Hugo Gruson
| Snapshot Date: 2026-03-10 13:40 -0400 (Tue, 10 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/Rhdf5lib |
| git_branch: devel |
| git_last_commit: e2d0017 |
| git_last_commit_date: 2026-03-10 12:35:16 -0400 (Tue, 10 Mar 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-11 11:33 -0400 (Wed, 11 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4719 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences" | 2847 |
| 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 1793/2360 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rhdf5lib 1.33.2 (landing page) Hugo Gruson
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
| See other builds for Rhdf5lib in R Universe. | ||||||||||||||
|
To the developers/maintainers of the Rhdf5lib package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rhdf5lib.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. |
| Package: Rhdf5lib |
| Version: 1.33.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data Rhdf5lib |
| StartedAt: 2026-03-10 15:38:05 -0400 (Tue, 10 Mar 2026) |
| EndedAt: 2026-03-10 15:38:09 -0400 (Tue, 10 Mar 2026) |
| EllapsedTime: 4.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data Rhdf5lib
###
##############################################################################
##############################################################################
* checking for file ‘Rhdf5lib/DESCRIPTION’ ... OK
* preparing ‘Rhdf5lib’:
* checking DESCRIPTION meta-information ... OK
* running ‘cleanup’
* installing the package (it is needed to build vignettes)
-----------------------------------
* installing *source* package ‘Rhdf5lib’ ...
** this is package ‘Rhdf5lib’ version ‘1.33.2’
** using staged installation
-- The C compiler identification is unknown
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - failed
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/clang
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/clang - broken
-- Configuring incomplete, errors occurred!
Error: failed to configure the libaec library with CMake
Execution halted
-- The C compiler identification is unknown
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - failed
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/clang
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/clang - broken
CMake Error at /Applications/CMake.app/Contents/share/cmake-3.31/Modules/CMakeTestCCompiler.cmake:67 (message):
The C compiler
"/Library/Developer/CommandLineTools/usr/bin/clang"
is not able to compile a simple test program.
It fails with the following output:
Change Dir: '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpHYHYrJ/Rbuild13dc83127ccb5/Rhdf5lib/_build_hdf5/CMakeFiles/CMakeScratch/TryCompile-yqVvAS'
Run Build Command(s): /Applications/CMake.app/Contents/bin/cmake -E env VERBOSE=1 make -f Makefile cmTC_0484e/fast
make -f CMakeFiles/cmTC_0484e.dir/build.make CMakeFiles/cmTC_0484e.dir/build
Building C object CMakeFiles/cmTC_0484e.dir/testCCompiler.c.o
/Library/Developer/CommandLineTools/usr/bin/clang -arch arm64 -std=gnu23 -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -fPIC -arch arm64 -o CMakeFiles/cmTC_0484e.dir/testCCompiler.c.o -c /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpHYHYrJ/Rbuild13dc83127ccb5/Rhdf5lib/_build_hdf5/CMakeFiles/CMakeScratch/TryCompile-yqVvAS/testCCompiler.c
error: invalid value 'gnu23' in '-std=gnu23'
note: use 'c89', 'c90', or 'iso9899:1990' for 'ISO C 1990' standard
note: use 'iso9899:199409' for 'ISO C 1990 with amendment 1' standard
note: use 'gnu89' or 'gnu90' for 'ISO C 1990 with GNU extensions' standard
note: use 'c99' or 'iso9899:1999' for 'ISO C 1999' standard
note: use 'gnu99' for 'ISO C 1999 with GNU extensions' standard
note: use 'c11' or 'iso9899:2011' for 'ISO C 2011' standard
note: use 'gnu11' for 'ISO C 2011 with GNU extensions' standard
note: use 'c17', 'iso9899:2017', 'c18', or 'iso9899:2018' for 'ISO C 2017' standard
note: use 'gnu17' or 'gnu18' for 'ISO C 2017 with GNU extensions' standard
note: use 'c2x' for 'Working Draft for ISO C2x' standard
note: use 'gnu2x' for 'Working Draft for ISO C2x with GNU extensions' standard
make[1]: *** [CMakeFiles/cmTC_0484e.dir/testCCompiler.c.o] Error 1
make: *** [cmTC_0484e/fast] Error 2
CMake will not be able to correctly generate this project.
Call Stack (most recent call first):
CMakeLists.txt:2 (project)
-- Configuring incomplete, errors occurred!
Error: failed to configure the HDF5 library with CMake
Execution halted
ERROR: configuration failed for package ‘Rhdf5lib’
* removing ‘/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpHYHYrJ/Rinst13dc82bf09849/Rhdf5lib’
-----------------------------------
ERROR: package installation failed