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This page was generated on 2026-03-12 16:11 -0400 (Thu, 12 Mar 2026).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2026-03-06 r89561) -- "Unsuffered Consequences" 903
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Package 119/230HostnameOS / ArchINSTALLBUILDCHECK
h5mread 1.3.2  (landing page)
Hervé Pagès
Snapshot Date: 2026-03-12 12:00 -0400 (Thu, 12 Mar 2026)
git_url: https://git.bioconductor.org/packages/h5mread
git_branch: devel
git_last_commit: 7fe3454
git_last_commit_date: 2026-03-06 18:54:23 -0400 (Fri, 06 Mar 2026)
teran2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  

INSTALL 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: 1.3.2
Command: /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL h5mread
StartedAt: 2026-03-12 12:16:22 -0400 (Thu, 12 Mar 2026)
EndedAt: 2026-03-12 12:16:39 -0400 (Thu, 12 Mar 2026)
EllapsedTime: 17.4 seconds
RetCode: 0
Status:   OK  

Command output

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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL h5mread
###
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library’
* installing *source* package ‘h5mread’ ...
** this is package ‘h5mread’ version ‘1.3.2’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 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
H5DSetDescriptor.c: In function ‘C_show_H5DSetDescriptor_xp’:
H5DSetDescriptor.c:1192:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘hsize_t’ {aka ‘long unsigned int’} [-Wformat=]
 1192 |                 Rprintf(" %llu", h5dset->h5dim[h5along]);
      |                           ~~~^   ~~~~~~~~~~~~~~~~~~~~~~
      |                              |                |
      |                              |                hsize_t {aka long unsigned int}
      |                              long long unsigned int
      |                           %lu
H5DSetDescriptor.c:1202:38: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘hsize_t’ {aka ‘long unsigned int’} [-Wformat=]
 1202 |                         Rprintf(" %llu",
      |                                   ~~~^
      |                                      |
      |                                      long long unsigned int
      |                                   %lu
 1203 |                                 h5dset->h5chunkdim[h5along]);
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                   |
      |                                                   hsize_t {aka long unsigned int}
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
In file included from TouchedChunks.c:9:
TouchedChunks.c: In function ‘read_h5chunk’:
TouchedChunks.c:312:37: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘hsize_t’ {aka ‘long unsigned int’} [-Wformat=]
  312 |                 PRINT_TO_ERRMSG_BUF("chunk storage size (%llu) bigger "
      |                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  313 |                                     "than expected (%llu + %d)",
  314 |                                     chunk_storage_size,
      |                                     ~~~~~~~~~~~~~~~~~~
      |                                     |
      |                                     hsize_t {aka long unsigned int}
global_errmsg_buf.h:9:67: note: in definition of macro ‘PRINT_TO_ERRMSG_BUF’
    9 |         snprintf(_h5mread_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
      |                                                                   ^~~~~~~~~~~
TouchedChunks.c:312:61: note: format string is defined here
  312 |                 PRINT_TO_ERRMSG_BUF("chunk storage size (%llu) bigger "
      |                                                          ~~~^
      |                                                             |
      |                                                             long long unsigned int
      |                                                          %lu
TouchedChunks.c: In function ‘_print_tchunk_info’:
TouchedChunks.c:569:35: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘hsize_t’ {aka ‘long unsigned int’} [-Wformat=]
  569 |                 Rprintf("#%lld=%llu:%llu", tchunkidx + 1,
      |                                ~~~^
      |                                   |
      |                                   long long unsigned int
      |                                %lu
  570 |                         tchunk_iter->tchunk_vps.h5chunk_vp.h5off[h5along] + 1,
      |                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                           |
      |                                                                           hsize_t {aka long unsigned int}
TouchedChunks.c:569:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘hsize_t’ {aka ‘long unsigned int’} [-Wformat=]
  569 |                 Rprintf("#%lld=%llu:%llu", tchunkidx + 1,
      |                                     ~~~^
      |                                        |
      |                                        long long unsigned int
      |                                     %lu
  570 |                         tchunk_iter->tchunk_vps.h5chunk_vp.h5off[h5along] + 1,
  571 |                         tchunk_iter->tchunk_vps.h5chunk_vp.h5off[h5along] +
      |                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                           |
      |                                                                           hsize_t {aka long unsigned int}
  572 |                             tchunk_iter->tchunk_vps.h5chunk_vp.h5dim[h5along]);
      |                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -lsz -lm -ldl -lcurl -lssl -lcrypto
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/00LOCK-h5mread/00new/h5mread/libs
** 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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (h5mread)