Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 1735/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Rhtslib 3.3.1 (landing page) Hervé Pagès
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
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: 3.3.1 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL Rhtslib |
StartedAt: 2024-12-23 15:04:27 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 15:06:01 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 93.4 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL Rhtslib ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘Rhtslib’ ... ** using non-staged installation via StagedInstall field ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ cd "htslib-1.18" && make -f "Makefile.Rhtslib" make[1]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/Rhtslib/src/htslib-1.18' echo '/* Default config.h generated by Makefile */' > config.h echo '#ifndef _XOPEN_SOURCE' >> config.h echo '#define _XOPEN_SOURCE 600' >> config.h echo '#endif' >> config.h echo '#define HAVE_LIBBZ2 1' >> config.h echo '#define HAVE_LIBLZMA 1' >> config.h echo '#ifndef __APPLE__' >> config.h echo '#define HAVE_LZMA_H 1' >> config.h echo '#endif' >> config.h echo '#define HAVE_LIBCURL 1' >> config.h if [ "x" != "x" ] && \ [ "x" != "x" ] && \ [ "x" != "x" ]; then \ echo '#define HAVE_POPCNT 1' >> config.h ; \ echo '#define HAVE_SSE4_1 1' >> config.h ; \ echo '#define HAVE_SSSE3 1' >> config.h ; \ echo '#if defined(HTS_ALLOW_UNALIGNED) && HTS_ALLOW_UNALIGNED == 0' >> config.h ; \ echo '#define UBSAN 1' >> config.h ; \ echo '#endif' >> config.h ; \ fi if [ "x" != "x" ] ; then \ echo '#define HAVE_AVX2 1' >> config.h ; \ fi if [ "x" != "x" ] ; then \ echo '#define HAVE_AVX512 1' >> config.h ; \ fi gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -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 -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o header.o header.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile.o hfile.c echo '#define HTS_VERSION_TEXT "1.18"' > version.h printf '#define HTS_CC "%s"\n#define HTS_CPPFLAGS "%s"\n#define HTS_CFLAGS "%s"\n#define HTS_LDFLAGS "%s"\n#define HTS_LIBS "%s"\n' \ 'gcc' \ '-I/usr/local/include -D_FILE_OFFSET_BITS=64' \ '-g -O2 -Wall -fpic -fvisibility=hidden' \ '-L/usr/local/lib -fvisibility=hidden' \ '-lz -lm -lbz2 -llzma -lcurl' > config_vars.h gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_expr.o hts_expr.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o region.o region.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o sam_mods.o sam_mods.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -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 -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -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 -fvisibility=hidden -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 -fvisibility=hidden -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 -fvisibility=hidden -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 -fvisibility=hidden -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 -fvisibility=hidden -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 -fvisibility=hidden -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 -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.o cram/mFILE.c gcc -g -O2 -Wall -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 gcc -g -O2 -Wall -fpic -fvisibility=hidden -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 -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.o cram/string_alloc.c gcc -g -O2 -Wall -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 gcc -g -O2 -Wall -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 gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c gcc -g -O2 -Wall -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 gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c gcc -g -O2 -Wall -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 gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c gcc -g -O2 -Wall -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 gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c gcc -g -O2 -Wall -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 sam_mods.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_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o hfile_libcurl.o ranlib libhts.a gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kfunc.pico kfunc.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kstring.pico kstring.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -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 -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bgzf.pico bgzf.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o errmod.pico errmod.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o faidx.pico faidx.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o header.pico header.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile.pico hfile.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts.pico hts.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_expr.pico hts_expr.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_os.pico hts_os.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o md5.pico md5.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o multipart.pico multipart.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o probaln.pico probaln.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o realn.pico realn.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o regidx.pico regidx.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o region.pico region.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o sam.pico sam.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o sam_mods.pico sam_mods.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -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 -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.pico vcf_sweep.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o tbx.pico tbx.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o textutils.pico textutils.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o thread_pool.pico thread_pool.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf.pico vcf.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcfutils.pico vcfutils.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -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 -fvisibility=hidden -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 -fvisibility=hidden -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 -fvisibility=hidden -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 -fvisibility=hidden -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 -fvisibility=hidden -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 -fvisibility=hidden -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 -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.pico cram/mFILE.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -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 -fvisibility=hidden -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 -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.pico cram/string_alloc.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/arith_dynamic.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/fqzcomp_qual.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/htscodecs.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/pack.pico htscodecs/htscodecs/pack.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static4x16pr.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.pico htscodecs/htscodecs/rANS_static32x16pr_avx2.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.pico htscodecs/htscodecs/rANS_static32x16pr_avx512.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.pico htscodecs/htscodecs/rANS_static32x16pr_sse4.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.pico htscodecs/htscodecs/rANS_static32x16pr_neon.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr.pico htscodecs/htscodecs/rANS_static32x16pr.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rANS_static.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rle.pico htscodecs/htscodecs/rle.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/tokenise_name3.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/utils.pico htscodecs/htscodecs/utils.c gcc -g -O2 -Wall -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile_libcurl.pico hfile_libcurl.c gcc -shared -Wl,-soname,libhts.so.3 -Wl,-version-script,htslib.map -L/usr/local/lib -fvisibility=hidden -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico sam_mods.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_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/pack.pico htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static32x16pr_avx2.pico htscodecs/htscodecs/rANS_static32x16pr_avx512.pico htscodecs/htscodecs/rANS_static32x16pr_sse4.pico htscodecs/htscodecs/rANS_static32x16pr_neon.pico htscodecs/htscodecs/rANS_static32x16pr.pico htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rle.pico htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/utils.pico hfile_libcurl.pico -lz -lm -lbz2 -llzma -lcurl -lpthread ln -sf libhts.so libhts.so.3 sed -e '/^static_libs=/s/@static_LIBS@/-lz -lm -lbz2 -llzma -lcurl/;s#@[^-][^@]*@##g' htslib.pc.in > htslib.pc.tmp sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc make[1]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rhtslib/src/htslib-1.18' mkdir -p "/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include/htslib" cd "htslib-1.18/htslib" && cp * "/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include/htslib" gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include" -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c R_init_Rhtslib.c -o R_init_Rhtslib.o mkdir -p "/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/usrlib" cd "htslib-1.18" && cp libhts.so libhts.a "/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/usrlib" cd "/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/usrlib" && ln -s libhts.so libhts.so.2 gcc -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o Rhtslib.so R_init_Rhtslib.o /home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR mkdir -p "/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/testdata/tabix" cd "htslib-1.18/test" && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/testdata" 2>/dev/null || true) && cd tabix && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/testdata/tabix" 2>/dev/null || true) installing to /home/biocbuild/bbs-3.21-bioc/R/site-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)