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This page was generated on 2023-10-20 09:38:10 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 1713/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rhtslib 2.2.0  (landing page)
Hervé Pagès
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/Rhtslib
git_branch: RELEASE_3_17
git_last_commit: ac2e2a6
git_last_commit_date: 2023-04-25 10:37:54 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

BUILD BIN results for Rhtslib on kjohnson2


To the developers/maintainers of the Rhtslib package:
- 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: Rhtslib
Version: 2.2.0
Command: rm -rf Rhtslib.buildbin-libdir && mkdir Rhtslib.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rhtslib_2.2.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Rhtslib.buildbin-libdir
StartedAt: 2023-10-19 16:29:42 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 16:31:10 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 87.7 seconds
RetCode: 0
Status:   OK  
PackageFile: Rhtslib_2.2.0.tgz
PackageFileSize: 2.959 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Rhtslib.buildbin-libdir && mkdir Rhtslib.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rhtslib_2.2.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Rhtslib.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rhtslib.buildbin-libdir Rhtslib_2.2.0.tar.gz'
>>>>>>> 

* installing *source* package ‘Rhtslib’ ...
** using non-staged installation via StagedInstall field
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
cd "htslib-1.15.1" && make -f "Makefile.Rhtslib"
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.o bcf_sr_sort.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o header.o header.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o hfile.o hfile.c
echo '#define HTS_VERSION_TEXT "1.15.1"' > version.h
echo '#define HTS_CC "clang -arch arm64"' > config_vars.h
echo '#define HTS_CPPFLAGS "-I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64"' >> config_vars.h
echo '#define HTS_CFLAGS "-falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden"' >> config_vars.h
echo '#define HTS_LDFLAGS "-L/opt/R/arm64/lib -fvisibility=hidden"' >> config_vars.h
echo '#define HTS_LIBS "-lz -lm -lbz2 -llzma -lcurl"' >> config_vars.h
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o hts_expr.o hts_expr.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o region.o region.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.o synced_bcf_reader.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.o cram/cram_codecs.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.o cram/cram_decode.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.o cram/cram_encode.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.o cram/cram_external.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.o cram/cram_index.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.o cram/cram_io.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_stats.o cram/cram_stats.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.o cram/mFILE.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/open_trace_file.o cram/open_trace_file.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/pooled_alloc.o cram/pooled_alloc.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.o cram/string_alloc.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o hfile_libcurl.o hfile_libcurl.c
ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o hfile_libcurl.o
ranlib libhts.a
clang -arch arm64 -dynamiclib -install_name /usr/local/lib/libhts.3.dylib -current_version 3.1.15 -compatibility_version 3.1.15 -L/opt/R/arm64/lib -fvisibility=hidden -o libhts.dylib kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o hfile_libcurl.o -lz -lm -lbz2 -llzma -lcurl
ln -sf libhts.dylib libhts.3.dylib
mkdir -p "/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/Rhtslib.buildbin-libdir/Rhtslib/include/htslib"
cd "htslib-1.15.1/htslib" && cp * "/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/Rhtslib.buildbin-libdir/Rhtslib/include/htslib"
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/Rhtslib.buildbin-libdir/Rhtslib/include" -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_Rhtslib.c -o R_init_Rhtslib.o
mkdir -p "/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/Rhtslib.buildbin-libdir/Rhtslib/usrlib"
cd "htslib-1.15.1" && cp libhts.a "/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/Rhtslib.buildbin-libdir/Rhtslib/usrlib"
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o Rhtslib.so R_init_Rhtslib.o /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/Rhtslib.buildbin-libdir/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
mkdir -p "/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/Rhtslib.buildbin-libdir/Rhtslib/testdata/tabix"
cd "htslib-1.15.1/test" && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/Rhtslib.buildbin-libdir/Rhtslib/testdata" 2>/dev/null || true) && cd tabix && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/Rhtslib.buildbin-libdir/Rhtslib/testdata/tabix" 2>/dev/null || true)
installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/Rhtslib.buildbin-libdir/Rhtslib/libs
** R
** 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
* DONE (Rhtslib)


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

>>>>>>> Paths before fix:
Rhtslib.buildbin-libdir/Rhtslib/libs/Rhtslib.so:
	Rhtslib.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/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/4.3-arm64/Resources/lib/libgcc_s.1.1.dylib" "Rhtslib.buildbin-libdir/Rhtslib/libs/Rhtslib.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "Rhtslib.buildbin-libdir/Rhtslib/libs/Rhtslib.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "Rhtslib.buildbin-libdir/Rhtslib/libs/Rhtslib.so"

>>>>>>> Paths after fix:

Rhtslib.buildbin-libdir/Rhtslib/libs/Rhtslib.so:
	Rhtslib.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/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)