Hervé Pagès
| Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/Rhtslib |
| git_branch: RELEASE_3_18 |
| git_last_commit: 33bf5d1 |
| git_last_commit_date: 2024-01-18 13:15:54 -0400 (Thu, 18 Jan 2024) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-29 11:38:09 -0400 (Fri, 29 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
| 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 1745/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rhtslib 2.4.1 (landing page) Hervé Pagès
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the Rhtslib package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rhtslib.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: Rhtslib |
| Version: 2.4.1 |
| Command: rm -rf Rhtslib.buildbin-libdir && mkdir Rhtslib.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rhtslib_2.4.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Rhtslib.buildbin-libdir |
| StartedAt: 2024-03-28 12:15:24 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 12:16:46 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 81.7 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: Rhtslib_2.4.1.tgz |
| PackageFileSize: 3.176 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf Rhtslib.buildbin-libdir && mkdir Rhtslib.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rhtslib_2.4.1.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_2.4.1.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 x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.o bcf_sr_sort.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o header.o header.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/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 x86_64"' > config_vars.h echo '#define HTS_CPPFLAGS "-I/opt/R/x86_64/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/x86_64/lib -fvisibility=hidden"' >> config_vars.h echo '#define HTS_LIBS "-lz -lm -lbz2 -llzma -lcurl"' >> config_vars.h clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o hts_expr.o hts_expr.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o region.o region.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.o synced_bcf_reader.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.o cram/cram_codecs.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.o cram/cram_decode.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.o cram/cram_encode.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.o cram/cram_external.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.o cram/cram_index.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.o cram/cram_io.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_stats.o cram/cram_stats.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.o cram/mFILE.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/open_trace_file.o cram/open_trace_file.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/pooled_alloc.o cram/pooled_alloc.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.o cram/string_alloc.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/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 x86_64 -dynamiclib -install_name /usr/local/lib/libhts.3.dylib -current_version 3.1.15 -compatibility_version 3.1.15 -L/opt/R/x86_64/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-3.18-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include/htslib" cd "htslib-1.15.1/htslib" && cp * "/Users/biocbuild/bbs-3.18-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include/htslib" clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Users/biocbuild/bbs-3.18-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include" -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_Rhtslib.c -o R_init_Rhtslib.o mkdir -p "/Users/biocbuild/bbs-3.18-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/usrlib" cd "htslib-1.15.1" && cp libhts.a "/Users/biocbuild/bbs-3.18-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/usrlib" clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o Rhtslib.so R_init_Rhtslib.o /Users/biocbuild/bbs-3.18-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation mkdir -p "/Users/biocbuild/bbs-3.18-bioc/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-3.18-bioc/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-3.18-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/testdata/tabix" 2>/dev/null || true) installing to /Users/biocbuild/bbs-3.18-bioc/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) /usr/lib/libbz2.1.0.dylib (compatibility version 1.0.0, current version 1.0.5) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11) /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.3) /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-x86_64/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-x86_64/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-x86_64/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) /usr/lib/libbz2.1.0.dylib (compatibility version 1.0.0, current version 1.0.5) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11) /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.3) /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)