Rapid builds (Linux only) of a subset of BioC 3.23<BR>Report updated every 6 hours

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-28 r88973) -- "Unsuffered Consequences"	925
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BUILD results for h5mread on teran2

To the developers/maintainers of the h5mread 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: h5mread

Version: 1.3.1

Command: /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data h5mread

StartedAt: 2025-12-09 12:39:00 -0500 (Tue, 09 Dec 2025)

EndedAt: 2025-12-09 12:39:05 -0500 (Tue, 09 Dec 2025)

EllapsedTime: 5.3 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data h5mread
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* checking for file ‘h5mread/DESCRIPTION’ ... OK
* preparing ‘h5mread’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
      -----------------------------------
* installing *source* package ‘h5mread’ ...
** this is package ‘h5mread’ version ‘1.3.1’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c H5File.c -o H5File.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c global_errmsg_buf.c -o global_errmsg_buf.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c H5DSetDescriptor.c -o H5DSetDescriptor.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c h5dimscales.c -o h5dimscales.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c uaselection.c -o uaselection.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c h5mread_helpers.c -o h5mread_helpers.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c h5mread_startscounts.c -o h5mread_startscounts.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c TouchedChunks.c -o TouchedChunks.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c h5mread_index.c -o h5mread_index.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c h5mread_sparse.c -o h5mread_sparse.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c h5mread.c -o h5mread.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c h5summarize.c -o h5summarize.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c R_init_h5mread.c -o R_init_h5mread.o
gcc -std=gnu2x -shared -L/usr/local/lib -o h5mread.so S4Vectors_stubs.o H5File.o global_errmsg_buf.o H5DSetDescriptor.o h5dimscales.o uaselection.o h5mread_helpers.o h5mread_startscounts.o TouchedChunks.o h5mread_index.o h5mread_sparse.o h5mread.o h5summarize.o R_init_h5mread.o /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/lib/libhdf5_hl.a /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/lib/libhdf5.a -L/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm
/usr/bin/ld: final link failed: No space left on device
collect2: error: ld returned 1 exit status
make: *** [/home/rapidbuild/bbs-3.23-bioc-rapid/R/share/make/shlib.mk:10: h5mread.so] Error 1
ERROR: compilation failed for package ‘h5mread’
* removing ‘/tmp/RtmpsaFH53/Rinst202bc2387cb82d/h5mread’
      -----------------------------------
ERROR: package installation failed