Hervé Pagès
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/Rhtslib |
| git_branch: RELEASE_3_16 |
| git_last_commit: 1757333 |
| git_last_commit_date: 2022-11-01 11:11:11 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:06:23 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
To the developers/maintainers of the Rhtslib package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1675/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rhtslib 2.0.0 (landing page) Hervé Pagès
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: Rhtslib |
| Version: 2.0.0 |
| Command: rm -rf Rhtslib.buildbin-libdir && mkdir Rhtslib.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rhtslib_2.0.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Rhtslib.buildbin-libdir |
| StartedAt: 2023-04-11 00:00:27 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 00:01:17 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 49.6 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: Rhtslib_2.0.0.tgz |
| PackageFileSize: 3.095 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf Rhtslib.buildbin-libdir && mkdir Rhtslib.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rhtslib_2.0.0.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_2.0.0.tar.gz' >>>>>>> * installing *source* package ‘Rhtslib’ ... ** using non-staged installation via StagedInstall field ** libs cd "htslib-1.15.1" && make -f "Makefile.Rhtslib" clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.o bcf_sr_sort.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o header.o header.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/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 -mmacosx-version-min=10.13"' > config_vars.h echo '#define HTS_CPPFLAGS "-I/usr/local/include -D_FILE_OFFSET_BITS=64"' >> config_vars.h echo '#define HTS_CFLAGS "-Wall -g -O2 -fpic -fvisibility=hidden"' >> config_vars.h echo '#define HTS_LDFLAGS "-L/usr/local/lib -fvisibility=hidden"' >> config_vars.h echo '#define HTS_LIBS "-lz -lm -lbz2 -llzma -lcurl"' >> config_vars.h clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_expr.o hts_expr.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o region.o region.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.o synced_bcf_reader.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.o cram/cram_codecs.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.o cram/cram_decode.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.o cram/cram_encode.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.o cram/cram_external.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.o cram/cram_index.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.o cram/cram_io.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_stats.o cram/cram_stats.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.o cram/mFILE.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/open_trace_file.o cram/open_trace_file.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/pooled_alloc.o cram/pooled_alloc.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.o cram/string_alloc.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c clang -mmacosx-version-min=10.13 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/usr/local/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 -mmacosx-version-min=10.13 -dynamiclib -install_name /usr/local/lib/libhts.3.dylib -current_version 3.1.15 -compatibility_version 3.1.15 -L/usr/local/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 ld: warning: dylib (/usr/local/lib/liblzma.dylib) was built for newer macOS version (12.0) than being linked (10.13) ln -sf libhts.dylib libhts.3.dylib mkdir -p "/Users/biocbuild/bbs-3.16-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include/htslib" cd "htslib-1.15.1/htslib" && cp * "/Users/biocbuild/bbs-3.16-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include/htslib" clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Users/biocbuild/bbs-3.16-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include" -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c R_init_Rhtslib.c -o R_init_Rhtslib.o mkdir -p "/Users/biocbuild/bbs-3.16-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/usrlib" cd "htslib-1.15.1" && cp libhts.a "/Users/biocbuild/bbs-3.16-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/usrlib" clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Rhtslib.so R_init_Rhtslib.o /Users/biocbuild/bbs-3.16-bioc/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-3.16-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-3.16-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-3.16-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/testdata/tabix" 2>/dev/null || true) installing to /Users/biocbuild/bbs-3.16-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 LINKS FOR Rhtslib.buildbin-libdir/Rhtslib/libs/Rhtslib.so >>>>>>> install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib" "Rhtslib.buildbin-libdir/Rhtslib/libs/Rhtslib.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/lib/libquadmath.0.dylib" "Rhtslib.buildbin-libdir/Rhtslib/libs/Rhtslib.so"