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This page was generated on 2025-04-01 18:16 -0400 (Tue, 01 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 871
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Package 174/217HostnameOS / ArchINSTALLBUILDCHECK
Rhtslib 3.3.2  (landing page)
Hervé Pagès
Snapshot Date: 2025-04-01 18:00 -0400 (Tue, 01 Apr 2025)
git_url: https://git.bioconductor.org/packages/Rhtslib
git_branch: devel
git_last_commit: 90f07ae
git_last_commit_date: 2025-03-05 01:33:30 -0400 (Wed, 05 Mar 2025)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  ERROR    ERROR  skipped

INSTALL results for Rhtslib on teran2

To the developers/maintainers of the Rhtslib package:
- 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.

raw results


Summary

Package: Rhtslib
Version: 3.3.2
Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL Rhtslib
StartedAt: 2025-04-01 18:04:21 -0400 (Tue, 01 Apr 2025)
EndedAt: 2025-04-01 18:04:29 -0400 (Tue, 01 Apr 2025)
EllapsedTime: 7.5 seconds
RetCode: 1
Status:   ERROR  

Command output

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###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL Rhtslib
###
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘Rhtslib’ ...
** this is package ‘Rhtslib’ version ‘3.3.2’
** 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 '/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/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 -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c
gcc -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c
gcc -g -O2 -Wall -Werror=format-security -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 -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c
gcc -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c
gcc -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c
gcc -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o header.o header.c
gcc -g -O2 -Wall -Werror=format-security -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 -Werror=format-security -fpic -fvisibility=hidden' \
'-L/usr/local/lib -fvisibility=hidden' \
'-lz -lm -lbz2 -llzma -lcurl' > config_vars.h
gcc -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c
hts.c:4969:1: fatal error: error writing to /tmp/ccfgdefN.s: No space left on device
 4969 | }                                                                  /* H.P. */
      | ^
compilation terminated.
make[1]: *** [Makefile.Rhtslib:160: hts.o] Error 1
make[1]: Leaving directory '/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/Rhtslib/src/htslib-1.18'
make: *** [Makevars.common:22: htslib] Error 2
ERROR: compilation failed for package ‘Rhtslib’
* removing ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhtslib’
* restoring previous ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhtslib’