Hugo Gruson
| Snapshot Date: 2026-04-17 13:40 -0400 (Fri, 17 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/rhdf5 |
| git_branch: devel |
| git_last_commit: 34ead97 |
| git_last_commit_date: 2026-03-14 07:37:29 -0400 (Sat, 14 Mar 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 1818/2404 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rhdf5 2.55.16 (landing page) Hugo Gruson
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | ERROR | ERROR | skipped | ||||||||||
| See other builds for rhdf5 in R Universe. | ||||||||||||||
|
To the developers/maintainers of the rhdf5 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rhdf5.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: rhdf5 |
| Version: 2.55.16 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL rhdf5 |
| StartedAt: 2026-04-16 20:19:52 -0000 (Thu, 16 Apr 2026) |
| EndedAt: 2026-04-16 20:20:30 -0000 (Thu, 16 Apr 2026) |
| EllapsedTime: 38.5 seconds |
| RetCode: 1 |
| Status: ERROR |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD INSTALL rhdf5
###
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘rhdf5’ ...
** this is package ‘rhdf5’ version ‘2.55.16’
** using staged installation
configure: creating ./config.status
config.status: creating src/external_filters.h
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (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/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c H5.c -o H5.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/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c H5A.c -o H5A.o
In file included from H5A.h:12,
from H5A.c:2:
utils.h:19:5: error: unknown type name ‘H5L_info2_t’; did you mean ‘H5F_info2_t’?
19 | H5L_info2_t info;
| ^~~~~~~~~~~
| H5F_info2_t
utils.h:25:5: error: unknown type name ‘H5O_token_t’; did you mean ‘H5O_type_t’?
25 | H5O_token_t token; /* Object token */
| ^~~~~~~~~~~
| H5O_type_t
utils.h:61:47: error: unknown type name ‘H5O_token_t’; did you mean ‘H5O_type_t’?
61 | int group_check(struct opObjListElement *od, H5O_token_t target_token, unsigned long target_fileno, hid_t loc_id);
| ^~~~~~~~~~~
| H5O_type_t
make: *** [/home/biocbuild/R/R/etc/Makeconf:201: H5A.o] Error 1
ERROR: compilation failed for package ‘rhdf5’
* removing ‘/home/biocbuild/R/R-devel_2025-02-19/site-library/rhdf5’
* restoring previous ‘/home/biocbuild/R/R-devel_2025-02-19/site-library/rhdf5’