Package: Rhtslib

Version: 1.15.5

Command: rm -rf Rhtslib.buildbin-libdir && mkdir Rhtslib.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rhtslib_1.15.5.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Rhtslib.buildbin-libdir

StartedAt: 2019-04-09 07:39:31 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 07:40:17 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 45.8 seconds

RetCode: 0

Status:  OK

PackageFile: Rhtslib_1.15.5.tgz

PackageFileSize: 2.154 MiB

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### Running command:
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###   rm -rf Rhtslib.buildbin-libdir && mkdir Rhtslib.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rhtslib_1.15.5.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Rhtslib.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rhtslib.buildbin-libdir Rhtslib_1.15.5.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:166: warning: ignoring old commands for target `.c.o'
clang -g -Wall -O2 -I.  -c -o kfunc.o kfunc.c
clang -g -Wall -O2 -I.  -c -o knetfile.o knetfile.c
clang -g -Wall -O2 -I.  -c -o kstring.o kstring.c
clang -g -Wall -O2 -I.  -c -o bcf_sr_sort.o bcf_sr_sort.c
clang -g -Wall -O2 -I.  -c -o bgzf.o bgzf.c
clang -g -Wall -O2 -I.  -c -o errmod.o errmod.c
clang -g -Wall -O2 -I.  -c -o faidx.o faidx.c
clang -g -Wall -O2 -I.  -c -o hfile.o hfile.c
clang -g -Wall -O2 -I.  -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.7"' > version.h
clang -g -Wall -O2 -I.  -c -o hts.o hts.c
clang -g -Wall -O2 -I.  -c -o hts_os.o hts_os.c
clang -g -Wall -O2 -I.  -c -o md5.o md5.c
clang -g -Wall -O2 -I.  -c -o multipart.o multipart.c
clang -g -Wall -O2 -I.  -c -o probaln.o probaln.c
clang -g -Wall -O2 -I.  -c -o realn.o realn.c
clang -g -Wall -O2 -I.  -c -o regidx.o regidx.c
clang -g -Wall -O2 -I.  -c -o sam.o sam.c
clang -g -Wall -O2 -I.  -c -o synced_bcf_reader.o synced_bcf_reader.c
clang -g -Wall -O2 -I.  -c -o vcf_sweep.o vcf_sweep.c
clang -g -Wall -O2 -I.  -c -o tbx.o tbx.c
clang -g -Wall -O2 -I.  -c -o textutils.o textutils.c
clang -g -Wall -O2 -I.  -c -o thread_pool.o thread_pool.c
clang -g -Wall -O2 -I.  -c -o vcf.o vcf.c
clang -g -Wall -O2 -I.  -c -o vcfutils.o vcfutils.c
clang -g -Wall -O2 -I.  -c -o cram/cram_codecs.o cram/cram_codecs.c
clang -g -Wall -O2 -I.  -c -o cram/cram_decode.o cram/cram_decode.c
clang -g -Wall -O2 -I.  -c -o cram/cram_encode.o cram/cram_encode.c
clang -g -Wall -O2 -I.  -c -o cram/cram_external.o cram/cram_external.c
clang -g -Wall -O2 -I.  -c -o cram/cram_index.o cram/cram_index.c
clang -g -Wall -O2 -I.  -c -o cram/cram_io.o cram/cram_io.c
clang -g -Wall -O2 -I.  -c -o cram/cram_samtools.o cram/cram_samtools.c
clang -g -Wall -O2 -I.  -c -o cram/cram_stats.o cram/cram_stats.c
clang -g -Wall -O2 -I.  -c -o cram/files.o cram/files.c
clang -g -Wall -O2 -I.  -c -o cram/mFILE.o cram/mFILE.c
clang -g -Wall -O2 -I.  -c -o cram/open_trace_file.o cram/open_trace_file.c
clang -g -Wall -O2 -I.  -c -o cram/pooled_alloc.o cram/pooled_alloc.c
clang -g -Wall -O2 -I.  -c -o cram/rANS_static.o cram/rANS_static.c
clang -g -Wall -O2 -I.  -c -o cram/sam_header.o cram/sam_header.c
clang -g -Wall -O2 -I.  -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  -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 -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" -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"