopt1.Tpo -c -o uniqscan-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c getopt1.c:71:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt_long (argc, argv, options, long_options, opt_index) ^ getopt1.c:87:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt_long_only (argc, argv, options, long_options, opt_index) ^ 2 warnings generated. mv -f .deps/uniqscan-getopt1.Tpo .deps/uniqscan-getopt1.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-uniqscan.o -MD -MP -MF .deps/uniqscan-uniqscan.Tpo -c -o uniqscan-uniqscan.o `test -f 'uniqscan.c' || echo './'`uniqscan.c In file included from uniqscan.c:55: ./getopt.h:147:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a previous declaration [-Wdeprecated-non-prototype] extern int getopt (); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/unistd.h:509:6: note: conflicting prototype is here int getopt(int, char * const [], const char *) __DARWIN_ALIAS(getopt); ^ 1 warning generated. mv -f .deps/uniqscan-uniqscan.Tpo .deps/uniqscan-uniqscan.Po /bin/sh ../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -o uniqscan uniqscan-except.o uniqscan-assert.o uniqscan-mem.o uniqscan-intlist.o uniqscan-list.o uniqscan-littleendian.o uniqscan-bigendian.o uniqscan-univinterval.o uniqscan-interval.o uniqscan-uintlist.o uniqscan-stopwatch.o uniqscan-access.o uniqscan-iit-read-univ.o uniqscan-iit-read.o uniqscan-md5.o uniqscan-bzip2.o uniqscan-sequence.o uniqscan-reader.o uniqscan-genomicpos.o uniqscan-compress.o uniqscan-genome.o uniqscan-genome_hr.o uniqscan-genome_sites.o uniqscan-bitpack64-read.o uniqscan-indexdb.o uniqscan-indexdb_hr.o uniqscan-oligo.o uniqscan-chrom.o uniqscan-segmentpos.o uniqscan-chrnum.o uniqscan-maxent_hr.o uniqscan-mapq.o uniqscan-shortread.o uniqscan-substring.o uniqscan-stage3hr.o uniqscan-spanningelt.o uniqscan-cmet.o uniqscan-atoi.o uniqscan-maxent.o uniqscan-pair.o uniqscan-pairpool.o uniqscan-diag.o uniqscan-diagpool.o uniqscan-orderstat.o uniqscan-oligoindex_hr.o uniqscan-cellpool.o uniqscan-stage2.o uniqscan-intron.o uniqscan-boyer-moore.o uniqscan-changepoint.o uniqscan-pbinom.o uniqscan-dynprog.o uniqscan-translation.o uniqscan-doublelist.o uniqscan-smooth.o uniqscan-chimera.o uniqscan-stage3.o uniqscan-splicestringpool.o uniqscan-splicetrie_build.o uniqscan-splicetrie.o uniqscan-splice.o uniqscan-indel.o uniqscan-bitpack64-access.o uniqscan-sarray-read.o uniqscan-stage1hr.o uniqscan-resulthr.o uniqscan-datadir.o uniqscan-getopt.o uniqscan-getopt1.o uniqscan-uniqscan.o -lz -lbz2 -lm libtool: link: gcc -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -o uniqscan uniqscan-except.o uniqscan-assert.o uniqscan-mem.o uniqscan-intlist.o uniqscan-list.o uniqscan-littleendian.o uniqscan-bigendian.o uniqscan-univinterval.o uniqscan-interval.o uniqscan-uintlist.o uniqscan-stopwatch.o uniqscan-access.o uniqscan-iit-read-univ.o uniqscan-iit-read.o uniqscan-md5.o uniqscan-bzip2.o uniqscan-sequence.o uniqscan-reader.o uniqscan-genomicpos.o uniqscan-compress.o uniqscan-genome.o uniqscan-genome_hr.o uniqscan-genome_sites.o uniqscan-bitpack64-read.o uniqscan-indexdb.o uniqscan-indexdb_hr.o uniqscan-oligo.o uniqscan-chrom.o uniqscan-segmentpos.o uniqscan-chrnum.o uniqscan-maxent_hr.o uniqscan-mapq.o uniqscan-shortread.o uniqscan-substring.o uniqscan-stage3hr.o uniqscan-spanningelt.o uniqscan-cmet.o uniqscan-atoi.o uniqscan-maxent.o uniqscan-pair.o uniqscan-pairpool.o uniqscan-diag.o uniqscan-diagpool.o uniqscan-orderstat.o uniqscan-oligoindex_hr.o uniqscan-cellpool.o uniqscan-stage2.o uniqscan-intron.o uniqscan-boyer-moore.o uniqscan-changepoint.o uniqscan-pbinom.o uniqscan-dynprog.o uniqscan-translation.o uniqscan-doublelist.o uniqscan-smooth.o uniqscan-chimera.o uniqscan-stage3.o uniqscan-splicestringpool.o uniqscan-splicetrie_build.o uniqscan-splicetrie.o uniqscan-splice.o uniqscan-indel.o uniqscan-bitpack64-access.o uniqscan-sarray-read.o uniqscan-stage1hr.o uniqscan-resulthr.o uniqscan-datadir.o uniqscan-getopt.o uniqscan-getopt1.o uniqscan-uniqscan.o -lz -lbz2 -lm gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-except.o -MD -MP -MF .deps/uniqscanl-except.Tpo -c -o uniqscanl-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/uniqscanl-except.Tpo .deps/uniqscanl-except.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-assert.o -MD -MP -MF .deps/uniqscanl-assert.Tpo -c -o uniqscanl-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/uniqscanl-assert.Tpo .deps/uniqscanl-assert.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-mem.o -MD -MP -MF .deps/uniqscanl-mem.Tpo -c -o uniqscanl-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/uniqscanl-mem.Tpo .deps/uniqscanl-mem.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-intlist.o -MD -MP -MF .deps/uniqscanl-intlist.Tpo -c -o uniqscanl-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/uniqscanl-intlist.Tpo .deps/uniqscanl-intlist.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-list.o -MD -MP -MF .deps/uniqscanl-list.Tpo -c -o uniqscanl-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/uniqscanl-list.Tpo .deps/uniqscanl-list.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-littleendian.o -MD -MP -MF .deps/uniqscanl-littleendian.Tpo -c -o uniqscanl-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c mv -f .deps/uniqscanl-littleendian.Tpo .deps/uniqscanl-littleendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-bigendian.o -MD -MP -MF .deps/uniqscanl-bigendian.Tpo -c -o uniqscanl-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c mv -f .deps/uniqscanl-bigendian.Tpo .deps/uniqscanl-bigendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-univinterval.o -MD -MP -MF .deps/uniqscanl-univinterval.Tpo -c -o uniqscanl-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~ %llu univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~~ %llu 2 warnings generated. mv -f .deps/uniqscanl-univinterval.Tpo .deps/uniqscanl-univinterval.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-interval.o -MD -MP -MF .deps/uniqscanl-interval.Tpo -c -o uniqscanl-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/uniqscanl-interval.Tpo .deps/uniqscanl-interval.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-uintlist.o -MD -MP -MF .deps/uniqscanl-uintlist.Tpo -c -o uniqscanl-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/uniqscanl-uintlist.Tpo .deps/uniqscanl-uintlist.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-uint8list.o -MD -MP -MF .deps/uniqscanl-uint8list.Tpo -c -o uniqscanl-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c uint8list.c:202:28: warning: format specifies type 'unsigned int' but the argument has type 'UINT8' (aka 'unsigned long long') [-Wformat] sprintf(Buffer,"%u,",Uint8list_head(p)); ~~ ^~~~~~~~~~~~~~~~~ %llu /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^~~~~~~~~~~ uint8list.c:205:25: warning: format specifies type 'unsigned int' but the argument has type 'UINT8' (aka 'unsigned long long') [-Wformat] sprintf(Buffer,"%u",Uint8list_head(p)); ~~ ^~~~~~~~~~~~~~~~~ %llu /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^~~~~~~~~~~ uint8list.c:211:28: warning: format specifies type 'unsigned int' but the argument has type 'UINT8' (aka 'unsigned long long') [-Wformat] sprintf(Buffer,"%u,",Uint8list_head(p)); ~~ ^~~~~~~~~~~~~~~~~ %llu /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^~~~~~~~~~~ uint8list.c:214:25: warning: format specifies type 'unsigned int' but the argument has type 'UINT8' (aka 'unsigned long long') [-Wformat] sprintf(Buffer,"%u",Uint8list_head(p)); ~~ ^~~~~~~~~~~~~~~~~ %llu /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^~~~~~~~~~~ 4 warnings generated. mv -f .deps/uniqscanl-uint8list.Tpo .deps/uniqscanl-uint8list.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-stopwatch.o -MD -MP -MF .deps/uniqscanl-stopwatch.Tpo -c -o uniqscanl-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/uniqscanl-stopwatch.Tpo .deps/uniqscanl-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-access.o -MD -MP -MF .deps/uniqscanl-access.Tpo -c -o uniqscanl-access.o `test -f 'access.c' || echo './'`access.c access.c:358:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] length,length,errno,strerror(errno)); ^~~~~~ access.c:358:15: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] length,length,errno,strerror(errno)); ^~~~~~ access.c:423:11: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] fd,offset,length,errno,strerror(errno)); ^~~~~~ access.c:493:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] *len,length,errno,strerror(errno)); ^~~~~~ access.c:556:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] offset,length,errno,strerror(errno)); ^~~~~~ access.c:641:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] *len,length,errno,strerror(errno)); ^~~~~~ 6 warnings generated. mv -f .deps/uniqscanl-access.Tpo .deps/uniqscanl-access.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-iit-read-univ.o -MD -MP -MF .deps/uniqscanl-iit-read-univ.Tpo -c -o uniqscanl-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~~~ %llu iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~ %llu iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~~~ %llu iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~ %llu iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %llu iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~ %llu iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %llu 10 warnings generated. mv -f .deps/uniqscanl-iit-read-univ.Tpo .deps/uniqscanl-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-iit-read.o -MD -MP -MF .deps/uniqscanl-iit-read.Tpo -c -o uniqscanl-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c mv -f .deps/uniqscanl-iit-read.Tpo .deps/uniqscanl-iit-read.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-md5.o -MD -MP -MF .deps/uniqscanl-md5.Tpo -c -o uniqscanl-md5.o `test -f 'md5.c' || echo './'`md5.c mv -f .deps/uniqscanl-md5.Tpo .deps/uniqscanl-md5.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-bzip2.o -MD -MP -MF .deps/uniqscanl-bzip2.Tpo -c -o uniqscanl-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c mv -f .deps/uniqscanl-bzip2.Tpo .deps/uniqscanl-bzip2.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-sequence.o -MD -MP -MF .deps/uniqscanl-sequence.Tpo -c -o uniqscanl-sequence.o `test -f 'sequence.c' || echo './'`sequence.c mv -f .deps/uniqscanl-sequence.Tpo .deps/uniqscanl-sequence.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-reader.o -MD -MP -MF .deps/uniqscanl-reader.Tpo -c -o uniqscanl-reader.o `test -f 'reader.c' || echo './'`reader.c mv -f .deps/uniqscanl-reader.Tpo .deps/uniqscanl-reader.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-genomicpos.o -MD -MP -MF .deps/uniqscanl-genomicpos.Tpo -c -o uniqscanl-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/uniqscanl-genomicpos.Tpo .deps/uniqscanl-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-compress.o -MD -MP -MF .deps/uniqscanl-compress.Tpo -c -o uniqscanl-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/uniqscanl-compress.Tpo .deps/uniqscanl-compress.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-genome.o -MD -MP -MF .deps/uniqscanl-genome.Tpo -c -o uniqscanl-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c:10292:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu genome.c:10292:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu genome.c:10392:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu genome.c:10392:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu 4 warnings generated. mv -f .deps/uniqscanl-genome.Tpo .deps/uniqscanl-genome.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-genome_hr.o -MD -MP -MF .deps/uniqscanl-genome_hr.Tpo -c -o uniqscanl-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c mv -f .deps/uniqscanl-genome_hr.Tpo .deps/uniqscanl-genome_hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-genome_sites.o -MD -MP -MF .deps/uniqscanl-genome_sites.Tpo -c -o uniqscanl-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c genome_sites.c:24729:17: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%u\t",startblock/3*32U); ~~ ^~~~~~~~~~~~~~~~ %llu genome_sites.c:24744:19: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%u\t",ptr/3*32U); ~~ ^~~~~~~~~ %llu genome_sites.c:24751:17: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%u\t",(endblock+3)/3*32U); ~~ ^~~~~~~~~~~~~~~~~~ %llu 3 warnings generated. mv -f .deps/uniqscanl-genome_sites.Tpo .deps/uniqscanl-genome_sites.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-bitpack64-read.o -MD -MP -MF .deps/uniqscanl-bitpack64-read.Tpo -c -o uniqscanl-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c mv -f .deps/uniqscanl-bitpack64-read.Tpo .deps/uniqscanl-bitpack64-read.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-indexdb.o -MD -MP -MF .deps/uniqscanl-indexdb.Tpo -c -o uniqscanl-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c:1363:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1483:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1653:63: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1792:6: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] ptr,sizeof(Univcoord_T),offset); ^~~ indexdb.c:1792:30: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] ptr,sizeof(Univcoord_T),offset); ^~~~~~ indexdb.c:1934:76: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, ~~~ ^~~~~~~~~~~~~~ %llu indexdb.c:2026:76: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, ~~~ ^~~~~~~~~~~~~~ %llu 7 warnings generated. mv -f .deps/uniqscanl-indexdb.Tpo .deps/uniqscanl-indexdb.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-indexdb_hr.o -MD -MP -MF .deps/uniqscanl-indexdb_hr.Tpo -c -o uniqscanl-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c indexdb_hr.c:1008:43: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" compound%d.%d:%u+%d\n",i,j,compoundpos->positions[i][j],diagterm); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ %llu indexdb_hr.c:1232:45: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("#%d--%d:%u ",i,batch->nentries,batch->position); ~~ ^~~~~~~~~~~~~~~ %llu 2 warnings generated. mv -f .deps/uniqscanl-indexdb_hr.Tpo .deps/uniqscanl-indexdb_hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-oligo.o -MD -MP -MF .deps/uniqscanl-oligo.Tpo -c -o uniqscanl-oligo.o `test -f 'oligo.c' || echo './'`oligo.c mv -f .deps/uniqscanl-oligo.Tpo .deps/uniqscanl-oligo.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-chrom.o -MD -MP -MF .deps/uniqscanl-chrom.Tpo -c -o uniqscanl-chrom.o `test -f 'chrom.c' || echo './'`chrom.c chrom.c:116:15: warning: comparing a pointer to a null character constant; did you mean to compare to NULL? [-Wpointer-compare] while (p != '\0' && *p >= '0' && *p <= '9') { ^~~~ (void *)0 1 warning generated. mv -f .deps/uniqscanl-chrom.Tpo .deps/uniqscanl-chrom.