Hervé Pagès
| Snapshot Date: 2026-04-17 13:40 -0400 (Fri, 17 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/h5mread |
| git_branch: devel |
| git_last_commit: 288d616 |
| git_last_commit_date: 2026-04-07 01:16:56 -0400 (Tue, 07 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-18 11:37 -0400 (Sat, 18 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4957 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4686 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4627 |
| 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 972/2404 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| h5mread 1.3.3 (landing page) Hervé Pagès
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
| See other builds for h5mread in R Universe. | ||||||||||||||
|
To the developers/maintainers of the h5mread package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/h5mread.git to reflect on this report. See Troubleshooting Build Report for more information. - 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: h5mread |
| Version: 1.3.3 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL h5mread |
| StartedAt: 2026-04-16 20:55:34 -0000 (Thu, 16 Apr 2026) |
| EndedAt: 2026-04-16 20:56:04 -0000 (Thu, 16 Apr 2026) |
| EllapsedTime: 30.4 seconds |
| RetCode: 0 |
| Status: OK |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD INSTALL h5mread
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘h5mread’ ...
** this is package ‘h5mread’ version ‘1.3.3’
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c H5File.c -o H5File.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-devel_2025-02-19/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
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-devel_2025-02-19/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:1192:29: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘hsize_t’ {aka ‘long long unsigned int’} [-Wformat=]
1192 | Rprintf(" %lu", h5dset->h5dim[h5along]);
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~
| | |
| | hsize_t {aka long long unsigned int}
| long unsigned int
| %llu
H5DSetDescriptor.c:1202:37: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘hsize_t’ {aka ‘long long unsigned int’} [-Wformat=]
1202 | Rprintf(" %lu", h5dset->h5chunkdim[h5along]);
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int hsize_t {aka long long unsigned int}
| %llu
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c h5dimscales.c -o h5dimscales.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c uaselection.c -o uaselection.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c h5mread_helpers.c -o h5mread_helpers.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c h5mread_startscounts.c -o h5mread_startscounts.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-devel_2025-02-19/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 ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘hsize_t’ {aka ‘long long unsigned int’} [-Wformat=]
312 | PRINT_TO_ERRMSG_BUF("chunk storage size (%lu) bigger "
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
313 | "than expected (%llu + %d)",
314 | chunk_storage_size,
| ~~~~~~~~~~~~~~~~~~
| |
| hsize_t {aka long 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:312:60: note: format string is defined here
312 | PRINT_TO_ERRMSG_BUF("chunk storage size (%lu) bigger "
| ~~^
| |
| long unsigned int
| %llu
TouchedChunks.c: In function ‘_print_tchunk_info’:
TouchedChunks.c:569:34: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘hsize_t’ {aka ‘long long unsigned int’} [-Wformat=]
569 | Rprintf("#%lld=%lu:%lu", tchunkidx + 1,
| ~~^
| |
| long unsigned int
| %llu
570 | tchunk_iter->tchunk_vps.h5chunk_vp.h5off[h5along] + 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| hsize_t {aka long long unsigned int}
TouchedChunks.c:569:38: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘hsize_t’ {aka ‘long long unsigned int’} [-Wformat=]
569 | Rprintf("#%lld=%lu:%lu", tchunkidx + 1,
| ~~^
| |
| long unsigned int
| %llu
570 | tchunk_iter->tchunk_vps.h5chunk_vp.h5off[h5along] + 1,
571 | tchunk_iter->tchunk_vps.h5chunk_vp.h5off[h5along] +
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| hsize_t {aka long long unsigned int}
572 | tchunk_iter->tchunk_vps.h5chunk_vp.h5dim[h5along]);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c h5mread_index.c -o h5mread_index.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c h5mread_sparse.c -o h5mread_sparse.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c h5mread.c -o h5mread.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c h5summarize.c -o h5summarize.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-devel_2025-02-19/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
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R/lib -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 /home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/lib/libhdf5_hl.a /home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/lib -lsz -laec -lz -ldl -lm -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/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)