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 12:06:14 -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: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL Rhtslib |
| StartedAt: 2019-10-15 18:09:51 -0400 (Tue, 15 Oct 2019) |
| EndedAt: 2019-10-15 18:11:08 -0400 (Tue, 15 Oct 2019) |
| EllapsedTime: 77.5 seconds |
| RetCode: 0 |
| Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL Rhtslib ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘Rhtslib’ ... ** using non-staged installation via StagedInstall field ** libs cd "htslib-1.7" && make -f "/home/biocbuild/bbs-3.9-bioc/R/etc/Makeconf" -f "Makefile.Rhtslib" make[1]: Entering directory '/home/biocbuild/bbs-3.9-bioc/meat/Rhtslib/src/htslib-1.7' Makefile.Rhtslib:128: warning: overriding recipe for target '.c.o' /home/biocbuild/bbs-3.9-bioc/R/etc/Makeconf:167: warning: ignoring old recipe for target '.c.o' echo '/* Default config.h generated by Makefile */' > config.h echo '#define HAVE_LIBBZ2 1' >> config.h echo '#define HAVE_LIBLZMA 1' >> config.h echo '#define HAVE_LZMA_H 1' >> config.h echo '#define HAVE_FSEEKO 1' >> config.h echo '#define HAVE_DRAND48 1' >> config.h gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o knetfile.o knetfile.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile.o hfile.c gcc -g -O2 -Wall -fpic -I. -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 gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.o cram/cram_decode.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.o cram/cram_encode.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.o cram/cram_external.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.o cram/cram_index.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.o cram/cram_io.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_samtools.o cram/cram_samtools.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_stats.o cram/cram_stats.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/files.o cram/files.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.o cram/mFILE.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/rANS_static.o cram/rANS_static.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/sam_header.o cram/sam_header.c gcc -g -O2 -Wall -fpic -I. -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 gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kfunc.pico kfunc.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o knetfile.pico knetfile.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kstring.pico kstring.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.pico bcf_sr_sort.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bgzf.pico bgzf.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o errmod.pico errmod.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o faidx.pico faidx.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile.pico hfile.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile_net.pico hfile_net.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts.pico hts.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_os.pico hts_os.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o md5.pico md5.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o multipart.pico multipart.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o probaln.pico probaln.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o realn.pico realn.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o regidx.pico regidx.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o sam.pico sam.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.pico vcf_sweep.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o tbx.pico tbx.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o textutils.pico textutils.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o thread_pool.pico thread_pool.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf.pico vcf.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcfutils.pico vcfutils.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.pico cram/cram_decode.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.pico cram/cram_encode.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.pico cram/cram_external.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.pico cram/cram_index.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.pico cram/cram_io.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_samtools.pico cram/cram_samtools.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_stats.pico cram/cram_stats.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/files.pico cram/files.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.pico cram/mFILE.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/rANS_static.pico cram/rANS_static.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/sam_header.pico cram/sam_header.c gcc -g -O2 -Wall -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.pico cram/string_alloc.c gcc -shared -Wl,-soname,libhts.so.2 -L/usr/local/lib -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico -lz -lm -lbz2 -llzma -lpthread ln -sf libhts.so libhts.so.2 make[1]: Leaving directory '/home/biocbuild/bbs-3.9-bioc/meat/Rhtslib/src/htslib-1.7' mkdir -p "/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include/htslib" cd "htslib-1.7/htslib" && cp * "/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include/htslib" && cd .. && cp textutils_internal.h hts_internal.h "/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I/usr/local/include -fpic -g -O2 -Wall -c R_init_Rhtslib.c -o R_init_Rhtslib.o mkdir -p "/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib" cd "htslib-1.7" && cp libhts.so libhts.a "/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib" cd "/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib" && ln -s libhts.so libhts.so.2 gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o Rhtslib.so R_init_Rhtslib.o /home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib/libhts.a -lz -lm -lbz2 -llzma -lpthread -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR mkdir -p "/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/testdata/tabix" cd "htslib-1.7/test" && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/testdata" 2>/dev/null || true) && cd tabix && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/testdata/tabix" 2>/dev/null || true) installing to /home/biocbuild/bbs-3.9-bioc/R/library/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)