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-segmentpos.o -MD -MP -MF .deps/uniqscanl-segmentpos.Tpo -c -o uniqscanl-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c segmentpos.c:90:41: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"%s\t%u\t%s\t%u\t%u\n",acc,chroffset+this->chrpos1,Chrom_string(this->chrom),this->chrpos1,this->length); ~~ ^~~~~~~~~~~~~~~~~~~~~~~ %llu 1 warning generated. mv -f .deps/uniqscanl-segmentpos.Tpo .deps/uniqscanl-segmentpos.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-chrnum.o -MD -MP -MF .deps/uniqscanl-chrnum.Tpo -c -o uniqscanl-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c mv -f .deps/uniqscanl-chrnum.Tpo .deps/uniqscanl-chrnum.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-maxent_hr.o -MD -MP -MF .deps/uniqscanl-maxent_hr.Tpo -c -o uniqscanl-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c mv -f .deps/uniqscanl-maxent_hr.Tpo .deps/uniqscanl-maxent_hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-mapq.o -MD -MP -MF .deps/uniqscanl-mapq.Tpo -c -o uniqscanl-mapq.o `test -f 'mapq.c' || echo './'`mapq.c mv -f .deps/uniqscanl-mapq.Tpo .deps/uniqscanl-mapq.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-shortread.o -MD -MP -MF .deps/uniqscanl-shortread.Tpo -c -o uniqscanl-shortread.o `test -f 'shortread.c' || echo './'`shortread.c mv -f .deps/uniqscanl-shortread.Tpo .deps/uniqscanl-shortread.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-substring.o -MD -MP -MF .deps/uniqscanl-substring.Tpo -c -o uniqscanl-substring.o `test -f 'substring.c' || echo './'`substring.c substring.c:1005:33: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("#%d:%u..%u ",chrnum,this->alignstart,this->alignend); ~~ ^~~~~~~~~~~~~~~~ %llu substring.c:1005:50: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("#%d:%u..%u ",chrnum,this->alignstart,this->alignend); ~~ ^~~~~~~~~~~~~~ %llu substring.c:3536:35: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"+%s:%u..%u",chr,substring->alignstart_trim - substring->chroffset + 1U, ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %llu substring.c:3537:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] substring->alignend_trim - substring->chroffset); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ substring.c:3539:35: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"-%s:%u..%u",chr,substring->alignend_trim - substring->chroffset, ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %llu substring.c:3540:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] substring->alignstart_trim - substring->chroffset + 1U); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ substring.c:3544:35: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"-%s:%u..%u",chr,substring->alignstart_trim - substring->chroffset, ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %llu substring.c:3545:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] substring->alignend_trim - substring->chroffset + 1U); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ substring.c:3547:35: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"+%s:%u..%u",chr,substring->alignend_trim - substring->chroffset + 1U, ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %llu substring.c:3548:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] substring->alignstart_trim - substring->chroffset); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 10 warnings generated. mv -f .deps/uniqscanl-substring.Tpo .deps/uniqscanl-substring.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-stage3hr.o -MD -MP -MF .deps/uniqscanl-stage3hr.Tpo -c -o uniqscanl-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c mv -f .deps/uniqscanl-stage3hr.Tpo .deps/uniqscanl-stage3hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-spanningelt.o -MD -MP -MF .deps/uniqscanl-spanningelt.Tpo -c -o uniqscanl-spanningelt.o `test -f 'spanningelt.c' || echo './'`spanningelt.c mv -f .deps/uniqscanl-spanningelt.Tpo .deps/uniqscanl-spanningelt.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-cmet.o -MD -MP -MF .deps/uniqscanl-cmet.Tpo -c -o uniqscanl-cmet.o `test -f 'cmet.c' || echo './'`cmet.c mv -f .deps/uniqscanl-cmet.Tpo .deps/uniqscanl-cmet.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-atoi.o -MD -MP -MF .deps/uniqscanl-atoi.Tpo -c -o uniqscanl-atoi.o `test -f 'atoi.c' || echo './'`atoi.c mv -f .deps/uniqscanl-atoi.Tpo .deps/uniqscanl-atoi.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-maxent.o -MD -MP -MF .deps/uniqscanl-maxent.Tpo -c -o uniqscanl-maxent.o `test -f 'maxent.c' || echo './'`maxent.c mv -f .deps/uniqscanl-maxent.Tpo .deps/uniqscanl-maxent.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-pair.o -MD -MP -MF .deps/uniqscanl-pair.Tpo -c -o uniqscanl-pair.o `test -f 'pair.c' || echo './'`pair.c pair.c:546:25: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP); ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %llu /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^~~~~~~~~~~ pair.c:573:25: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP); ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %llu /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^~~~~~~~~~~ pair.c:600:25: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] sprintf(Buffer,"%u",chroffset + start->genomepos + ONEBASEDP); ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %llu /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^~~~~~~~~~~ pair.c:607:25: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] sprintf(Buffer,"%u",chroffset + end->genomepos + ONEBASEDP); ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %llu /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^~~~~~~~~~~ pair.c:1273:3: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] chroffset + this->genomepos + ONEBASEDP, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:1278:3: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] chroffset + this->genomepos + ONEBASEDP, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:1790:25: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~ %llu pair.c:1790:52: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~ %llu pair.c:1799:27: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~ %llu pair.c:1799:54: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~ %llu pair.c:1913:26: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~ %llu pair.c:1913:53: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~ %llu pair.c:1922:28: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~ %llu pair.c:1922:55: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~ %llu pair.c:2419:24: warning: taking the absolute value of unsigned type 'Chrpos_T' (aka 'unsigned int') has no effect [-Wabsolute-value] sprintf(token,"N%u",abs(intron_end - intron_start) + 1); ^ pair.c:2419:24: note: remove the call to 'abs' since unsigned values cannot be negative sprintf(token,"N%u",abs(intron_end - intron_start) + 1); ^~~ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ pair.c:4651:17: warning: taking the absolute value of unsigned type 'Chrpos_T' (aka 'unsigned int') has no effect [-Wabsolute-value] genome_gap = abs(intron_end - intron_start) + 1; ^ pair.c:4651:17: note: remove the call to 'abs' since unsigned values cannot be negative genome_gap = abs(intron_end - intron_start) + 1; ^~~ pair.c:6986:24: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp," %u%s%u",position1 + ONEBASEDP,"..",position2 + ONEBASEDP); ~~ ^~~~~~~~~~~~~~~~~~~~~ %llu pair.c:6986:51: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(fp," %u%s%u",position1 + ONEBASEDP,"..",position2 + ONEBASEDP); ~~ ^~~~~~~~~~~~~~~~~~~~~ %llu 18 warnings generated. mv -f .deps/uniqscanl-pair.Tpo .deps/uniqscanl-pair.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-pairpool.o -MD -MP -MF .deps/uniqscanl-pairpool.Tpo -c -o uniqscanl-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c mv -f .deps/uniqscanl-pairpool.Tpo .deps/uniqscanl-pairpool.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-diag.o -MD -MP -MF .deps/uniqscanl-diag.Tpo -c -o uniqscanl-diag.o `test -f 'diag.c' || echo './'`diag.c mv -f .deps/uniqscanl-diag.Tpo .deps/uniqscanl-diag.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-diagpool.o -MD -MP -MF .deps/uniqscanl-diagpool.Tpo -c -o uniqscanl-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c mv -f .deps/uniqscanl-diagpool.Tpo .deps/uniqscanl-diagpool.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-orderstat.o -MD -MP -MF .deps/uniqscanl-orderstat.Tpo -c -o uniqscanl-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c mv -f .deps/uniqscanl-orderstat.Tpo .deps/uniqscanl-orderstat.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-oligoindex_hr.o -MD -MP -MF .deps/uniqscanl-oligoindex_hr.Tpo -c -o uniqscanl-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c mv -f .deps/uniqscanl-oligoindex_hr.Tpo .deps/uniqscanl-oligoindex_hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-cellpool.o -MD -MP -MF .deps/uniqscanl-cellpool.Tpo -c -o uniqscanl-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c mv -f .deps/uniqscanl-cellpool.Tpo .deps/uniqscanl-cellpool.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-stage2.o -MD -MP -MF .deps/uniqscanl-stage2.Tpo -c -o uniqscanl-stage2.o `test -f 'stage2.c' || echo './'`stage2.c stage2.c:1329:19: warning: taking the absolute value of unsigned type 'Chrpos_T' (aka 'unsigned int') has no effect [-Wabsolute-value] diffdistance = abs(gendistance - querydistance); ^ stage2.c:1329:19: note: remove the call to 'abs' since unsigned values cannot be negative diffdistance = abs(gendistance - querydistance); ^~~ stage2.c:1812:19: warning: taking the absolute value of unsigned type 'Chrpos_T' (aka 'unsigned int') has no effect [-Wabsolute-value] diffdistance = abs(gendistance - querydistance); ^ stage2.c:1812:19: note: remove the call to 'abs' since unsigned values cannot be negative diffdistance = abs(gendistance - querydistance); ^~~ 2 warnings generated. mv -f .deps/uniqscanl-stage2.Tpo .deps/uniqscanl-stage2.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-intron.o -MD -MP -MF .deps/uniqscanl-intron.Tpo -c -o uniqscanl-intron.o `test -f 'intron.c' || echo './'`intron.c mv -f .deps/uniqscanl-intron.Tpo .deps/uniqscanl-intron.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-boyer-moore.o -MD -MP -MF .deps/uniqscanl-boyer-moore.Tpo -c -o uniqscanl-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c mv -f .deps/uniqscanl-boyer-moore.Tpo .deps/uniqscanl-boyer-moore.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-changepoint.o -MD -MP -MF .deps/uniqscanl-changepoint.Tpo -c -o uniqscanl-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c mv -f .deps/uniqscanl-changepoint.Tpo .deps/uniqscanl-changepoint.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-pbinom.o -MD -MP -MF .deps/uniqscanl-pbinom.Tpo -c -o uniqscanl-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c mv -f .deps/uniqscanl-pbinom.Tpo .deps/uniqscanl-pbinom.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-dynprog.o -MD -MP -MF .deps/uniqscanl-dynprog.Tpo -c -o uniqscanl-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c mv -f .deps/uniqscanl-dynprog.Tpo .deps/uniqscanl-dynprog.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-translation.o -MD -MP -MF .deps/uniqscanl-translation.Tpo -c -o uniqscanl-translation.o `test -f 'translation.c' || echo './'`translation.c mv -f .deps/uniqscanl-translation.Tpo .deps/uniqscanl-translation.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-doublelist.o -MD -MP -MF .deps/uniqscanl-doublelist.Tpo -c -o uniqscanl-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c mv -f .deps/uniqscanl-doublelist.Tpo .deps/uniqscanl-doublelist.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-smooth.o -MD -MP -MF .deps/uniqscanl-smooth.Tpo -c -o uniqscanl-smooth.o `test -f 'smooth.c' || echo './'`smooth.c mv -f .deps/uniqscanl-smooth.Tpo .deps/uniqscanl-smooth.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-chimera.o -MD -MP -MF .deps/uniqscanl-chimera.Tpo -c -o uniqscanl-chimera.o `test -f 'chimera.c' || echo './'`chimera.c mv -f .deps/uniqscanl-chimera.Tpo .deps/uniqscanl-chimera.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-stage3.o -MD -MP -MF .deps/uniqscanl-stage3.Tpo -c -o uniqscanl-stage3.o `test -f 'stage3.c' || echo './'`stage3.c mv -f .deps/uniqscanl-stage3.Tpo .deps/uniqscanl-stage3.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-splicestringpool.o -MD -MP -MF .deps/uniqscanl-splicestringpool.Tpo -c -o uniqscanl-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c mv -f .deps/uniqscanl-splicestringpool.Tpo .deps/uniqscanl-splicestringpool.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-splicetrie_build.o -MD -MP -MF .deps/uniqscanl-splicetrie_build.Tpo -c -o uniqscanl-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c splicetrie_build.c:132:31: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%d %u",(int) leaf,position); ~~ ^~~~~~~~ %llu splicetrie_build.c:146:33: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%d %u",(int) leaf,position); ~~ ^~~~~~~~ %llu 2 warnings generated. mv -f .deps/uniqscanl-splicetrie_build.Tpo .deps/uniqscanl-splicetrie_build.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-splicetrie.o -MD -MP -MF .deps/uniqscanl-splicetrie.Tpo -c -o uniqscanl-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c mv -f .deps/uniqscanl-splicetrie.Tpo .deps/uniqscanl-splicetrie.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-splice.o -MD -MP -MF .deps/uniqscanl-splice.Tpo -c -o uniqscanl-splice.o `test -f 'splice.c' || echo './'`splice.c mv -f .deps/uniqscanl-splice.Tpo .deps/uniqscanl-splice.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-indel.o -MD -MP -MF .deps/uniqscanl-indel.Tpo -c -o uniqscanl-indel.o `test -f 'indel.c' || echo './'`indel.c mv -f .deps/uniqscanl-indel.Tpo .deps/uniqscanl-indel.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-bitpack64-access.o -MD -MP -MF .deps/uniqscanl-bitpack64-access.Tpo -c -o uniqscanl-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c mv -f .deps/uniqscanl-bitpack64-access.Tpo .deps/uniqscanl-bitpack64-access.