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 11:05:48 -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: set _R_INSTALL_TIME_PATCHES_=no&& F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL Rhtslib |
| StartedAt: 2023-04-10 15:30:25 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 15:31:42 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 76.2 seconds |
| RetCode: 0 |
| Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### set _R_INSTALL_TIME_PATCHES_=no&& F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL Rhtslib ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library' * installing *source* package 'Rhtslib' ... ** using non-staged installation via StagedInstall field ** libs cd "htslib-1.15.1" && /usr/bin/make -f "Makefile.Rhtslib.win" make[1]: Entering directory '/f/biocbuild/bbs-3.16-bioc/meat/Rhtslib/src/htslib-1.15.1' 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 gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o kfunc.o kfunc.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o kstring.o kstring.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o bgzf.o bgzf.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o errmod.o errmod.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o faidx.o faidx.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o header.o header.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o hfile.o hfile.c echo '#define HTS_VERSION_TEXT "1.15.1"' > version.h echo '#define HTS_CC "gcc"' > config_vars.h echo '#define HTS_CPPFLAGS "-D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB"' >> config_vars.h echo '#define HTS_CFLAGS "-O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden"' >> config_vars.h echo '#define HTS_LDFLAGS "-fvisibility=hidden"' >> config_vars.h echo '#define HTS_LIBS "-lz -lm -lbz2 -llzma -lcurl -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex"' >> config_vars.h gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o hts.o hts.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o hts_expr.o hts_expr.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o hts_os.o hts_os.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o md5.o md5.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o multipart.o multipart.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o probaln.o probaln.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o realn.o realn.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o regidx.o regidx.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o region.o region.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o sam.o sam.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o vcf_sweep.o vcf_sweep.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o tbx.o tbx.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o textutils.o textutils.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o thread_pool.o thread_pool.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o vcf.o vcf.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o vcfutils.o vcfutils.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_decode.o cram/cram_decode.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_encode.o cram/cram_encode.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_external.o cram/cram_external.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_index.o cram/cram_index.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_io.o cram/cram_io.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_stats.o cram/cram_stats.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/mFILE.o cram/mFILE.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/string_alloc.o cram/string_alloc.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -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 gcc -shared -Wl,--out-implib=hts.dll.a -Wl,--enable-auto-import -Wl,--exclude-all-symbols -fvisibility=hidden -o hts-3.dll -Wl,--whole-archive 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 -Wl,--no-whole-archive -lz -lm -lbz2 -llzma -lcurl -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -lpthread gendef hts-3.dll * [hts-3.dll] Found PE+ image dlltool -m i386:x86-64 -d hts-3.def -l hts-3.lib sed -e '/^static_libs=/s/@static_LIBS@/-lz -lm -lbz2 -llzma -lcurl -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex/;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 '/f/biocbuild/bbs-3.16-bioc/meat/Rhtslib/src/htslib-1.15.1' mkdir -p "F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/usrlib/x64" cd "htslib-1.15.1" && cp libhts.a "F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/usrlib/x64" mkdir -p "F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include/htslib" cd "htslib-1.15.1/htslib" && cp * "F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include/htslib" gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include" -I'F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_Rhtslib.c -o R_init_Rhtslib.o mkdir -p "F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/testdata/tabix" cd "htslib-1.15.1/test" && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/testdata" 2>/dev/null || true) && cd tabix && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/testdata/tabix" 2>/dev/null || true) gcc -shared -s -static-libgcc -o Rhtslib.dll tmp.def R_init_Rhtslib.o F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lz -lm -lbz2 -llzma -lcurl -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/libs/x64 ** 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)