Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
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 560/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DiffBind 3.15.0 (landing page) Rory Stark
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the DiffBind package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DiffBind.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: DiffBind |
Version: 3.15.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DiffBind.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DiffBind_3.15.0.tar.gz |
StartedAt: 2024-08-26 20:53:28 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 20:57:02 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 213.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DiffBind.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DiffBind.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DiffBind_3.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/DiffBind.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 ‘DiffBind/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DiffBind’ version ‘3.15.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘DiffBind’ can be installed ... OK * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... NOTE installed size is 5.3Mb sub-directories of 1Mb or more: data 2.0Mb extra 1.3Mb libs 1.1Mb * 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 ... OK * 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... NOTE checkRd: (-1) NEWS.Rd:106-115: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:431-438: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:440-446: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:450-456: Lost braces in \itemize; meant \describe ? checkRd: (-1) DiffBind3.Rd:96-98: Lost braces in \itemize; meant \describe ? checkRd: (-1) DiffBind3.Rd:99-101: Lost braces in \itemize; meant \describe ? checkRd: (-1) DiffBind3.Rd:102-104: Lost braces in \itemize; meant \describe ? checkRd: (-1) DiffBind3.Rd:126-127: Lost braces in \itemize; meant \describe ? checkRd: (-1) DiffBind3.Rd:128-132: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:54-55: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:56: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:57: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:58: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:59: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:60: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:61: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:62: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:63: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:64: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:65-66: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:67-69: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:71: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:72: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:73: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:74: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:75: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:76: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:77: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:78: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:80-81: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:82: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:83: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:84-86: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:101: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:102-103: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:104-105: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:106-107: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:108-110: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:111-113: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:114-115: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:116-117: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:118-119: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:120-121: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:122-123: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.analyze.Rd:56: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.analyze.Rd:57: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.analyze.Rd:58-59: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.analyze.Rd:94: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.analyze.Rd:95: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.analyze.Rd:96-97: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.blacklist.Rd:37: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.blacklist.Rd:38: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.blacklist.Rd:39: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.blacklist.Rd:40: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.blacklist.Rd:41: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.blacklist.Rd:42: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.blacklist.Rd:43: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.blacklist.Rd:44: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.blacklist.Rd:45: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.blacklist.Rd:46: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.blacklist.Rd:107: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.blacklist.Rd:108: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.blacklist.Rd:109: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:31: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:32-33: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:45-46: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:48-49: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:51-53: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:55-60: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:62-64: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:66-67: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:69-71: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:83: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:85: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:87-90: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:92-95: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:217-219: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:221: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:223-226: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:228: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:233-234: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:236-237: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:253: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:255: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:257-258: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:267-268: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:270-271: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:85: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:86: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:87: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:88: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:89: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:90: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:91: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:92: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:93: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:94: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:95: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:102: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:103: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:104: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:105: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:106: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:107: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:108: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:109: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:110: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:111: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:112: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.plotHeatmap.Rd:148: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.plotHeatmap.Rd:149: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.plotHeatmap.Rd:150: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.plotProfile.rd:50-51: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.plotProfile.rd:53-56: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.plotProfile.rd:58-62: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.plotProfile.rd:64-68: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.plotProfile.rd:70-71: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:47: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:50: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:53-54: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:57-58: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:61: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:64-66: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:69-71: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:74-75: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:78: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:81-82: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:85-86: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:89-90: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:102-109: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:112-113: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:116-120: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:123-127: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:130-133: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:136-139: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:142-145: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:148-150: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:153-155: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:158-159: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:162-163: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:166-167: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:170-171: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:174-175: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:178-180: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:183-185: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:188-190: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:193-195: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:198-200: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:203-204: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:207-208: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:211-212: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:215-216: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:219-220: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:223-224: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:227-228: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:231-232: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:235-236: Lost braces in \itemize; meant \describe ? * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/DiffBind/libs/DiffBind.so’: Found ‘___assert_rtn’, possibly from ‘assert’ (C) Found ‘___stderrp’, possibly from ‘stderr’ (C) Found ‘___stdoutp’, possibly from ‘stdout’ (C) Found ‘_abort’, possibly from ‘abort’ (C) Found ‘_exit’, possibly from ‘exit’ (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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed dba.contrast 11.127 0.231 11.361 dba.plotVenn 7.055 0.132 7.207 dba.normalize 6.157 0.110 6.271 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/DiffBind.Rcheck/00check.log’ for details.
DiffBind.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DiffBind ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘DiffBind’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bamReader.cpp -o bamReader.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bam_plbuf.c -o bam_plbuf.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bedReader.cpp -o bedReader.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bitBucket.cpp -o bitBucket.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c croi_func.cpp -o croi_func.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c croi_main.cpp -o croi_main.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c densitySet.cpp -o densitySet.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c iBucket.cpp -o iBucket.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c interval.cpp -o interval.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c intervalDensity.cpp -o intervalDensity.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c intervalNode.cpp -o intervalNode.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c intervalSet.cpp -o intervalSet.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c intervalTree.cpp -o intervalTree.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c merge.cpp -o merge.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c mergeOne.c -o mergeOne.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nodeGroup.cpp -o nodeGroup.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c peakOrder.cpp -o peakOrder.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c reader.cpp -o reader.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sequence.cpp -o sequence.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c util.cpp -o util.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o DiffBind.so RcppExports.o bamReader.o bam_plbuf.o bedReader.o bitBucket.o croi_func.o croi_main.o densitySet.o iBucket.o interval.o intervalDensity.o intervalNode.o intervalSet.o intervalTree.o merge.o mergeOne.o nodeGroup.o peakOrder.o reader.o sequence.o util.o /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-DiffBind/00new/DiffBind/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** 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 (DiffBind)
DiffBind.Rcheck/tests/testthat.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. > library(testthat) > library(DiffBind) Loading required package: GenomicRanges Loading required package: stats4 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 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: GenomeInfoDb Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars 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")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians >>> DiffBind 3.15.0 > > test_check("DiffBind") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 141 ] > > proc.time() user system elapsed 33.745 0.845 34.644
DiffBind.Rcheck/DiffBind-Ex.timings
name | user | system | elapsed | |
dba | 0.545 | 0.019 | 0.568 | |
dba.analyze | 3.881 | 0.088 | 3.971 | |
dba.blacklist | 2.251 | 0.024 | 2.282 | |
dba.contrast | 11.127 | 0.231 | 11.361 | |
dba.count | 0.557 | 0.027 | 0.585 | |
dba.load | 0.029 | 0.004 | 0.037 | |
dba.mask | 0.022 | 0.005 | 0.027 | |
dba.normalize | 6.157 | 0.110 | 6.271 | |
dba.overlap | 0.187 | 0.011 | 0.202 | |
dba.peakset | 0.376 | 0.026 | 0.406 | |
dba.plotBox | 0.158 | 0.007 | 0.165 | |
dba.plotHeatmap | 2.216 | 0.047 | 2.208 | |
dba.plotMA | 3.901 | 0.093 | 3.996 | |
dba.plotPCA | 0.428 | 0.014 | 0.442 | |
dba.plotProfile | 0.096 | 0.002 | 0.098 | |
dba.plotVenn | 7.055 | 0.132 | 7.207 | |
dba.plotVolcano | 1.401 | 0.035 | 1.437 | |
dba.report | 1.235 | 0.049 | 1.285 | |
dba.save | 0 | 0 | 0 | |
dba.show | 0.213 | 0.007 | 0.220 | |
print.DBA | 0.036 | 0.002 | 0.039 | |
tamoxifen | 0.212 | 0.014 | 0.228 | |