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-sarray-read.o -MD -MP -MF .deps/uniqscanl-sarray-read.Tpo -c -o uniqscanl-sarray-read.o `test -f 'sarray-read.c' || echo './'`sarray-read.c sarray-read.c:302:15: warning: incompatible pointer types assigning to 'UINT4 *' (aka 'unsigned int *') from 'Univcoord_T *' (aka 'unsigned long long *') [-Wincompatible-pointer-types] new->lcpcomp = (Univcoord_T *) Access_allocated(&new->lcpcomp_len,&seconds2,filename,sizeof(Univcoord_T)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sarray-read.c:368:15: warning: incompatible pointer types assigning to 'UINT4 *' (aka 'unsigned int *') from 'Univcoord_T *' (aka 'unsigned long long *') [-Wincompatible-pointer-types] new->lcpcomp = (Univcoord_T *) Access_mmap_and_preload(&new->lcpcomp_fd,&new->lcpcomp_len,&npages,&seconds2, ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sarray-read.c:434:15: warning: incompatible pointer types assigning to 'UINT4 *' (aka 'unsigned int *') from 'Univcoord_T *' (aka 'unsigned long long *') [-Wincompatible-pointer-types] new->lcpcomp = (Univcoord_T *) Access_mmap(&new->lcpcomp_fd,&new->lcpcomp_len,filename,sizeof(Univcoord_T), ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sarray-read.c:526:15: warning: incompatible pointer types assigning to 'UINT4 *' (aka 'unsigned int *') from 'Univcoord_T *' (aka 'unsigned long long *') [-Wincompatible-pointer-types] new->lcpcomp = (Univcoord_T *) Access_allocated(&new->lcpcomp_len,&seconds2,filename,sizeof(Univcoord_T)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sarray-read.c:653:15: warning: incompatible pointer types assigning to 'UINT4 *' (aka 'unsigned int *') from 'Univcoord_T *' (aka 'unsigned long long *') [-Wincompatible-pointer-types] new->lcpcomp = (Univcoord_T *) Access_mmap(&new->lcpcomp_fd,&new->lcpcomp_len, ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sarray-read.c:1667:53: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%d..%d:%u\t",elt->querystart,elt->queryend,elt->positions[k]); ~~ ^~~~~~~~~~~~~~~~~ %llu sarray-read.c:1682:56: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%d..%d:%u\n",elt->querystart,elt->queryend,elt->positions[k]); ~~ ^~~~~~~~~~~~~~~~~ %llu sarray-read.c:2170:11: warning: incompatible pointer types assigning to 'Univcoord_T *' (aka 'unsigned long long *') from 'UINT4 *' (aka 'unsigned int *') [-Wincompatible-pointer-types] array = Uintlist_to_array(&n,difflist); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sarray-read.c:2442:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); ^~~~~~~~~ ./uint8list.h:11:19: note: passing argument to parameter 'list' here Uint8list_push (T list, UINT8 x); ^ sarray-read.c:2442:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sarray-read.c:2456:34: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] /*ambcoords_donor*/NULL,ambcoords, ^~~~~~~~~ ./stage3hr.h:296:50: note: passing argument to parameter 'ambcoords_acceptor' here Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, ^ sarray-read.c:2499:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); ^~~~~~~~~ ./uint8list.h:11:19: note: passing argument to parameter 'list' here Uint8list_push (T list, UINT8 x); ^ sarray-read.c:2499:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sarray-read.c:2513:10: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords,/*ambcoords_acceptor*/NULL, ^~~~~~~~~ ./stage3hr.h:296:21: note: passing argument to parameter 'ambcoords_donor' here Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, ^ sarray-read.c:2643:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); ^~~~~~~~~ ./uint8list.h:11:19: note: passing argument to parameter 'list' here Uint8list_push (T list, UINT8 x); ^ sarray-read.c:2643:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sarray-read.c:2656:36: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] /*ambcoords_donor*/NULL,ambcoords, ^~~~~~~~~ ./stage3hr.h:296:50: note: passing argument to parameter 'ambcoords_acceptor' here Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, ^ sarray-read.c:2699:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); ^~~~~~~~~ ./uint8list.h:11:19: note: passing argument to parameter 'list' here Uint8list_push (T list, UINT8 x); ^ sarray-read.c:2699:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sarray-read.c:2712:12: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords,/*ambcoords_acceptor*/NULL, ^~~~~~~~~ ./stage3hr.h:296:21: note: passing argument to parameter 'ambcoords_donor' here Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, ^ sarray-read.c:2752:11: warning: incompatible pointer types assigning to 'Univcoord_T *' (aka 'unsigned long long *') from 'UINT4 *' (aka 'unsigned int *') [-Wincompatible-pointer-types] array = Uintlist_to_array(&n,difflist); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sarray-read.c:3024:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); ^~~~~~~~~ ./uint8list.h:11:19: note: passing argument to parameter 'list' here Uint8list_push (T list, UINT8 x); ^ sarray-read.c:3024:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sarray-read.c:3038:34: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] /*ambcoords_donor*/NULL,ambcoords, ^~~~~~~~~ ./stage3hr.h:296:50: note: passing argument to parameter 'ambcoords_acceptor' here Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, ^ sarray-read.c:3082:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); ^~~~~~~~~ ./uint8list.h:11:19: note: passing argument to parameter 'list' here Uint8list_push (T list, UINT8 x); ^ sarray-read.c:3082:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sarray-read.c:3096:10: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords,/*ambcoords_acceptor*/NULL, ^~~~~~~~~ ./stage3hr.h:296:21: note: passing argument to parameter 'ambcoords_donor' here Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, ^ sarray-read.c:3217:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); ^~~~~~~~~ ./uint8list.h:11:19: note: passing argument to parameter 'list' here Uint8list_push (T list, UINT8 x); ^ sarray-read.c:3217:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sarray-read.c:3231:34: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] /*ambcoords_donor*/NULL,ambcoords, ^~~~~~~~~ ./stage3hr.h:296:50: note: passing argument to parameter 'ambcoords_acceptor' here Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, ^ sarray-read.c:3274:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); ^~~~~~~~~ ./uint8list.h:11:19: note: passing argument to parameter 'list' here Uint8list_push (T list, UINT8 x); ^ sarray-read.c:3274:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sarray-read.c:3288:10: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types] ambcoords,/*ambcoords_acceptor*/NULL, ^~~~~~~~~ ./stage3hr.h:296:21: note: passing argument to parameter 'ambcoords_donor' here Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, ^ 33 warnings generated. mv -f .deps/uniqscanl-sarray-read.Tpo .deps/uniqscanl-sarray-read.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-stage1hr.o -MD -MP -MF .deps/uniqscanl-stage1hr.Tpo -c -o uniqscanl-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c stage1hr.c:6630:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stage1hr.c:6630:40: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stage1hr.c:6630:76: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stage1hr.c:6769:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Substring_genomicstart(donor),Substring_genomicend(donor),Substring_plusp(donor), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stage1hr.c:6769:37: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Substring_genomicstart(donor),Substring_genomicend(donor),Substring_plusp(donor), ^~~~~~~~~~~~~~~~~~~~~~~~~~~ stage1hr.c:6770:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Substring_genomicstart(acceptor),Substring_genomicend(acceptor),Substring_plusp(acceptor), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stage1hr.c:6770:40: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Substring_genomicstart(acceptor),Substring_genomicend(acceptor),Substring_plusp(acceptor), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stage1hr.c:6771:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] segmenti->diagonal - querylength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stage1hr.c:7146:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stage1hr.c:7146:40: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stage1hr.c:7146:76: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stage1hr.c:7285:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stage1hr.c:7285:40: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stage1hr.c:7285:76: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 14 warnings generated. mv -f .deps/uniqscanl-stage1hr.Tpo .deps/uniqscanl-stage1hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-resulthr.o -MD -MP -MF .deps/uniqscanl-resulthr.Tpo -c -o uniqscanl-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c mv -f .deps/uniqscanl-resulthr.Tpo .deps/uniqscanl-resulthr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-datadir.o -MD -MP -MF .deps/uniqscanl-datadir.Tpo -c -o uniqscanl-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/uniqscanl-datadir.Tpo .deps/uniqscanl-datadir.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-getopt.o -MD -MP -MF .deps/uniqscanl-getopt.Tpo -c -o uniqscanl-getopt.o `test -f 'getopt.c' || echo './'`getopt.c getopt.c:208:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] my_index (str, chr) ^ getopt.c:291:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] exchange (argv) ^ getopt.c:376:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] _getopt_initialize (argc, argv, optstring) ^ getopt.c:389:28: warning: passing arguments to 'getenv' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] posixly_correct = getenv ("POSIXLY_CORRECT"); ^ getopt.c:498:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] _getopt_internal (argc, argv, optstring, longopts, longind, long_only) ^ getopt.c:1179:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt (argc, argv, optstring) ^ In file included from getopt.c:97: ./getopt.h:147:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent definition [-Wdeprecated-non-prototype] extern int getopt (); ^ 7 warnings generated. mv -f .deps/uniqscanl-getopt.Tpo .deps/uniqscanl-getopt.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-getopt1.o -MD -MP -MF .deps/uniqscanl-getopt1.Tpo -c -o uniqscanl-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c getopt1.c:71:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt_long (argc, argv, options, long_options, opt_index) ^ getopt1.c:87:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt_long_only (argc, argv, options, long_options, opt_index) ^ 2 warnings generated. mv -f .deps/uniqscanl-getopt1.Tpo .deps/uniqscanl-getopt1.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-uniqscan.o -MD -MP -MF .deps/uniqscanl-uniqscan.Tpo -c -o uniqscanl-uniqscan.o `test -f 'uniqscan.c' || echo './'`uniqscan.c In file included from uniqscan.c:55: ./getopt.h:147:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a previous declaration [-Wdeprecated-non-prototype] extern int getopt (); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/unistd.h:509:6: note: conflicting prototype is here int getopt(int, char * const [], const char *) __DARWIN_ALIAS(getopt); ^ 1 warning generated. mv -f .deps/uniqscanl-uniqscan.Tpo .deps/uniqscanl-uniqscan.Po /bin/sh ../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -o uniqscanl uniqscanl-except.o uniqscanl-assert.o uniqscanl-mem.o uniqscanl-intlist.o uniqscanl-list.o uniqscanl-littleendian.o uniqscanl-bigendian.o uniqscanl-univinterval.o uniqscanl-interval.o uniqscanl-uintlist.o uniqscanl-uint8list.o uniqscanl-stopwatch.o uniqscanl-access.o uniqscanl-iit-read-univ.o uniqscanl-iit-read.o uniqscanl-md5.o uniqscanl-bzip2.o uniqscanl-sequence.o uniqscanl-reader.o uniqscanl-genomicpos.o uniqscanl-compress.o uniqscanl-genome.o uniqscanl-genome_hr.o uniqscanl-genome_sites.o uniqscanl-bitpack64-read.o uniqscanl-indexdb.o uniqscanl-indexdb_hr.o uniqscanl-oligo.o uniqscanl-chrom.o uniqscanl-segmentpos.o uniqscanl-chrnum.o uniqscanl-maxent_hr.o uniqscanl-mapq.o uniqscanl-shortread.o uniqscanl-substring.o uniqscanl-stage3hr.o uniqscanl-spanningelt.o uniqscanl-cmet.o uniqscanl-atoi.o uniqscanl-maxent.o uniqscanl-pair.o uniqscanl-pairpool.o uniqscanl-diag.o uniqscanl-diagpool.o uniqscanl-orderstat.o uniqscanl-oligoindex_hr.o uniqscanl-cellpool.o uniqscanl-stage2.o uniqscanl-intron.o uniqscanl-boyer-moore.o uniqscanl-changepoint.o uniqscanl-pbinom.o uniqscanl-dynprog.o uniqscanl-translation.o uniqscanl-doublelist.o uniqscanl-smooth.o uniqscanl-chimera.o uniqscanl-stage3.o uniqscanl-splicestringpool.o uniqscanl-splicetrie_build.o uniqscanl-splicetrie.o uniqscanl-splice.o uniqscanl-indel.o uniqscanl-bitpack64-access.o uniqscanl-sarray-read.o uniqscanl-stage1hr.o uniqscanl-resulthr.o uniqscanl-datadir.o uniqscanl-getopt.o uniqscanl-getopt1.o uniqscanl-uniqscan.o -lz -lbz2 -lm libtool: link: gcc -D_THREAD_SAFE -DTARGET=\"arm-apple-darwin22.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -o uniqscanl uniqscanl-except.o uniqscanl-assert.o uniqscanl-mem.o uniqscanl-intlist.o uniqscanl-list.o uniqscanl-littleendian.o uniqscanl-bigendian.o uniqscanl-univinterval.o uniqscanl-interval.o uniqscanl-uintlist.o uniqscanl-uint8list.o uniqscanl-stopwatch.o uniqscanl-access.o uniqscanl-iit-read-univ.o uniqscanl-iit-read.o uniqscanl-md5.o uniqscanl-bzip2.o uniqscanl-sequence.o uniqscanl-reader.o uniqscanl-genomicpos.o uniqscanl-compress.o uniqscanl-genome.o uniqscanl-genome_hr.o uniqscanl-genome_sites.o uniqscanl-bitpack64-read.o uniqscanl-indexdb.o uniqscanl-indexdb_hr.o uniqscanl-oligo.o uniqscanl-chrom.o uniqscanl-segmentpos.o uniqscanl-chrnum.o uniqscanl-maxent_hr.o uniqscanl-mapq.o uniqscanl-shortread.o uniqscanl-substring.o uniqscanl-stage3hr.o uniqscanl-spanningelt.o uniqscanl-cmet.o uniqscanl-atoi.o uniqscanl-maxent.o uniqscanl-pair.o uniqscanl-pairpool.o uniqscanl-diag.o uniqscanl-diagpool.o uniqscanl-orderstat.o uniqscanl-oligoindex_hr.o uniqscanl-cellpool.o uniqscanl-stage2.o uniqscanl-intron.o uniqscanl-boyer-moore.o uniqscanl-changepoint.o uniqscanl-pbinom.o uniqscanl-dynprog.o uniqscanl-translation.o uniqscanl-doublelist.o uniqscanl-smooth.o uniqscanl-chimera.o uniqscanl-stage3.o uniqscanl-splicestringpool.o uniqscanl-splicetrie_build.o uniqscanl-splicetrie.o uniqscanl-splice.o uniqscanl-indel.o uniqscanl-bitpack64-access.o uniqscanl-sarray-read.o uniqscanl-stage1hr.o uniqscanl-resulthr.o uniqscanl-datadir.o uniqscanl-getopt.o uniqscanl-getopt1.o uniqscanl-uniqscan.o -lz -lbz2 -lm gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-except.o -MD -MP -MF .deps/snpindex-except.Tpo -c -o snpindex-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/snpindex-except.Tpo .deps/snpindex-except.