Multiple platform build/check report for BioC 3.20 - BUILD BIN results for rtracklayer on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4501
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4761
palomino8	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4504
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4535
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4483
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4491
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*
BUILD BIN results for rtracklayer on kjohnson3

To the developers/maintainers of the rtracklayer package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rtracklayer.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.
raw results
Summary

Package: rtracklayer
Version: 1.65.0
Command: rm -rf rtracklayer.buildbin-libdir && mkdir rtracklayer.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh rtracklayer_1.65.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R rtracklayer.buildbin-libdir
StartedAt: 2024-10-28 06:00:54 -0400 (Mon, 28 Oct 2024)
EndedAt: 2024-10-28 06:01:15 -0400 (Mon, 28 Oct 2024)
EllapsedTime: 21.3 seconds
RetCode: 0
Status: OK
PackageFile: rtracklayer_1.65.0.tgz
PackageFileSize: 6.374 MiB
Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf rtracklayer.buildbin-libdir && mkdir rtracklayer.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh rtracklayer_1.65.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R rtracklayer.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=rtracklayer.buildbin-libdir rtracklayer_1.65.0.tar.gz'
>>>>>>> 

* installing *source* package ‘rtracklayer’ ...
** using staged installation
checking for pkg-config... /opt/R/arm64/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for OPENSSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c XVector_stubs.c -o XVector_stubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_rtracklayer.c -o R_init_rtracklayer.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c readGFF.c -o readGFF.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bbiHelper.c -o bbiHelper.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bigWig.c -o bigWig.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bigBedHelper.c -o bigBedHelper.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bigBed.c -o bigBed.o
bigBed.c:338:10: warning: variable 'extraIndexListEndOffset' set but not used [-Wunused-but-set-variable]
  bits64 extraIndexListEndOffset = 0;
         ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c chain_io.c -o chain_io.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c twoBit.c -o twoBit.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c handlers.c -o handlers.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c utils.c -o utils.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/memgfx.c -o ucsc/memgfx.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/binRange.c -o ucsc/binRange.o
ucsc/binRange.c:28:12: warning: unused function 'binFromRangeStandard' [-Wunused-function]
static int binFromRangeStandard(int start, int end)
           ^
ucsc/binRange.c:49:12: warning: unused function 'binFromRangeExtended' [-Wunused-function]
static int binFromRangeExtended(int start, int end)
           ^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/htmlColor.c -o ucsc/htmlColor.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/sqlList.c -o ucsc/sqlList.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/tokenizer.c -o ucsc/tokenizer.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/asParse.c -o ucsc/asParse.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/basicBed.c -o ucsc/basicBed.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/bigBed.c -o ucsc/bigBed.o
ucsc/bigBed.c:150:28: warning: unused function 'bigBedCoverageIntervals' [-Wunused-function]
static struct bbiInterval *bigBedCoverageIntervals(struct bbiFile *bbi,
                           ^
ucsc/bigBed.c:241:31: warning: unused function 'bigBedChunksMatchingName' [-Wunused-function]
static struct fileOffsetSize *bigBedChunksMatchingName(struct bbiFile *bbi, 
                              ^
ucsc/bigBed.c:252:31: warning: unused function 'bigBedChunksMatchingNames' [-Wunused-function]
static struct fileOffsetSize *bigBedChunksMatchingNames(struct bbiFile *bbi, 
                              ^
ucsc/bigBed.c:301:16: warning: unused function 'bbWordMatchesName' [-Wunused-function]
static boolean bbWordMatchesName(char *line, int fieldIx, void *target)
               ^
ucsc/bigBed.c:311:16: warning: unused function 'bbWordIsInHash' [-Wunused-function]
static boolean bbWordIsInHash(char *line, int fieldIx, void *target)
               ^
ucsc/bigBed.c:326:31: warning: unused function 'bigBedIntervalsMatchingName' [-Wunused-function]
static struct bigBedInterval *bigBedIntervalsMatchingName(struct bbiFile *bbi, 
                              ^
