Bioconductor Package Maintainer
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/Rhtslib |
| Branch: RELEASE_3_9 |
| Last Commit: 3ed0b5d |
| Last Changed Date: 2019-09-27 00:55:03 -0400 (Fri, 27 Sep 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:55:05 -0400 (Wed, 16 Oct 2019).
| Package 1375/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Rhtslib 1.16.3 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | [ OK ] | |
| Package: Rhtslib |
| Version: 1.16.3 |
| Command: rm -rf Rhtslib.buildbin-libdir && mkdir Rhtslib.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rhtslib_1.16.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Rhtslib.buildbin-libdir |
| StartedAt: 2019-10-16 09:16:56 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 09:17:32 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 35.9 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: Rhtslib_1.16.3.tgz |
| PackageFileSize: 2.157 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf Rhtslib.buildbin-libdir && mkdir Rhtslib.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rhtslib_1.16.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Rhtslib.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rhtslib.buildbin-libdir Rhtslib_1.16.3.tar.gz' >>>>>>> * installing *source* package ‘Rhtslib’ ... ** using non-staged installation via StagedInstall field ** libs cd "htslib-1.7" && make -f "/Library/Frameworks/R.framework/Resources/etc/Makeconf" -f "Makefile.Rhtslib" Makefile.Rhtslib:128: warning: overriding commands for target `.c.o' /Library/Frameworks/R.framework/Resources/etc/Makeconf:167: warning: ignoring old commands for target `.c.o' clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o knetfile.o knetfile.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.o bcf_sr_sort.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile.o hfile.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.7"' > version.h clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.o synced_bcf_reader.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.o cram/cram_codecs.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.o cram/cram_decode.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.o cram/cram_encode.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.o cram/cram_external.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.o cram/cram_index.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.o cram/cram_io.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_samtools.o cram/cram_samtools.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_stats.o cram/cram_stats.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/files.o cram/files.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.o cram/mFILE.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/open_trace_file.o cram/open_trace_file.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/pooled_alloc.o cram/pooled_alloc.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/rANS_static.o cram/rANS_static.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/sam_header.o cram/sam_header.c clang -Wall -g -O2 -fpic -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.o cram/string_alloc.c ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.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_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o ranlib libhts.a clang -dynamiclib -install_name /usr/local/lib/libhts.2.dylib -current_version 1.7 -compatibility_version 2 -L/usr/local/lib -o libhts.dylib kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.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_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o -lz -lm -lbz2 -llzma ln -sf libhts.dylib libhts.2.dylib mkdir -p "/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include/htslib" cd "htslib-1.7/htslib" && cp * "/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include/htslib" && cd .. && cp textutils_internal.h hts_internal.h "/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include" clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/zlibbioc/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c R_init_Rhtslib.c -o R_init_Rhtslib.o mkdir -p "/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/usrlib" cd "htslib-1.7" && cp libhts.a "/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/usrlib" clang -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-3.9-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/usrlib/libhts.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation mkdir -p "/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/testdata/tabix" cd "htslib-1.7/test" && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/Users/biocbuild/bbs-3.9-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-3.9-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/testdata/tabix" 2>/dev/null || true) installing to /Users/biocbuild/bbs-3.9-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/3.6/Resources/lib/libgcc_s.1.dylib" "Rhtslib.buildbin-libdir/Rhtslib/libs//Rhtslib.so" install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "Rhtslib.buildbin-libdir/Rhtslib/libs//Rhtslib.so" install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.5.2.dylib" "Rhtslib.buildbin-libdir/Rhtslib/libs//Rhtslib.so" install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "Rhtslib.buildbin-libdir/Rhtslib/libs//Rhtslib.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "Rhtslib.buildbin-libdir/Rhtslib/libs//Rhtslib.so"