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-assert.o -MD -MP -MF .deps/snpindex-assert.Tpo -c -o snpindex-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/snpindex-assert.Tpo .deps/snpindex-assert.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-mem.o -MD -MP -MF .deps/snpindex-mem.Tpo -c -o snpindex-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/snpindex-mem.Tpo .deps/snpindex-mem.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-intlist.o -MD -MP -MF .deps/snpindex-intlist.Tpo -c -o snpindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/snpindex-intlist.Tpo .deps/snpindex-intlist.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-list.o -MD -MP -MF .deps/snpindex-list.Tpo -c -o snpindex-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/snpindex-list.Tpo .deps/snpindex-list.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-littleendian.o -MD -MP -MF .deps/snpindex-littleendian.Tpo -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c mv -f .deps/snpindex-littleendian.Tpo .deps/snpindex-littleendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-bigendian.o -MD -MP -MF .deps/snpindex-bigendian.Tpo -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c mv -f .deps/snpindex-bigendian.Tpo .deps/snpindex-bigendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-univinterval.o -MD -MP -MF .deps/snpindex-univinterval.Tpo -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~ %llu univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~~ %llu 2 warnings generated. mv -f .deps/snpindex-univinterval.Tpo .deps/snpindex-univinterval.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-interval.o -MD -MP -MF .deps/snpindex-interval.Tpo -c -o snpindex-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/snpindex-interval.Tpo .deps/snpindex-interval.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-uintlist.o -MD -MP -MF .deps/snpindex-uintlist.Tpo -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/snpindex-uintlist.Tpo .deps/snpindex-uintlist.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-stopwatch.o -MD -MP -MF .deps/snpindex-stopwatch.Tpo -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/snpindex-stopwatch.Tpo .deps/snpindex-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-access.o -MD -MP -MF .deps/snpindex-access.Tpo -c -o snpindex-access.o `test -f 'access.c' || echo './'`access.c access.c:358:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] length,length,errno,strerror(errno)); ^~~~~~ access.c:358:15: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] length,length,errno,strerror(errno)); ^~~~~~ access.c:423:11: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] fd,offset,length,errno,strerror(errno)); ^~~~~~ access.c:493:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] *len,length,errno,strerror(errno)); ^~~~~~ access.c:556:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] offset,length,errno,strerror(errno)); ^~~~~~ access.c:641:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] *len,length,errno,strerror(errno)); ^~~~~~ 6 warnings generated. mv -f .deps/snpindex-access.Tpo .deps/snpindex-access.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-iit-read-univ.o -MD -MP -MF .deps/snpindex-iit-read-univ.Tpo -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~~~ %llu iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~ %llu iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~~~ %llu iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~ %llu iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %llu iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~ %llu iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %llu 10 warnings generated. mv -f .deps/snpindex-iit-read-univ.Tpo .deps/snpindex-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-iit-read.o -MD -MP -MF .deps/snpindex-iit-read.Tpo -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c mv -f .deps/snpindex-iit-read.Tpo .deps/snpindex-iit-read.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-genomicpos.o -MD -MP -MF .deps/snpindex-genomicpos.Tpo -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/snpindex-genomicpos.Tpo .deps/snpindex-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-compress.o -MD -MP -MF .deps/snpindex-compress.Tpo -c -o snpindex-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/snpindex-compress.Tpo .deps/snpindex-compress.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-compress-write.o -MD -MP -MF .deps/snpindex-compress-write.Tpo -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c compress-write.c:73:80: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i); ~~~ ^~~~~~~~~~ %llu compress-write.c:252:13: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Buffer[i],position+i); ^~~~~~~~~~ compress-write.c:300:13: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Buffer[i],position+i); ^~~~~~~~~~ 3 warnings generated. mv -f .deps/snpindex-compress-write.Tpo .deps/snpindex-compress-write.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-genome_hr.o -MD -MP -MF .deps/snpindex-genome_hr.Tpo -c -o snpindex-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c mv -f .deps/snpindex-genome_hr.Tpo .deps/snpindex-genome_hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-bitpack64-read.o -MD -MP -MF .deps/snpindex-bitpack64-read.Tpo -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c mv -f .deps/snpindex-bitpack64-read.Tpo .deps/snpindex-bitpack64-read.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-bitpack64-write.o -MD -MP -MF .deps/snpindex-bitpack64-write.Tpo -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c bitpack64-write.c:4146:38: warning: passing 'const UINT4 *' (aka 'const unsigned int *') to parameter of type 'Positionsptr_T *' (aka 'unsigned int *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] reorder_values_vertically(vertical,horizontal); ^~~~~~~~~~ bitpack64-write.c:4091:70: note: passing argument to parameter 'horizontal' here reorder_values_vertically (Positionsptr_T *vertical, Positionsptr_T *horizontal) { ^ 1 warning generated. mv -f .deps/snpindex-bitpack64-write.Tpo .deps/snpindex-bitpack64-write.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-indexdb.o -MD -MP -MF .deps/snpindex-indexdb.Tpo -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c:1363:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1483:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1653:63: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1792:6: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] ptr,sizeof(Univcoord_T),offset); ^~~ indexdb.c:1792:30: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] ptr,sizeof(Univcoord_T),offset); ^~~~~~ indexdb.c:1934:76: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, ~~~ ^~~~~~~~~~~~~~ %llu indexdb.c:2026:76: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, ~~~ ^~~~~~~~~~~~~~ %llu 7 warnings generated. mv -f .deps/snpindex-indexdb.Tpo .deps/snpindex-indexdb.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-indexdb-write.o -MD -MP -MF .deps/snpindex-indexdb-write.Tpo -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c indexdb-write.c:2495:3: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]); ^~~~~~ indexdb-write.c:2495:10: warning: format specifies type 'int' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]); ^ indexdb-write.c:2495:12: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]); ^~~~~~~~ indexdb-write.c:2727:8: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligok,offsetscomp[gammaptrs[p-1]],cum); ^~~~~~ indexdb-write.c:2738:8: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligok-1UL,offsets[oligok-1],cum); ^~~~~~~~~~ indexdb-write.c:2761:3: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligok-1UL,offsets[oligok-1],cum); ^~~~~~~~~~ indexdb-write.c:2788:6: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligok,offsetscomp[gammaptrs[p-1]],cum); ^~~~~~ indexdb-write.c:2799:6: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligok,offsets[oligok],*ptr); ^~~~~~ indexdb-write.c:2888:59: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Allocating %lu*%lu bytes for offsets\n",oligospace+1UL,sizeof(Positionsptr_T)); ~~~ ^~~~~~~~~~~~~~ %llu indexdb-write.c:2895:101: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Unable to allocate %lu bytes of memory, needed to build offsets with %d-mers\n",oligospace+1UL,index1part); ~~~ ^~~~~~~~~~~~~~ %llu indexdb-write.c:2972:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Bad character %c at position %lu\n",c,position); ~~~ ^~~~~~~~ %llu indexdb-write.c:3094:79: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Writing %lu offsets to file with total of %u k-mers...",oligospace+1,offsets[oligospace]); ~~~ ^~~~~~~~~~~~ %llu indexdb-write.c:3127:101: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Writing %lu offsets compressed via gammas to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]); ~~~ ^~~~~~~~~~~~~~ %llu indexdb-write.c:3171:102: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Writing %lu offsets compressed via bitpack to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]); ~~~ ^~~~~~~~~~~~~~ %llu indexdb-write.c:3234:85: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] fprintf(stderr,"Attempted to do lseek on offset %u*%lu=%lu\n",ptr,sizeof(UINT4),offset); ~~~ ^~~~~~ %lld indexdb-write.c:3246:85: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] fprintf(stderr,"Attempted to do lseek on offset %u*%lu=%lu\n",ptr,sizeof(UINT8),offset); ~~~ ^~~~~~ %lld indexdb-write.c:3371:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Bad character %c at position %lu\n",c,position); ~~~ ^~~~~~~~ %llu indexdb-write.c:3601:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Bad character %c at position %lu\n",c,position); ~~~ ^~~~~~~~ %llu indexdb-write.c:3796:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] positionsfile,totalcounts*sizeof(UINT8),filesize); ^~~~~~~~ indexdb-write.c:3823:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] positionsfile,totalcounts*sizeof(UINT8),filesize); ^~~~~~~~ indexdb-write.c:3838:45: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] positionsfile,totalcounts*sizeof(UINT8),filesize); ^~~~~~~~ indexdb-write.c:3865:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] positionsfile,totalcounts*sizeof(UINT4),filesize); ^~~~~~~~ indexdb-write.c:3892:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] positionsfile,totalcounts*sizeof(UINT4),filesize); ^~~~~~~~ indexdb-write.c:3907:45: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] positionsfile,totalcounts*sizeof(UINT4),filesize); ^~~~~~~~ 24 warnings generated. mv -f .deps/snpindex-indexdb-write.Tpo .deps/snpindex-indexdb-write.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-chrom.o -MD -MP -MF .deps/snpindex-chrom.Tpo -c -o snpindex-chrom.o `test -f 'chrom.c' || echo './'`chrom.c chrom.c:116:15: warning: comparing a pointer to a null character constant; did you mean to compare to NULL? [-Wpointer-compare] while (p != '\0' && *p >= '0' && *p <= '9') { ^~~~ (void *)0 1 warning generated. mv -f .deps/snpindex-chrom.Tpo .deps/snpindex-chrom.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-md5.o -MD -MP -MF .deps/snpindex-md5.Tpo -c -o snpindex-md5.o `test -f 'md5.c' || echo './'`md5.c mv -f .deps/snpindex-md5.Tpo .deps/snpindex-md5.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-bzip2.o -MD -MP -MF .deps/snpindex-bzip2.Tpo -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c mv -f .deps/snpindex-bzip2.Tpo .deps/snpindex-bzip2.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-sequence.o -MD -MP -MF .deps/snpindex-sequence.Tpo -c -o snpindex-sequence.o `test -f 'sequence.c' || echo './'`sequence.c mv -f .deps/snpindex-sequence.Tpo .deps/snpindex-sequence.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-genome.o -MD -MP -MF .deps/snpindex-genome.Tpo -c -o snpindex-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c:10292:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu genome.c:10292:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu genome.c:10392:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu genome.c:10392:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu 4 warnings generated. mv -f .deps/snpindex-genome.Tpo .deps/snpindex-genome.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-datadir.o -MD -MP -MF .deps/snpindex-datadir.Tpo -c -o snpindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/snpindex-datadir.Tpo .deps/snpindex-datadir.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-getopt.o -MD -MP -MF .deps/snpindex-getopt.Tpo -c -o snpindex-getopt.o `test -f 'getopt.c' || echo './'`getopt.c getopt.c:208:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] my_index (str, chr) ^ getopt.c:291:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] exchange (argv) ^ getopt.c:376:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] _getopt_initialize (argc, argv, optstring) ^ getopt.c:389:28: warning: passing arguments to 'getenv' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] posixly_correct = getenv ("POSIXLY_CORRECT"); ^ getopt.c:498:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] _getopt_internal (argc, argv, optstring, longopts, longind, long_only) ^ getopt.c:1179:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt (argc, argv, optstring) ^ In file included from getopt.c:97: ./getopt.h:147:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent definition [-Wdeprecated-non-prototype] extern int getopt (); ^ 7 warnings generated. mv -f .deps/snpindex-getopt.Tpo .deps/snpindex-getopt.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-getopt1.o -MD -MP -MF .deps/snpindex-getopt1.Tpo -c -o snpindex-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c getopt1.c:71:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt_long (argc, argv, options, long_options, opt_index) ^ getopt1.c:87:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt_long_only (argc, argv, options, long_options, opt_index) ^ 2 warnings generated. mv -f .deps/snpindex-getopt1.Tpo .deps/snpindex-getopt1.