6 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
ucsc/bPlusTree.c:476:9: warning: variable 'slotsUsed' set but not used [-Wunused-but-set-variable]
    int slotsUsed = 0;
        ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/bbiRead.c -o ucsc/bbiRead.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
ucsc/bwgQuery.c:164:18: warning: variable 'blockEnd' set but not used [-Wunused-but-set-variable]
        char *blockPt, *blockEnd;
                        ^
ucsc/bwgQuery.c:47:12: warning: unused function 'bigWigBlockDumpIntersectingRange' [-Wunused-function]
static int bigWigBlockDumpIntersectingRange(boolean isSwapped, char *blockPt, char *blockEnd, 
           ^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c:530:13: warning: function 'rEnumerateBlocks' is not needed and will not be emitted [-Wunneeded-internal-declaration]
static void rEnumerateBlocks(struct cirTreeFile *crt, int level, bits64 indexFileOffset,
            ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/common.c -o ucsc/common.o
ucsc/common.c:249:13: 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]
        free(el);
            ^
ucsc/common.c:1900:14: warning: unused variable 'naStr' [-Wunused-variable]
static char *naStr = "n/a";
             ^
ucsc/common.c:1901:14: warning: unused variable 'emptyStr' [-Wunused-variable]
static char *emptyStr = "";
             ^
ucsc/common.c:1971:13: warning: unused function 'dateAdd' [-Wunused-function]
static void dateAdd(struct tm *tp,int addYears,int addMonths,int addDays)
            ^
4 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/dnaseq.c -o ucsc/dnaseq.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/dnautil.c -o ucsc/dnautil.o
ucsc/dnautil.c:465:12: warning: unused function 'findTailPolyAMaybeMask' [-Wunused-function]
static int findTailPolyAMaybeMask(DNA *dna, int size, boolean doMask,
           ^
ucsc/dnautil.c:521:12: warning: unused function 'findHeadPolyTMaybeMask' [-Wunused-function]
static int findHeadPolyTMaybeMask(DNA *dna, int size, boolean doMask,
           ^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/errAbort.c -o ucsc/errAbort.o
ucsc/errAbort.c:210:13: warning: unused function 'debugAbort' [-Wunused-function]
static void debugAbort()
            ^
ucsc/errAbort.c:218:13: warning: unused function 'warnAbortHandler' [-Wunused-function]
static void warnAbortHandler(char *format, va_list args)
            ^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/hash.c -o ucsc/hash.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/linefile.c -o ucsc/linefile.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/localmem.c -o ucsc/localmem.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/sqlNum.c -o ucsc/sqlNum.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/zlibFace.c -o ucsc/zlibFace.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/dystring.c -o ucsc/dystring.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/hmmstats.c -o ucsc/hmmstats.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c:14:12: warning: unused variable '_dotForUserMod' [-Wunused-variable]
static int _dotForUserMod = 100; /* How often does dotForUser() output a dot. */
           ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/pipeline.c -o ucsc/pipeline.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/rangeTree.c -o ucsc/rangeTree.o
ucsc/rangeTree.c:36:14: warning: unused function 'sumInt' [-Wunused-function]
static void *sumInt(void *a, void *b)
             ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/rbTree.c -o ucsc/rbTree.o
ucsc/rbTree.c:576:13: warning: function 'rTreeDump' is not needed and will not be emitted [-Wunneeded-internal-declaration]
static void rTreeDump(struct rbTreeNode *n)
            ^
ucsc/rbTree.c:674:13: warning: unused function 'addRef' [-Wunused-function]
static void addRef(void *item)
            ^
ucsc/rbTree.c:680:13: warning: unused function 'addRefWithContext' [-Wunused-function]
static void addRefWithContext(void *item, void *context)
            ^
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/memalloc.c -o ucsc/memalloc.o
ucsc/memalloc.c:220:13: warning: unused function 'carefulMemInit' [-Wunused-function]
static void carefulMemInit(size_t maxToAlloc)
            ^
ucsc/memalloc.c:314:26: warning: unused variable 'carefulMemHandler' [-Wunused-variable]
static struct memHandler carefulMemHandler = 
                         ^
ucsc/memalloc.c:348:13: warning: unused function 'memTrackerFree' [-Wunused-function]
static void memTrackerFree(void *vpt)
            ^
ucsc/memalloc.c:357:14: warning: unused function 'memTrackerRealloc' [-Wunused-function]
static void *memTrackerRealloc(void *vpt, size_t size)
             ^
4 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/dlist.c -o ucsc/dlist.o
ucsc/dlist.c:124:12: warning: unused function 'dlNodeCmp' [-Wunused-function]
