Hervé Pagès
| Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/Rhtslib |
| git_branch: RELEASE_3_18 |
| git_last_commit: 33bf5d1 |
| git_last_commit_date: 2024-01-18 13:15:54 -0400 (Thu, 18 Jan 2024) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-29 11:37:13 -0400 (Fri, 29 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
| 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 1745/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rhtslib 2.4.1 (landing page) Hervé Pagès
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 2.4.1 |
| Command: set _R_INSTALL_TIME_PATCHES_=no&& rm -rf Rhtslib.buildbin-libdir && mkdir Rhtslib.buildbin-libdir && F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL --build --library=Rhtslib.buildbin-libdir Rhtslib_2.4.1.tar.gz |
| StartedAt: 2024-03-28 07:36:34 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 07:37:53 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 79.8 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: Rhtslib_2.4.1.zip |
| PackageFileSize: 5.751 MiB |
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###
### Running command:
###
### set _R_INSTALL_TIME_PATCHES_=no&& rm -rf Rhtslib.buildbin-libdir && mkdir Rhtslib.buildbin-libdir && F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL --build --library=Rhtslib.buildbin-libdir Rhtslib_2.4.1.tar.gz
###
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* installing *source* package 'Rhtslib' ...
** using non-staged installation via StagedInstall field
** libs
using C compiler: 'gcc.exe (GCC) 12.3.0'
cd "htslib-1.15.1" && /usr/bin/make -f "Makefile.Rhtslib.win"
make[1]: Entering directory '/f/biocbuild/bbs-3.18-bioc/tmpdir/RtmpkXWE9o/R.INSTALL28c832ff1b46/Rhtslib/src/htslib-1.15.1'
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o kfunc.o kfunc.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o kstring.o kstring.c
gcc -O2 -Wall -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 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o bgzf.o bgzf.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o errmod.o errmod.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o faidx.o faidx.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o header.o header.c
gcc -O2 -Wall -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 -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 -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex"' >> config_vars.h
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o hts.o hts.c
gcc -O2 -Wall -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 -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 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o md5.o md5.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o multipart.o multipart.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o probaln.o probaln.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o realn.o realn.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o regidx.o regidx.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o region.o region.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o sam.o sam.c
gcc -O2 -Wall -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 -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 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o tbx.o tbx.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o textutils.o textutils.c
gcc -O2 -Wall -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 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o vcf.o vcf.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o vcfutils.o vcfutils.c
gcc -O2 -Wall -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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
In file included from htscodecs/htscodecs/rANS_static4x16pr.c:74:
In function 'RansEncFlush',
inlined from 'rans_compress_O1_4x16.isra' at htscodecs/htscodecs/rANS_static4x16pr.c:840:5:
htscodecs/htscodecs/rANS_word.h:109:9: warning: 'ptr' may be used uninitialized [-Wmaybe-uninitialized]
109 | ptr -= 4;
| ~~~~^~~~
htscodecs/htscodecs/rANS_static4x16pr.c: In function 'rans_compress_O1_4x16.isra':
htscodecs/htscodecs/rANS_static4x16pr.c:793:14: note: 'ptr' was declared here
793 | uint8_t* ptr = out_end;
| ^~~
gcc -O2 -Wall -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 -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 -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 -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o hfile_libcurl.o hfile_libcurl.c
hfile_libcurl.c: In function 'libcurl_open':
hfile_libcurl.c:1335:9: warning: 'CURLINFO_CONTENT_LENGTH_DOWNLOAD' is deprecated: since 7.55.0. Use CURLINFO_CONTENT_LENGTH_DOWNLOAD_T [-Wdeprecated-declarations]
1335 | if (curl_easy_getinfo(fp->easy, CURLINFO_CONTENT_LENGTH_DOWNLOAD,
| ^~
In file included from hfile_libcurl.c:47:
c:\rtools43\x86_64-w64-mingw32.static.posix\include\curl\curl.h:2874:3: note: declared here
2874 | CURLINFO_CONTENT_LENGTH_DOWNLOAD
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
make[1]: Leaving directory '/f/biocbuild/bbs-3.18-bioc/tmpdir/RtmpkXWE9o/R.INSTALL28c832ff1b46/Rhtslib/src/htslib-1.15.1'
mkdir -p "F:/biocbuild/bbs-3.18-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/usrlib/x64"
cd "htslib-1.15.1" && cp libhts.a "F:/biocbuild/bbs-3.18-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/usrlib/x64"
mkdir -p "F:/biocbuild/bbs-3.18-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include/htslib"
cd "htslib-1.15.1/htslib" && cp * "F:/biocbuild/bbs-3.18-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include/htslib"
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"F:/biocbuild/bbs-3.18-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include" -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_Rhtslib.c -o R_init_Rhtslib.o
mkdir -p "F:/biocbuild/bbs-3.18-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/testdata/tabix"
cd "htslib-1.15.1/test" && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "F:/biocbuild/bbs-3.18-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/testdata" 2>/dev/null || true) && cd tabix && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "F:/biocbuild/bbs-3.18-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/testdata/tabix" 2>/dev/null || true)
gcc -shared -s -static-libgcc -o Rhtslib.dll tmp.def R_init_Rhtslib.o F:/biocbuild/bbs-3.18-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/usrlib/x64/libhts.a -lz -lm -lbz2 -llzma -lcurl -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.18-bioc/meat/Rhtslib.buildbin-libdir/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
* MD5 sums
packaged installation of 'Rhtslib' as Rhtslib_2.4.1.zip
* DONE (Rhtslib)