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-snpindex.o -MD -MP -MF .deps/snpindex-snpindex.Tpo -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo './'`snpindex.c In file included from snpindex.c:69: ./getopt.h:147:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a previous declaration [-Wdeprecated-non-prototype] extern int getopt (); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/unistd.h:509:6: note: conflicting prototype is here int getopt(int, char * const [], const char *) __DARWIN_ALIAS(getopt); ^ snpindex.c:889:75: warning: format specifies type 'unsigned long' but the argument has type 'UINT8' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Problem: saw duplicate positions %lu in oligo %s\n",*ptr1,nt); ~~~ ^~~~~ %llu snpindex.c:1143:71: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Allocating %lu*3*%lu bytes for compressed genome\n",nblocks,sizeof(Genomecomp_T)); ~~~ ^~~~~~~ %llu snpindex.c:1270:66: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Writing %lu offsets with %u total positions\n",oligospace+1,offsets[oligospace]); ~~~ ^~~~~~~~~~~~ %llu 4 warnings generated. mv -f .deps/snpindex-snpindex.Tpo .deps/snpindex-snpindex.Po /bin/sh ../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-access.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-genome_hr.o snpindex-bitpack64-read.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-getopt.o snpindex-getopt1.o snpindex-snpindex.o -lz -lbz2 -lm libtool: link: gcc -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-access.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-genome_hr.o snpindex-bitpack64-read.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-getopt.o snpindex-getopt1.o snpindex-snpindex.o -lz -lbz2 -lm gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-except.o -MD -MP -MF .deps/cmetindex-except.Tpo -c -o cmetindex-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/cmetindex-except.Tpo .deps/cmetindex-except.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-assert.o -MD -MP -MF .deps/cmetindex-assert.Tpo -c -o cmetindex-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/cmetindex-assert.Tpo .deps/cmetindex-assert.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-mem.o -MD -MP -MF .deps/cmetindex-mem.Tpo -c -o cmetindex-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/cmetindex-mem.Tpo .deps/cmetindex-mem.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-littleendian.o -MD -MP -MF .deps/cmetindex-littleendian.Tpo -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c mv -f .deps/cmetindex-littleendian.Tpo .deps/cmetindex-littleendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-bigendian.o -MD -MP -MF .deps/cmetindex-bigendian.Tpo -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c mv -f .deps/cmetindex-bigendian.Tpo .deps/cmetindex-bigendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-genomicpos.o -MD -MP -MF .deps/cmetindex-genomicpos.Tpo -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/cmetindex-genomicpos.Tpo .deps/cmetindex-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-stopwatch.o -MD -MP -MF .deps/cmetindex-stopwatch.Tpo -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/cmetindex-stopwatch.Tpo .deps/cmetindex-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-access.o -MD -MP -MF .deps/cmetindex-access.Tpo -c -o cmetindex-access.o `test -f 'access.c' || echo './'`access.c access.c:358:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] length,length,errno,strerror(errno)); ^~~~~~ access.c:358:15: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] length,length,errno,strerror(errno)); ^~~~~~ access.c:423:11: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] fd,offset,length,errno,strerror(errno)); ^~~~~~ access.c:493:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] *len,length,errno,strerror(errno)); ^~~~~~ access.c:556:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] offset,length,errno,strerror(errno)); ^~~~~~ access.c:641:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] *len,length,errno,strerror(errno)); ^~~~~~ 6 warnings generated. mv -f .deps/cmetindex-access.Tpo .deps/cmetindex-access.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-univinterval.o -MD -MP -MF .deps/cmetindex-univinterval.Tpo -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~ %llu univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~~ %llu 2 warnings generated. mv -f .deps/cmetindex-univinterval.Tpo .deps/cmetindex-univinterval.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-interval.o -MD -MP -MF .deps/cmetindex-interval.Tpo -c -o cmetindex-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/cmetindex-interval.Tpo .deps/cmetindex-interval.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-iit-read-univ.o -MD -MP -MF .deps/cmetindex-iit-read-univ.Tpo -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~~~ %llu iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~ %llu iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~~~ %llu iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~ %llu iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %llu iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~ %llu iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %llu 10 warnings generated. mv -f .deps/cmetindex-iit-read-univ.Tpo .deps/cmetindex-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-iit-read.o -MD -MP -MF .deps/cmetindex-iit-read.Tpo -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c mv -f .deps/cmetindex-iit-read.Tpo .deps/cmetindex-iit-read.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-compress.o -MD -MP -MF .deps/cmetindex-compress.Tpo -c -o cmetindex-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/cmetindex-compress.Tpo .deps/cmetindex-compress.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-compress-write.o -MD -MP -MF .deps/cmetindex-compress-write.Tpo -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c compress-write.c:73:80: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i); ~~~ ^~~~~~~~~~ %llu compress-write.c:252:13: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Buffer[i],position+i); ^~~~~~~~~~ compress-write.c:300:13: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Buffer[i],position+i); ^~~~~~~~~~ 3 warnings generated. mv -f .deps/cmetindex-compress-write.Tpo .deps/cmetindex-compress-write.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-genome_hr.o -MD -MP -MF .deps/cmetindex-genome_hr.Tpo -c -o cmetindex-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c mv -f .deps/cmetindex-genome_hr.Tpo .deps/cmetindex-genome_hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-bitpack64-read.o -MD -MP -MF .deps/cmetindex-bitpack64-read.Tpo -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c mv -f .deps/cmetindex-bitpack64-read.Tpo .deps/cmetindex-bitpack64-read.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-bitpack64-write.o -MD -MP -MF .deps/cmetindex-bitpack64-write.Tpo -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c bitpack64-write.c:4146:38: warning: passing 'const UINT4 *' (aka 'const unsigned int *') to parameter of type 'Positionsptr_T *' (aka 'unsigned int *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] reorder_values_vertically(vertical,horizontal); ^~~~~~~~~~ bitpack64-write.c:4091:70: note: passing argument to parameter 'horizontal' here reorder_values_vertically (Positionsptr_T *vertical, Positionsptr_T *horizontal) { ^ 1 warning generated. mv -f .deps/cmetindex-bitpack64-write.Tpo .deps/cmetindex-bitpack64-write.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-indexdb.o -MD -MP -MF .deps/cmetindex-indexdb.Tpo -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c:1363:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1483:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1653:63: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1792:6: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] ptr,sizeof(Univcoord_T),offset); ^~~ indexdb.c:1792:30: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] ptr,sizeof(Univcoord_T),offset); ^~~~~~ indexdb.c:1934:76: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, ~~~ ^~~~~~~~~~~~~~ %llu indexdb.c:2026:76: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, ~~~ ^~~~~~~~~~~~~~ %llu 7 warnings generated. mv -f .deps/cmetindex-indexdb.Tpo .deps/cmetindex-indexdb.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-indexdb-write.o -MD -MP -MF .deps/cmetindex-indexdb-write.Tpo -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c indexdb-write.c:2495:3: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]); ^~~~~~ indexdb-write.c:2495:10: warning: format specifies type 'int' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]); ^ indexdb-write.c:2495:12: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]); ^~~~~~~~ indexdb-write.c:2727:8: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligok,offsetscomp[gammaptrs[p-1]],cum); ^~~~~~ indexdb-write.c:2738:8: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligok-1UL,offsets[oligok-1],cum); ^~~~~~~~~~ indexdb-write.c:2761:3: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligok-1UL,offsets[oligok-1],cum); ^~~~~~~~~~ indexdb-write.c:2788:6: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligok,offsetscomp[gammaptrs[p-1]],cum); ^~~~~~ indexdb-write.c:2799:6: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligok,offsets[oligok],*ptr); ^~~~~~ indexdb-write.c:2888:59: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Allocating %lu*%lu bytes for offsets\n",oligospace+1UL,sizeof(Positionsptr_T)); ~~~ ^~~~~~~~~~~~~~ %llu indexdb-write.c:2895:101: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Unable to allocate %lu bytes of memory, needed to build offsets with %d-mers\n",oligospace+1UL,index1part); ~~~ ^~~~~~~~~~~~~~ %llu indexdb-write.c:2972:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Bad character %c at position %lu\n",c,position); ~~~ ^~~~~~~~ %llu indexdb-write.c:3094:79: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Writing %lu offsets to file with total of %u k-mers...",oligospace+1,offsets[oligospace]); ~~~ ^~~~~~~~~~~~ %llu indexdb-write.c:3127:101: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Writing %lu offsets compressed via gammas to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]); ~~~ ^~~~~~~~~~~~~~ %llu indexdb-write.c:3171:102: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Writing %lu offsets compressed via bitpack to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]); ~~~ ^~~~~~~~~~~~~~ %llu indexdb-write.c:3234:85: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] fprintf(stderr,"Attempted to do lseek on offset %u*%lu=%lu\n",ptr,sizeof(UINT4),offset); ~~~ ^~~~~~ %lld indexdb-write.c:3246:85: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] fprintf(stderr,"Attempted to do lseek on offset %u*%lu=%lu\n",ptr,sizeof(UINT8),offset); ~~~ ^~~~~~ %lld indexdb-write.c:3371:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Bad character %c at position %lu\n",c,position); ~~~ ^~~~~~~~ %llu indexdb-write.c:3601:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Bad character %c at position %lu\n",c,position); ~~~ ^~~~~~~~ %llu indexdb-write.c:3796:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] positionsfile,totalcounts*sizeof(UINT8),filesize); ^~~~~~~~ indexdb-write.c:3823:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] positionsfile,totalcounts*sizeof(UINT8),filesize); ^~~~~~~~ indexdb-write.c:3838:45: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] positionsfile,totalcounts*sizeof(UINT8),filesize); ^~~~~~~~ indexdb-write.c:3865:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] positionsfile,totalcounts*sizeof(UINT4),filesize); ^~~~~~~~ indexdb-write.c:3892:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] positionsfile,totalcounts*sizeof(UINT4),filesize); ^~~~~~~~ indexdb-write.c:3907:45: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] positionsfile,totalcounts*sizeof(UINT4),filesize); ^~~~~~~~ 24 warnings generated. mv -f .deps/cmetindex-indexdb-write.Tpo .deps/cmetindex-indexdb-write.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-cmet.o -MD -MP -MF .deps/cmetindex-cmet.Tpo -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo './'`cmet.c mv -f .deps/cmetindex-cmet.Tpo .deps/cmetindex-cmet.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-list.o -MD -MP -MF .deps/cmetindex-list.Tpo -c -o cmetindex-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/cmetindex-list.Tpo .deps/cmetindex-list.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-datadir.o -MD -MP -MF .deps/cmetindex-datadir.Tpo -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/cmetindex-datadir.Tpo .deps/cmetindex-datadir.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-getopt.o -MD -MP -MF .deps/cmetindex-getopt.Tpo -c -o cmetindex-getopt.o `test -f 'getopt.c' || echo './'`getopt.c getopt.c:208:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] my_index (str, chr) ^ getopt.c:291:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] exchange (argv) ^ getopt.c:376:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] _getopt_initialize (argc, argv, optstring) ^ getopt.c:389:28: warning: passing arguments to 'getenv' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] posixly_correct = getenv ("POSIXLY_CORRECT"); ^ getopt.c:498:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] _getopt_internal (argc, argv, optstring, longopts, longind, long_only) ^ getopt.c:1179:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt (argc, argv, optstring) ^ In file included from getopt.c:97: ./getopt.h:147:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent definition [-Wdeprecated-non-prototype] extern int getopt (); ^ 7 warnings generated. mv -f .deps/cmetindex-getopt.Tpo .deps/cmetindex-getopt.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-getopt1.o -MD -MP -MF .deps/cmetindex-getopt1.Tpo -c -o cmetindex-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c getopt1.c:71:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt_long (argc, argv, options, long_options, opt_index) ^ getopt1.c:87:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt_long_only (argc, argv, options, long_options, opt_index) ^ 2 warnings generated. mv -f .deps/cmetindex-getopt1.Tpo .deps/cmetindex-getopt1.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-cmetindex.o -MD -MP -MF .deps/cmetindex-cmetindex.Tpo -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo './'`cmetindex.c In file included from cmetindex.c:61: ./getopt.h:147:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a previous declaration [-Wdeprecated-non-prototype] extern int getopt (); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/unistd.h:509:6: note: conflicting prototype is here int getopt(int, char * const [], const char *) __DARWIN_ALIAS(getopt); ^ 1 warning generated. mv -f .deps/cmetindex-cmetindex.Tpo .deps/cmetindex-cmetindex.Po /bin/sh ../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-genome_hr.o cmetindex-bitpack64-read.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-list.o cmetindex-datadir.o cmetindex-getopt.o cmetindex-getopt1.o cmetindex-cmetindex.o -lm libtool: link: gcc -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-genome_hr.o cmetindex-bitpack64-read.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-list.o cmetindex-datadir.o cmetindex-getopt.o cmetindex-getopt1.o cmetindex-cmetindex.o -lm gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-except.o -MD -MP -MF .deps/atoiindex-except.Tpo -c -o atoiindex-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/atoiindex-except.Tpo .deps/atoiindex-except.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-assert.o -MD -MP -MF .deps/atoiindex-assert.Tpo -c -o atoiindex-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/atoiindex-assert.Tpo .deps/atoiindex-assert.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-mem.o -MD -MP -MF .deps/atoiindex-mem.Tpo -c -o atoiindex-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/atoiindex-mem.Tpo .deps/atoiindex-mem.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-littleendian.o -MD -MP -MF .deps/atoiindex-littleendian.Tpo -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c mv -f .deps/atoiindex-littleendian.Tpo .deps/atoiindex-littleendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-bigendian.o -MD -MP -MF .deps/atoiindex-bigendian.Tpo -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c mv -f .deps/atoiindex-bigendian.Tpo .deps/atoiindex-bigendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-genomicpos.o -MD -MP -MF .deps/atoiindex-genomicpos.Tpo -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/atoiindex-genomicpos.Tpo .deps/atoiindex-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-stopwatch.o -MD -MP -MF .deps/atoiindex-stopwatch.Tpo -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/atoiindex-stopwatch.Tpo .deps/atoiindex-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-access.o -MD -MP -MF .deps/atoiindex-access.Tpo -c -o atoiindex-access.o `test -f 'access.c' || echo './'`access.c access.c:358:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] length,length,errno,strerror(errno)); ^~~~~~ access.c:358:15: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] length,length,errno,strerror(errno)); ^~~~~~ access.c:423:11: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] fd,offset,length,errno,strerror(errno)); ^~~~~~ access.c:493:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] *len,length,errno,strerror(errno)); ^~~~~~ access.c:556:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] offset,length,errno,strerror(errno)); ^~~~~~ access.c:641:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] *len,length,errno,strerror(errno)); ^~~~~~ 6 warnings generated. mv -f .deps/atoiindex-access.Tpo .deps/atoiindex-access.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-univinterval.o -MD -MP -MF .deps/atoiindex-univinterval.Tpo -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~ %llu univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~~ %llu 2 warnings generated. mv -f .deps/atoiindex-univinterval.Tpo .deps/atoiindex-univinterval.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-interval.o -MD -MP -MF .deps/atoiindex-interval.Tpo -c -o atoiindex-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/atoiindex-interval.Tpo .deps/atoiindex-interval.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-iit-read-univ.o -MD -MP -MF .deps/atoiindex-iit-read-univ.Tpo -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~~~ %llu iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~ %llu iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~~~ %llu iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~ %llu iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %llu iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~ %llu iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %llu 10 warnings generated. mv -f .deps/atoiindex-iit-read-univ.Tpo .deps/atoiindex-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-iit-read.o -MD -MP -MF .deps/atoiindex-iit-read.Tpo -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c mv -f .deps/atoiindex-iit-read.Tpo .deps/atoiindex-iit-read.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-compress.o -MD -MP -MF .deps/atoiindex-compress.Tpo -c -o atoiindex-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/atoiindex-compress.Tpo .deps/atoiindex-compress.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-compress-write.o -MD -MP -MF .deps/atoiindex-compress-write.Tpo -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c compress-write.c:73:80: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i); ~~~ ^~~~~~~~~~ %llu compress-write.c:252:13: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Buffer[i],position+i); ^~~~~~~~~~ compress-write.c:300:13: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Buffer[i],position+i); ^~~~~~~~~~ 3 warnings generated. mv -f .deps/atoiindex-compress-write.Tpo .deps/atoiindex-compress-write.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-genome_hr.o -MD -MP -MF .deps/atoiindex-genome_hr.Tpo -c -o atoiindex-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c mv -f .deps/atoiindex-genome_hr.Tpo .deps/atoiindex-genome_hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-bitpack64-read.o -MD -MP -MF .deps/atoiindex-bitpack64-read.Tpo -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c mv -f .deps/atoiindex-bitpack64-read.Tpo .deps/atoiindex-bitpack64-read.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-bitpack64-write.o -MD -MP -MF .deps/atoiindex-bitpack64-write.Tpo -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c bitpack64-write.c:4146:38: warning: passing 'const UINT4 *' (aka 'const unsigned int *') to parameter of type 'Positionsptr_T *' (aka 'unsigned int *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] reorder_values_vertically(vertical,horizontal); ^~~~~~~~~~ bitpack64-write.c:4091:70: note: passing argument to parameter 'horizontal' here reorder_values_vertically (Positionsptr_T *vertical, Positionsptr_T *horizontal) { ^ 1 warning generated. mv -f .deps/atoiindex-bitpack64-write.Tpo .deps/atoiindex-bitpack64-write.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-indexdb.o -MD -MP -MF .deps/atoiindex-indexdb.Tpo -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c:1363:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1483:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1653:63: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1792:6: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] ptr,sizeof(Univcoord_T),offset); ^~~ indexdb.c:1792:30: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] ptr,sizeof(Univcoord_T),offset); ^~~~~~ indexdb.c:1934:76: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, ~~~ ^~~~~~~~~~~~~~ %llu indexdb.c:2026:76: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, ~~~ ^~~~~~~~~~~~~~ %llu 7 warnings generated. mv -f .deps/atoiindex-indexdb.Tpo .deps/atoiindex-indexdb.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-indexdb-write.o -MD -MP -MF .deps/atoiindex-indexdb-write.Tpo -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c indexdb-write.c:2495:3: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]); ^~~~~~ indexdb-write.c:2495:10: warning: format specifies type 'int' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]); ^ indexdb-write.c:2495:12: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]); ^~~~~~~~ indexdb-write.c:2727:8: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligok,offsetscomp[gammaptrs[p-1]],cum); ^~~~~~ indexdb-write.c:2738:8: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligok-1UL,offsets[oligok-1],cum); ^~~~~~~~~~ indexdb-write.c:2761:3: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligok-1UL,offsets[oligok-1],cum); ^~~~~~~~~~ indexdb-write.c:2788:6: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligok,offsetscomp[gammaptrs[p-1]],cum); ^~~~~~ indexdb-write.c:2799:6: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligok,offsets[oligok],*ptr); ^~~~~~ indexdb-write.c:2888:59: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Allocating %lu*%lu bytes for offsets\n",oligospace+1UL,sizeof(Positionsptr_T)); ~~~ ^~~~~~~~~~~~~~ %llu indexdb-write.c:2895:101: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Unable to allocate %lu bytes of memory, needed to build offsets with %d-mers\n",oligospace+1UL,index1part); ~~~ ^~~~~~~~~~~~~~ %llu indexdb-write.c:2972:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Bad character %c at position %lu\n",c,position); ~~~ ^~~~~~~~ %llu indexdb-write.c:3094:79: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Writing %lu offsets to file with total of %u k-mers...",oligospace+1,offsets[oligospace]); ~~~ ^~~~~~~~~~~~ %llu indexdb-write.c:3127:101: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Writing %lu offsets compressed via gammas to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]); ~~~ ^~~~~~~~~~~~~~ %llu indexdb-write.c:3171:102: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Writing %lu offsets compressed via bitpack to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]); ~~~ ^~~~~~~~~~~~~~ %llu indexdb-write.c:3234:85: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] fprintf(stderr,"Attempted to do lseek on offset %u*%lu=%lu\n",ptr,sizeof(UINT4),offset); ~~~ ^~~~~~ %lld indexdb-write.c:3246:85: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] fprintf(stderr,"Attempted to do lseek on offset %u*%lu=%lu\n",ptr,sizeof(UINT8),offset); ~~~ ^~~~~~ %lld indexdb-write.c:3371:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Bad character %c at position %lu\n",c,position); ~~~ ^~~~~~~~ %llu indexdb-write.c:3601:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Bad character %c at position %lu\n",c,position); ~~~ ^~~~~~~~ %llu indexdb-write.c:3796:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] positionsfile,totalcounts*sizeof(UINT8),filesize); ^~~~~~~~ indexdb-write.c:3823:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] positionsfile,totalcounts*sizeof(UINT8),filesize); ^~~~~~~~ indexdb-write.c:3838:45: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] positionsfile,totalcounts*sizeof(UINT8),filesize); ^~~~~~~~ indexdb-write.c:3865:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] positionsfile,totalcounts*sizeof(UINT4),filesize); ^~~~~~~~ indexdb-write.c:3892:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] positionsfile,totalcounts*sizeof(UINT4),filesize); ^~~~~~~~ indexdb-write.c:3907:45: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] positionsfile,totalcounts*sizeof(UINT4),filesize); ^~~~~~~~ 24 warnings generated. mv -f .deps/atoiindex-indexdb-write.Tpo .deps/atoiindex-indexdb-write.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-atoi.o -MD -MP -MF .deps/atoiindex-atoi.Tpo -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo './'`atoi.c mv -f .deps/atoiindex-atoi.Tpo .deps/atoiindex-atoi.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-list.o -MD -MP -MF .deps/atoiindex-list.Tpo -c -o atoiindex-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/atoiindex-list.Tpo .deps/atoiindex-list.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-datadir.o -MD -MP -MF .deps/atoiindex-datadir.Tpo -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/atoiindex-datadir.Tpo .deps/atoiindex-datadir.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-getopt.o -MD -MP -MF .deps/atoiindex-getopt.Tpo -c -o atoiindex-getopt.o `test -f 'getopt.c' || echo './'`getopt.c getopt.c:208:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] my_index (str, chr) ^ getopt.c:291:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] exchange (argv) ^ getopt.c:376:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] _getopt_initialize (argc, argv, optstring) ^ getopt.c:389:28: warning: passing arguments to 'getenv' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] posixly_correct = getenv ("POSIXLY_CORRECT"); ^ getopt.c:498:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] _getopt_internal (argc, argv, optstring, longopts, longind, long_only) ^ getopt.c:1179:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt (argc, argv, optstring) ^ In file included from getopt.c:97: ./getopt.h:147:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent definition [-Wdeprecated-non-prototype] extern int getopt (); ^ 7 warnings generated. mv -f .deps/atoiindex-getopt.Tpo .deps/atoiindex-getopt.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-getopt1.o -MD -MP -MF .deps/atoiindex-getopt1.Tpo -c -o atoiindex-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c getopt1.c:71:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt_long (argc, argv, options, long_options, opt_index) ^ getopt1.c:87:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] getopt_long_only (argc, argv, options, long_options, opt_index) ^ 2 warnings generated. mv -f .deps/atoiindex-getopt1.Tpo .deps/atoiindex-getopt1.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-atoiindex.o -MD -MP -MF .deps/atoiindex-atoiindex.Tpo -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo './'`atoiindex.c In file included from atoiindex.c:61: ./getopt.h:147:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a previous declaration [-Wdeprecated-non-prototype] extern int getopt (); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/unistd.h:509:6: note: conflicting prototype is here int getopt(int, char * const [], const char *) __DARWIN_ALIAS(getopt); ^ 1 warning generated. mv -f .deps/atoiindex-atoiindex.Tpo .deps/atoiindex-atoiindex.Po /bin/sh ../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-genome_hr.o atoiindex-bitpack64-read.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-list.o atoiindex-datadir.o atoiindex-getopt.o atoiindex-getopt1.o atoiindex-atoiindex.o -lm libtool: link: gcc -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-genome_hr.o atoiindex-bitpack64-read.