Back to Rapid builds (Linux only) of a subset of BioC 3.21
Report updated every 6 hours

This page was generated on 2025-03-24 12:36 -0400 (Mon, 24 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 870
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 172/217HostnameOS / ArchINSTALLBUILDCHECK
rhdf5filters 1.19.2  (landing page)
Mike Smith
Snapshot Date: 2025-03-24 12:00 -0400 (Mon, 24 Mar 2025)
git_url: https://git.bioconductor.org/packages/rhdf5filters
git_branch: devel
git_last_commit: 9bda651
git_last_commit_date: 2025-03-24 11:10:54 -0400 (Mon, 24 Mar 2025)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  ERROR    ERROR  skipped


INSTALL results for rhdf5filters on teran2

To the developers/maintainers of the rhdf5filters 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: rhdf5filters
Version: 1.19.2
Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL rhdf5filters
StartedAt: 2025-03-24 12:05:10 -0400 (Mon, 24 Mar 2025)
EndedAt: 2025-03-24 12:05:30 -0400 (Mon, 24 Mar 2025)
EllapsedTime: 19.4 seconds
RetCode: 1
Status:   ERROR  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL rhdf5filters
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘rhdf5filters’ ...
** this is package ‘rhdf5filters’ version ‘1.19.2’
** using staged installation
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
configure: is Bioc build machine
configure: configuring BZIP2 filter...
configure: compiling bundled bzip2 library
configure: configuring the Zstd filter...
configure: compiling bundled Zstd library
configure: configuring the BLOSC filter...
configure: compiling bundled BLOSC library
checking whether C compiler accepts -msse2... yes
configure: Bioc build machine; disabling MAVX2
checking for gcc __builtin_cpu_init function... (cached) true
checking for x86 sse2 instruction support... yes
configure: configuring the VBZ filter
machine=x86_64
CPU_ARCH=x86
checking whether C compiler accepts -mavx... yes
checking for x86 avx instruction support... yes
VBZ_FLAGS=-mssse3
configure: creating ./config.status
config.status: creating src/bzip2/Makefile
config.status: creating src/zstd/Makefile
config.status: creating src/blosc/lib/blosc-1.20.1/Makefile
config.status: creating src/blosc/Makefile
config.status: creating src/vbz/Makefile
config.status: creating src/vbz/vbz/Makefile
config.status: creating src/vbz/third_party/streamvbyte/Makefile
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
make -C zstd
make[1]: Entering directory '/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/rhdf5filters/src/zstd'
gcc -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/debug.c -o common/debug.o
gcc -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/entropy_common.c -o common/entropy_common.o
gcc -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/error_private.c -o common/error_private.o
gcc -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/fse_decompress.c -o common/fse_decompress.o
gcc -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/pool.c -o common/pool.o -o common/pool.o
gcc -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/threading.c -o common/threading.o
gcc -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/xxhash.c -o common/xxhash.o
gcc -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/zstd_common.c -o common/zstd_common.o
gcc -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/fse_compress.c -o compress/fse_compress.o
gcc -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/hist.c -o compress/hist.o
gcc -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/huf_compress.c -o compress/huf_compress.o
gcc -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_compress.c -o compress/zstd_compress.o
gcc -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_compress_literals.c -o compress/zstd_compress_literals.o
gcc -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_compress_sequences.c -o compress/zstd_compress_sequences.o
gcc -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_compress_superblock.c -o compress/zstd_compress_superblock.o
gcc -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_double_fast.c -o compress/zstd_double_fast.o
gcc -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_fast.c -o compress/zstd_fast.o
gcc -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_lazy.c -o compress/zstd_lazy.o
compress/zstd_lazy.c:2157:1: fatal error: error writing to /tmp/cczvk4Ht.s: No space left on device
 2157 | }
      | ^
compilation terminated.
make[1]: *** [Makefile:51: compress/zstd_lazy.o] Error 1
make[1]: Leaving directory '/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/rhdf5filters/src/zstd'
make: *** [Makevars:38: libH5Zzstd.so] Error 2
ERROR: compilation failed for package ‘rhdf5filters’
* removing ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/rhdf5filters’
* restoring previous ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/rhdf5filters’