static int dlNodeCmp(const void *elem1, const void *elem2)
           ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/filePath.c -o ucsc/filePath.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/htmlPage.c -o ucsc/htmlPage.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/udc.c -o ucsc/udc.o
ucsc/udc.c:1070:14: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
    while (c = *str++)
           ~~^~~~~~~~
ucsc/udc.c:1070:14: note: place parentheses around the assignment to silence this warning
    while (c = *str++)
             ^
           (         )
ucsc/udc.c:1070:14: note: use '==' to turn this assignment into an equality comparison
    while (c = *str++)
             ^
             ==
ucsc/udc.c:1083:60: warning: taking the absolute value of unsigned type 'unsigned long' has no effect [-Wabsolute-value]
    int total_size = url_size + floor(1.0 + log10((double) llabs(hash_id))) + 1;
                                                           ^
ucsc/udc.c:1083:60: note: remove the call to 'llabs' since unsigned values cannot be negative
    int total_size = url_size + floor(1.0 + log10((double) llabs(hash_id))) + 1;
                                                           ^~~~~
ucsc/udc.c:1273:13: warning: unused function 'qDecode' [-Wunused-function]
static void qDecode(const char *input, char *buf, size_t size)
            ^
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/net.c -o ucsc/net.o
ucsc/net.c:36:1: warning: non-void function does not return a value in all control paths [-Wreturn-type]
}
^
ucsc/net.c:57:1: warning: non-void function does not return a value in all control paths [-Wreturn-type]
}
^
ucsc/net.c:168:22: warning: unused variable 'status' [-Wunused-variable]
            CURLcode status = wrapped_curl_request(curl, GET);
                     ^
ucsc/net.c:187:1: warning: non-void function does not return a value in all control paths [-Wreturn-type]
}
^
4 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/bits.c -o ucsc/bits.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/twoBit.c -o ucsc/twoBit.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/internet.c -o ucsc/internet.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/https.c -o ucsc/https.o
ucsc/https.c:22:22: warning: unused function 'openssl_id_callback' [-Wunused-function]
static unsigned long openssl_id_callback(void)
                     ^
ucsc/https.c:27:13: warning: unused function 'openssl_locking_callback' [-Wunused-function]
static void openssl_locking_callback(int mode, int n, const char * file, int line)
            ^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/base64.c -o ucsc/base64.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/verbose.c -o ucsc/verbose.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/os.c -o ucsc/os.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/wildcmp.c -o ucsc/wildcmp.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/_portimpl.c -o ucsc/_portimpl.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 rtracklayer.so S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_rtracklayer.o readGFF.o bbiHelper.o bigWig.o bigBedHelper.o bigBed.o chain_io.o twoBit.o handlers.o utils.o ucsc/memgfx.o ucsc/binRange.o ucsc/htmlColor.o ucsc/sqlList.o ucsc/tokenizer.o ucsc/asParse.o ucsc/basicBed.o ucsc/bigBed.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/errAbort.o ucsc/hash.o ucsc/linefile.o ucsc/localmem.o ucsc/sqlNum.o ucsc/zlibFace.o ucsc/dystring.o ucsc/hmmstats.o ucsc/obscure.o ucsc/pipeline.o ucsc/rangeTree.o ucsc/rbTree.o ucsc/memalloc.o ucsc/dlist.o ucsc/filePath.o ucsc/htmlPage.o ucsc/udc.o ucsc/net.o ucsc/bits.o ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -lz -pthread /opt/R/arm64/lib/libssl.a /opt/R/arm64/lib/libcrypto.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/rtracklayer.buildbin-libdir/00LOCK-rtracklayer/00new/rtracklayer/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘offset’ from package ‘stats’ in package ‘rtracklayer’
** 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 (rtracklayer)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR rtracklayer.buildbin-libdir/rtracklayer/libs/rtracklayer.so
>>>>>>> 

>>>>>>> Paths before fix:
rtracklayer.buildbin-libdir/rtracklayer/libs/rtracklayer.so:
	rtracklayer.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
	/usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "rtracklayer.buildbin-libdir/rtracklayer/libs/rtracklayer.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "rtracklayer.buildbin-libdir/rtracklayer/libs/rtracklayer.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "rtracklayer.buildbin-libdir/rtracklayer/libs/rtracklayer.so"

>>>>>>> Paths after fix:
rtracklayer.buildbin-libdir/rtracklayer/libs/rtracklayer.so:
	rtracklayer.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
	/usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)