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-list.o atoiindex-datadir.o atoiindex-getopt.o atoiindex-getopt1.o atoiindex-atoiindex.o -lm ../config/install-sh -c -d '/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/bin' /bin/sh ../libtool --mode=install /usr/bin/install -c gmap gmapl get-genome gmapindex iit_store iit_get iit_dump gsnap gsnapl uniqscan uniqscanl snpindex cmetindex atoiindex '/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/bin' libtool: install: /usr/bin/install -c gmap /Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/bin/gmap libtool: install: /usr/bin/install -c gmapl /Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/bin/gmapl libtool: install: /usr/bin/install -c get-genome /Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/bin/get-genome libtool: install: /usr/bin/install -c gmapindex /Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/bin/gmapindex libtool: install: /usr/bin/install -c iit_store /Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/bin/iit_store libtool: install: /usr/bin/install -c iit_get /Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/bin/iit_get libtool: install: /usr/bin/install -c iit_dump /Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/bin/iit_dump libtool: install: /usr/bin/install -c gsnap /Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/bin/gsnap libtool: install: /usr/bin/install -c gsnapl /Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/bin/gsnapl libtool: install: /usr/bin/install -c uniqscan /Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/bin/uniqscan libtool: install: /usr/bin/install -c uniqscanl /Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/bin/uniqscanl libtool: install: /usr/bin/install -c snpindex /Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/bin/snpindex libtool: install: /usr/bin/install -c cmetindex /Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/bin/cmetindex libtool: install: /usr/bin/install -c atoiindex /Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/bin/atoiindex make[3]: Nothing to be done for `install-data-am'. Making install in util cp gmap_compress.pl gmap_compress chmod +x gmap_compress cp gmap_uncompress.pl gmap_uncompress chmod +x gmap_uncompress cp gmap_process.pl gmap_process chmod +x gmap_process cp gmap_setup.pl gmap_setup chmod +x gmap_setup cp gmap_build.pl gmap_build chmod +x gmap_build cp gmap_reassemble.pl gmap_reassemble chmod +x gmap_reassemble cp md_coords.pl md_coords chmod +x md_coords cp fa_coords.pl fa_coords chmod +x fa_coords cp psl_splicesites.pl psl_splicesites chmod +x psl_splicesites cp psl_introns.pl psl_introns chmod +x psl_introns cp psl_genes.pl psl_genes chmod +x psl_genes cp gtf_splicesites.pl gtf_splicesites chmod +x gtf_splicesites cp gtf_introns.pl gtf_introns chmod +x gtf_introns cp gtf_genes.pl gtf_genes chmod +x gtf_genes cp gff3_splicesites.pl gff3_splicesites chmod +x gff3_splicesites cp gff3_introns.pl gff3_introns chmod +x gff3_introns cp gff3_genes.pl gff3_genes chmod +x gff3_genes cp dbsnp_iit.pl dbsnp_iit chmod +x dbsnp_iit cp gvf_iit.pl gvf_iit chmod +x gvf_iit cp vcf_iit.pl vcf_iit chmod +x vcf_iit ../config/install-sh -c -d '/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/bin' /usr/bin/install -c gmap_compress gmap_uncompress gmap_process gmap_setup gmap_build gmap_reassemble md_coords fa_coords psl_splicesites psl_introns psl_genes gtf_splicesites gtf_introns gtf_genes gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/Users/biocbuild/bbs-3.20-bioc/meat/gmapR/src/../inst/usr/bin' make[3]: Nothing to be done for `install-data-am'. Making install in tests make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-gmapR/00new/gmapR/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function from function ‘directory’ in package ‘gmapR’ Creating a generic function for ‘bamPaths’ from package ‘Rsamtools’ in package ‘gmapR’ Note: ... may be used in an incorrect context ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (gmapR)
gmapR.Rcheck/tests/gmapR_unit_tests.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > require("gmapR") || stop("unable to load gmapR package") Loading required package: gmapR Loading required package: GenomeInfoDb Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomicRanges Loading required package: Rsamtools Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit [1] TRUE > gmapR:::.test() NOTE: genome 'hg19.p53' already exists, not overwriting Loading required package: BSgenome Loading required package: BiocIO Loading required package: rtracklayer Attaching package: 'rtracklayer' The following object is masked from 'package:BiocIO': FileForFormat writing chrI sequence to file ... OK writing chrII sequence to file ... OK writing chrIII sequence to file ... OK writing chrIV sequence to file ... OK writing chrV sequence to file ... OK writing chrVI sequence to file ... OK writing chrVII sequence to file ... OK writing chrVIII sequence to file ... OK writing chrIX sequence to file ... OK writing chrX sequence to file ... OK writing chrXI sequence to file ... OK writing chrXII sequence to file ... OK writing chrXIII sequence to file ... OK writing chrXIV sequence to file ... OK writing chrXV sequence to file ... OK writing chrXVI sequence to file ... OK writing chrM sequence to file ... OK -k flag specified (not as 15), but not -b, so building with base size == kmer size Running /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//fa_coords -c chrM -o ./yeast.coords "/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpE2qvEU/gmap_build_fasta70ce729431a1" Opening file /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpE2qvEU/gmap_build_fasta70ce729431a1 Processed short contigs (<1000000 nt): ... Contig chrIV: concatenated at chromosome end: chrIV:1..1531933 (length = 1531933 nt) Processed short contigs (<1000000 nt): .. Contig chrVII: concatenated at chromosome end: chrVII:1..1090940 (length = 1090940 nt) Processed short contigs (<1000000 nt): .... Contig chrXII: concatenated at chromosome end: chrXII:1..1078177 (length = 1078177 nt) Processed short contigs (<1000000 nt): .. Contig chrXV: concatenated at chromosome end: chrXV:1..1091291 (length = 1091291 nt) Processed short contigs (<1000000 nt): .. ============================================================ Contig mapping information has been written to file ./yeast.coords. You should look at this file, and edit it if necessary If everything is okay, you should proceed by running make gmapdb ============================================================ Running /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//gmap_process -c ./yeast.coords "/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpE2qvEU/gmap_build_fasta70ce729431a1" | /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//gmapindex -d yeast -D . -A -s none Reading coordinates from file ./yeast.coords Logging contig chrI at chrI:1..230218 in genome yeast Logging contig chrII at chrII:1..813184 in genome yeast Logging contig chrIII at chrIII:1..316620 in genome yeast Logging contig chrIV at chrIV:1..1531933 in genome yeast Logging contig chrV at chrV:1..576874 in genome yeast Logging contig chrVI at chrVI:1..270161 in genome yeast Logging contig chrVII at chrVII:1..1090940 in genome yeast Logging contig chrVIII at chrVIII:1..562643 in genome yeast Logging contig chrIX at chrIX:1..439888 in genome yeast Logging contig chrX at chrX:1..745751 in genome yeast Logging contig chrXI at chrXI:1..666816 in genome yeast Logging contig chrXII at chrXII:1..1078177 in genome yeast Logging contig chrXIII at chrXIII:1..924431 in genome yeast Logging contig chrXIV at chrXIV:1..784333 in genome yeast Logging contig chrXV at chrXV:1..1091291 in genome yeast Logging contig chrXVI at chrXVI:1..948066 in genome yeast Logging contig chrM at chrM:1..85779 in genome yeast chrM is a circular chromosome Total genomic length = 12157105 bp Chromosome chrI has universal coordinates 1..230218 Chromosome chrII has universal coordinates 230219..1043402 Chromosome chrIII has universal coordinates 1043403..1360022 Chromosome chrIV has universal coordinates 1360023..2891955 Chromosome chrV has universal coordinates 2891956..3468829 Chromosome chrVI has universal coordinates 3468830..3738990 Chromosome chrVII has universal coordinates 3738991..4829930 Chromosome chrVIII has universal coordinates 4829931..5392573 Chromosome chrIX has universal coordinates 5392574..5832461 Chromosome chrX has universal coordinates 5832462..6578212 Chromosome chrXI has universal coordinates 6578213..7245028 Chromosome chrXII has universal coordinates 7245029..8323205 Chromosome chrXIII has universal coordinates 8323206..9247636 Chromosome chrXIV has universal coordinates 9247637..10031969 Chromosome chrXV has universal coordinates 10031970..11123260 Chromosome chrXVI has universal coordinates 11123261..12071326 Chromosome chrM has universal coordinates 12071327..12157105 Writing IIT file header information...coordinates require 4 bytes each...done Processing null division/chromosome...sorting...writing...done (17 intervals) Writing IIT file footer information...done Writing IIT file header information...coordinates require 4 bytes each...done Processing null division/chromosome...sorting...writing...done (17 intervals) Writing IIT file footer information...done Running /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//gmap_process -c ./yeast.coords "/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpE2qvEU/gmap_build_fasta70ce729431a1" | /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//gmapindex -d yeast -F . -D . -G Genome length is 12242884 nt Trying to allocate 1147773*4 bytes of memory...succeeded. Building genome in memory. Reading coordinates from file ./yeast.coords Writing contig chrI to universal coordinates 1..230218 in genome yeast Writing contig chrII to universal coordinates 230219..1043402 in genome yeast Writing contig chrIII to universal coordinates 1043403..1360022 in genome yeast Writing contig chrIV to universal coordinates 1360023..2891955 in genome yeast Writing contig chrV to universal coordinates 2891956..3468829 in genome yeast Writing contig chrVI to universal coordinates 3468830..3738990 in genome yeast Writing contig chrVII to universal coordinates 3738991..4829930 in genome yeast Writing contig chrVIII to universal coordinates 4829931..5392573 in genome yeast Writing contig chrIX to universal coordinates 5392574..5832461 in genome yeast Writing contig chrX to universal coordinates 5832462..6578212 in genome yeast Writing contig chrXI to universal coordinates 6578213..7245028 in genome yeast Writing contig chrXII to universal coordinates 7245029..8323205 in genome yeast Writing contig chrXIII to universal coordinates 8323206..9247636 in genome yeast Writing contig chrXIV to universal coordinates 9247637..10031969 in genome yeast Writing contig chrXV to universal coordinates 10031970..11123260 in genome yeast Writing contig chrXVI to universal coordinates 11123261..12071326 in genome yeast Writing contig chrM to universal coordinates 12071327..12157105 in genome yeast Chromosome chrM is circular. Copying 12071327..12157105 to 12157106..12242884 A total of 0 non-ACGTNX characters were seen in the genome. Running cat ./yeast.genomecomp | /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//gmapindex -d yeast -U > ./yeast.genomebits Running cat ./yeast.genomecomp | /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//gmapindex -b 12 -k 12 -q 3 -d yeast -F . -D . -O Note: since base size is equal to the k-mer size 12, offsets will not be compressed Offset compression types: Allocating 16777217*4 bytes for offsets Indexing offsets of oligomers in genome yeast (12 bp every 3 bp), position 0 Writing 16777217 offsets to file with total of 4080904 k-mers...done Running cat ./yeast.genomecomp | /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//gmapindex -b 12 -k 12 -q 3 -d yeast -F . -D . -P Looking for index files in directory . (offsets not compressed) Offsets file is yeast.ref123offsets Positions file is yeast.ref123positions Trying to allocate 4080904*4 bytes of memory...succeeded. Building positions in memory. Indexing positions of oligomers in genome yeast (12 bp every 3 bp), position 0 Writing 4080904 genomic positions to file ./yeast.ref123positions ... Running /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//gmapindex -d yeast -F . -D . -S SACA_K called with n = 12242885, K = 5, level 0 SACA_K called with n = 3442582, K = 0, level 1 SACA_K called with n = 1091915, K = 0, level 2 SACA_K called with n = 355699, K = 0, level 3 SACA_K called with n = 115942, K = 0, level 4 SACA_K called with n = 37652, K = 0, level 5 SACA_K called with n = 12156, K = 0, level 6 SACA_K called with n = 4037, K = 0, level 7 SACA_K called with n = 1305, K = 0, level 8 Computing lcp...done Computing saindex...done Copying files to directory /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpE2qvEU/110469943/yeast -k flag specified (not as 15), but not -b, so building with base size == kmer size Running /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//fa_coords -o ./thing.coords "/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpE2qvEU/file70ce5f467bcb" Opening file /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpE2qvEU/file70ce5f467bcb Processed short contigs (<1000000 nt): . ============================================================ Contig mapping information has been written to file ./thing.coords. You should look at this file, and edit it if necessary If everything is okay, you should proceed by running make gmapdb ============================================================ Running /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//gmap_process -c ./thing.coords "/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpE2qvEU/file70ce5f467bcb" | /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//gmapindex -d thing -D . -A -s none Reading coordinates from file ./thing.coords Logging contig sampleDNAStringSet at sampleDNAStringSet:1..2000 in genome thing Total genomic length = 2000 bp Chromosome sampleDNAStringSet has universal coordinates 1..2000 Writing IIT file header information...coordinates require 4 bytes each...done Processing null division/chromosome...sorting...writing...done (1 intervals) Writing IIT file footer information...done Writing IIT file header information...coordinates require 4 bytes each...done Processing null division/chromosome...sorting...writing...done (1 intervals) Writing IIT file footer information...done Running /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//gmap_process -c ./thing.coords "/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpE2qvEU/file70ce5f467bcb" | /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//gmapindex -d thing -F . -D . -G Genome length is 2000 nt Trying to allocate 189*4 bytes of memory...succeeded. Building genome in memory. Reading coordinates from file ./thing.coords Writing contig sampleDNAStringSet to universal coordinates 1..2000 in genome thing A total of 0 non-ACGTNX characters were seen in the genome. Running cat ./thing.genomecomp | /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//gmapindex -d thing -U > ./thing.genomebits Running cat ./thing.genomecomp | /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//gmapindex -b 12 -k 12 -q 3 -d thing -F . -D . -O Note: since base size is equal to the k-mer size 12, offsets will not be compressed Offset compression types: Allocating 16777217*4 bytes for offsets Indexing offsets of oligomers in genome thing (12 bp every 3 bp), position 0 Writing 16777217 offsets to file with total of 663 k-mers...done Running cat ./thing.genomecomp | /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//gmapindex -b 12 -k 12 -q 3 -d thing -F . -D . -P Looking for index files in directory . (offsets not compressed) Offsets file is thing.ref123offsets Positions file is thing.ref123positions Trying to allocate 663*4 bytes of memory...succeeded. Building positions in memory. Indexing positions of oligomers in genome thing (12 bp every 3 bp), position 0 Writing 663 genomic positions to file ./thing.ref123positions ... Running /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//gmapindex -d thing -F . -D . -S SACA_K called with n = 2001, K = 5, level 0 SACA_K called with n = 575, K = 0, level 1 Computing lcp...done Computing saindex...done Copying files to directory /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpE2qvEU/871805021/thing -k flag specified (not as 15), but not -b, so building with base size == kmer size Running /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//fa_coords -o ./testGenome.coords "/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpE2qvEU/file70ce61a0cd4a" Opening file /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpE2qvEU/file70ce61a0cd4a Processed short contigs (<1000000 nt): .. ============================================================ Contig mapping information has been written to file ./testGenome.coords. You should look at this file, and edit it if necessary If everything is okay, you should proceed by running make gmapdb ============================================================ Running /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//gmap_process -c ./testGenome.coords "/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpE2qvEU/file70ce61a0cd4a" | /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//gmapindex -d testGenome -D . -A -s none Reading coordinates from file ./testGenome.coords Logging contig testA at testA:1..26 in genome testGenome Logging contig testB at testB:1..13 in genome testGenome Total genomic length = 39 bp Chromosome testA has universal coordinates 1..26 Chromosome testB has universal coordinates 27..39 Writing IIT file header information...coordinates require 4 bytes each...done Processing null division/chromosome...sorting...writing...done (2 intervals) Writing IIT file footer information...done Writing IIT file header information...coordinates require 4 bytes each...done Processing null division/chromosome...sorting...writing...done (2 intervals) Writing IIT file footer information...done Running /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//gmap_process -c ./testGenome.coords "/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpE2qvEU/file70ce61a0cd4a" | /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//gmapindex -d testGenome -F . -D . -G Genome length is 39 nt Trying to allocate 6*4 bytes of memory...succeeded. Building genome in memory. Reading coordinates from file ./testGenome.coords Writing contig testA to universal coordinates 1..26 in genome testGenome Writing contig testB to universal coordinates 27..39 in genome testGenome A total of 0 non-ACGTNX characters were seen in the genome. Running cat ./testGenome.genomecomp | /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//gmapindex -d testGenome -U > ./testGenome.genomebits Running cat ./testGenome.genomecomp | /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//gmapindex -b 12 -k 12 -q 3 -d testGenome -F . -D . -O Note: since base size is equal to the k-mer size 12, offsets will not be compressed Offset compression types: Allocating 16777217*4 bytes for offsets Indexing offsets of oligomers in genome testGenome (12 bp every 3 bp), position 0 Writing 16777217 offsets to file with total of 6 k-mers...done Running cat ./testGenome.genomecomp | /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//gmapindex -b 12 -k 12 -q 3 -d testGenome -F . -D . -P Looking for index files in directory . (offsets not compressed) Offsets file is testGenome.ref123offsets Positions file is testGenome.ref123positions Trying to allocate 6*4 bytes of memory...succeeded. Building positions in memory. Indexing positions of oligomers in genome testGenome (12 bp every 3 bp), position 0 Writing 6 genomic positions to file ./testGenome.ref123positions ... Running /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//gmapindex -d testGenome -F . -D . -S SACA_K called with n = 40, K = 5, level 0 Computing lcp...done Computing saindex...done Copying files to directory /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpE2qvEU/file70cec697d4b/testGenome Loading required package: GenomicFeatures Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Finished reading FASTA file -- total entries: 4918 Maximum coordinate: 1968875 Total label length: 29508 + 4918 separators Total annotation length: 20152 + 4918 separators Saw 1 distinct divisions/chromosomes Saw 3 distinct tags/types Writing IIT file header information...done Processing null division/chromosome...sorting...writing...done (0 intervals) Processing division/chromosome chr17...sorting...writing...done (4918 intervals) Writing IIT file footer information...done NOTE: genome 'hg19.p53' already exists, not overwriting Creating directory /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpE2qvEU/66073 writing chrI sequence to file ... OK writing chrII sequence to file ... OK writing chrIII sequence to file ... OK writing chrIV sequence to file ... OK writing chrV sequence to file ... OK writing chrVI sequence to file ... OK writing chrVII sequence to file ... OK writing chrVIII sequence to file ... OK writing chrIX sequence to file ... OK writing chrX sequence to file ... OK writing chrXI sequence to file ... OK writing chrXII sequence to file ... OK writing chrXIII sequence to file ... OK writing chrXIV sequence to file ... OK writing chrXV sequence to file ... OK writing chrXVI sequence to file ... OK writing chrM sequence to file ... OK -k flag specified (not as 15), but not -b, so building with base size == kmer size Running /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//fa_coords -c chrM -o ./yeast.coords "/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpE2qvEU/gmap_build_fasta70ce510f2d37" Opening file /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpE2qvEU/gmap_build_fasta70ce510f2d37 Processed short contigs (<1000000 nt): ... Contig chrIV: concatenated at chromosome end: chrIV:1..1531933 (length = 1531933 nt) Processed short contigs (<1000000 nt): .. Contig chrVII: concatenated at chromosome end: chrVII:1..1090940 (length = 1090940 nt) Processed short contigs (<1000000 nt): .... Contig chrXII: concatenated at chromosome end: chrXII:1..1078177 (length = 1078177 nt) Processed short contigs (<1000000 nt): .. Contig chrXV: concatenated at chromosome end: chrXV:1..1091291 (length = 1091291 nt) Processed short contigs (<1000000 nt): .. ============================================================ Contig mapping information has been written to file ./yeast.coords. You should look at this file, and edit it if necessary If everything is okay, you should proceed by running make gmapdb ============================================================ Running /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//gmap_process -c ./yeast.coords "/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpE2qvEU/gmap_build_fasta70ce510f2d37" | /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//gmapindex -d yeast -D . -A -s none Reading coordinates from file ./yeast.coords Logging contig chrI at chrI:1..230218 in genome yeast Logging contig chrII at chrII:1..813184 in genome yeast Logging contig chrIII at chrIII:1..316620 in genome yeast Logging contig chrIV at chrIV:1..1531933 in genome yeast Logging contig chrV at chrV:1..576874 in genome yeast Logging contig chrVI at chrVI:1..270161 in genome yeast Logging contig chrVII at chrVII:1..1090940 in genome yeast Logging contig chrVIII at chrVIII:1..562643 in genome yeast Logging contig chrIX at chrIX:1..439888 in genome yeast Logging contig chrX at chrX:1..745751 in genome yeast Logging contig chrXI at chrXI:1..666816 in genome yeast Logging contig chrXII at chrXII:1..1078177 in genome yeast Logging contig chrXIII at chrXIII:1..924431 in genome yeast Logging contig chrXIV at chrXIV:1..784333 in genome yeast Logging contig chrXV at chrXV:1..1091291 in genome yeast Logging contig chrXVI at chrXVI:1..948066 in genome yeast Logging contig chrM at chrM:1..85779 in genome yeast chrM is a circular chromosome Total genomic length = 12157105 bp Chromosome chrI has universal coordinates 1..230218 Chromosome chrII has universal coordinates 230219..1043402 Chromosome chrIII has universal coordinates 1043403..1360022 Chromosome chrIV has universal coordinates 1360023..2891955 Chromosome chrV has universal coordinates 2891956..3468829 Chromosome chrVI has universal coordinates 3468830..3738990 Chromosome chrVII has universal coordinates 3738991..4829930 Chromosome chrVIII has universal coordinates 4829931..5392573 Chromosome chrIX has universal coordinates 5392574..5832461 Chromosome chrX has universal coordinates 5832462..6578212 Chromosome chrXI has universal coordinates 6578213..7245028 Chromosome chrXII has universal coordinates 7245029..8323205 Chromosome chrXIII has universal coordinates 8323206..9247636 Chromosome chrXIV has universal coordinates 9247637..10031969 Chromosome chrXV has universal coordinates 10031970..11123260 Chromosome chrXVI has universal coordinates 11123261..12071326 Chromosome chrM has universal coordinates 12071327..12157105 Writing IIT file header information...coordinates require 4 bytes each...done Processing null division/chromosome...sorting...writing...done (17 intervals) Writing IIT file footer information...done Writing IIT file header information...coordinates require 4 bytes each...done Processing null division/chromosome...sorting...writing...done (17 intervals) Writing IIT file footer information...done Running /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//gmap_process -c ./yeast.coords "/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpE2qvEU/gmap_build_fasta70ce510f2d37" | /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//gmapindex -d yeast -F . -D . -G Genome length is 12242884 nt Trying to allocate 1147773*4 bytes of memory...succeeded. Building genome in memory. Reading coordinates from file ./yeast.coords Writing contig chrI to universal coordinates 1..230218 in genome yeast Writing contig chrII to universal coordinates 230219..1043402 in genome yeast Writing contig chrIII to universal coordinates 1043403..1360022 in genome yeast Writing contig chrIV to universal coordinates 1360023..2891955 in genome yeast Writing contig chrV to universal coordinates 2891956..3468829 in genome yeast Writing contig chrVI to universal coordinates 3468830..3738990 in genome yeast Writing contig chrVII to universal coordinates 3738991..4829930 in genome yeast Writing contig chrVIII to universal coordinates 4829931..5392573 in genome yeast Writing contig chrIX to universal coordinates 5392574..5832461 in genome yeast Writing contig chrX to universal coordinates 5832462..6578212 in genome yeast Writing contig chrXI to universal coordinates 6578213..7245028 in genome yeast Writing contig chrXII to universal coordinates 7245029..8323205 in genome yeast Writing contig chrXIII to universal coordinates 8323206..9247636 in genome yeast Writing contig chrXIV to universal coordinates 9247637..10031969 in genome yeast Writing contig chrXV to universal coordinates 10031970..11123260 in genome yeast Writing contig chrXVI to universal coordinates 11123261..12071326 in genome yeast Writing contig chrM to universal coordinates 12071327..12157105 in genome yeast Chromosome chrM is circular. Copying 12071327..12157105 to 12157106..12242884 A total of 0 non-ACGTNX characters were seen in the genome. Running cat ./yeast.genomecomp | /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//gmapindex -d yeast -U > ./yeast.genomebits Running cat ./yeast.genomecomp | /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//gmapindex -b 12 -k 12 -q 3 -d yeast -F . -D . -O Note: since base size is equal to the k-mer size 12, offsets will not be compressed Offset compression types: Allocating 16777217*4 bytes for offsets Indexing offsets of oligomers in genome yeast (12 bp every 3 bp), position 0 Writing 16777217 offsets to file with total of 4080904 k-mers...done Running cat ./yeast.genomecomp | /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//gmapindex -b 12 -k 12 -q 3 -d yeast -F . -D . -P Looking for index files in directory . (offsets not compressed) Offsets file is yeast.ref123offsets Positions file is yeast.ref123positions Trying to allocate 4080904*4 bytes of memory...succeeded. Building positions in memory. Indexing positions of oligomers in genome yeast (12 bp every 3 bp), position 0 Writing 4080904 genomic positions to file ./yeast.ref123positions ... Running /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gmapR/usr/bin//gmapindex -d yeast -F . -D . -S SACA_K called with n = 12242885, K = 5, level 0 SACA_K called with n = 3442582, K = 0, level 1 SACA_K called with n = 1091915, K = 0, level 2 SACA_K called with n = 355699, K = 0, level 3 SACA_K called with n = 115942, K = 0, level 4 SACA_K called with n = 37652, K = 0, level 5 SACA_K called with n = 12156, K = 0, level 6 SACA_K called with n = 4037, K = 0, level 7 SACA_K called with n = 1305, K = 0, level 8 Computing lcp...done Computing saindex...done Copying files to directory /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpE2qvEU/66073/yeast Creating package in /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpE2qvEU/50224/GmapGenome.Scerevisiae.UCSC.sacCer3 RUNIT TEST PROTOCOL -- Mon Aug 26 21:42:51 2024 *********************************************** Number of test functions: 26 Number of errors: 0 Number of failures: 0 1 Test Suite : gmapR RUnit Tests - 26 test functions, 0 errors, 0 failures Number of test functions: 26 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 27.001 1.612 93.144
gmapR.Rcheck/gmapR-Ex.timings
name | user | system | elapsed | |
GmapGenome-class | 0.000 | 0.001 | 0.000 | |
GmapGenomeDirectory-class | 0.001 | 0.000 | 0.001 | |
TP53Genome | 0.002 | 0.001 | 0.004 | |
cmetindex | 0 | 0 | 0 | |
gmap_build-methods | 0 | 0 | 0 | |
makeGmapGenomePackage | 0 | 0 | 0 | |