Back to Rapid builds (Linux only) of a subset of BioC 3.23
Report updated every 6 hours

This page was generated on 2025-12-19 15:55 -0500 (Fri, 19 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-28 r88973) -- "Unsuffered Consequences" 926
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 182/230HostnameOS / ArchINSTALLBUILDCHECK
Rhtslib 3.7.0  (landing page)
Hervé Pagès
Snapshot Date: 2025-12-19 12:00 -0500 (Fri, 19 Dec 2025)
git_url: https://git.bioconductor.org/packages/Rhtslib
git_branch: devel
git_last_commit: 0dcad2a
git_last_commit_date: 2025-10-29 14:52:40 -0500 (Wed, 29 Oct 2025)
teran2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped

BUILD 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: 3.7.0
Command: /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data Rhtslib
StartedAt: 2025-12-19 13:15:34 -0500 (Fri, 19 Dec 2025)
EndedAt: 2025-12-19 13:16:08 -0500 (Fri, 19 Dec 2025)
EllapsedTime: 33.3 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data Rhtslib
###
##############################################################################
##############################################################################


* checking for file ‘Rhtslib/DESCRIPTION’ ... OK
* preparing ‘Rhtslib’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
      -----------------------------------
* installing *source* package ‘Rhtslib’ ...
** this is package ‘Rhtslib’ version ‘3.7.0’
** 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 '/tmp/Rtmpzom4vo/Rbuild195e68296836d7/Rhtslib/src/htslib-1.18'
gcc -std=gnu2x -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 -std=gnu2x -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 -std=gnu2x -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 -std=gnu2x -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 -std=gnu2x -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 -std=gnu2x -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 -std=gnu2x -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 -std=gnu2x -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 -std=gnu2x' \
'-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 -std=gnu2x -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
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_expr.o hts_expr.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o region.o region.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o sam_mods.o sam_mods.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.o cram/cram_decode.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.o cram/cram_encode.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.o cram/cram_external.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.o cram/cram_index.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.o cram/cram_io.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_stats.o cram/cram_stats.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.o cram/mFILE.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -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 -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.o cram/string_alloc.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -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 -std=gnu2x -g -O2 -Wall -Werror=format-security -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 -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -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 -std=gnu2x -g -O2 -Wall -Werror=format-security -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 -std=gnu2x -g -O2 -Wall -Werror=format-security -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 -std=gnu2x -g -O2 -Wall -Werror=format-security -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 -std=gnu2x -g -O2 -Wall -Werror=format-security -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 -std=gnu2x -g -O2 -Wall -Werror=format-security -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 -std=gnu2x -g -O2 -Wall -Werror=format-security -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 -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -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 -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -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
ar: libhts.a: error reading cram/cram_encode.o: No space left on device
make[1]: *** [Makefile.Rhtslib:317: libhts.a] Error 1
make[1]: Leaving directory '/tmp/Rtmpzom4vo/Rbuild195e68296836d7/Rhtslib/src/htslib-1.18'
make: *** [Makevars.common:22: htslib] Error 2
ERROR: compilation failed for package ‘Rhtslib’
* removing ‘/tmp/Rtmpzom4vo/Rinst195e6816ae995b/Rhtslib’
      -----------------------------------
ERROR: package installation failed