Multiple platform build/check report for BioC 3.22 - INSTALL results for rhdf5client on taishan

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.2 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4796
palomino8	Windows Server 2022 Datacenter	x64	4.5.1 (2025-06-13 ucrt) -- "Great Square Root"	4536
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4578
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4519
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4517
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*

INSTALL results for rhdf5client on taishan

To the developers/maintainers of the rhdf5client package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rhdf5client.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.

raw results

Summary

Package: rhdf5client

Version: 1.31.0

Command: /home/biocbuild/R/R/bin/R CMD INSTALL rhdf5client

StartedAt: 2025-07-31 20:35:19 -0000 (Thu, 31 Jul 2025)

EndedAt: 2025-07-31 20:35:44 -0000 (Thu, 31 Jul 2025)

EllapsedTime: 24.9 seconds

RetCode: 0

Status: OK

Command output

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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL rhdf5client
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘rhdf5client’ ...
** this is package ‘rhdf5client’ version ‘1.31.0’
** 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-4.5.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c extract.c -o extract.o
extract.c: In function ‘extractBin’:
extract.c:101:52: warning: ‘rip’ may be used uninitialized [-Wmaybe-uninitialized]
  101 |     A[ia] = (Rf_isReal(resvec_sexp) ? rdp[ib] : rip[ib]);
      |                                                    ^
extract.c:89:8: note: ‘rip’ was declared here
   89 |   int *rip;
      |        ^~~
extract.c:101:42: warning: ‘rdp’ may be used uninitialized [-Wmaybe-uninitialized]
  101 |     A[ia] = (Rf_isReal(resvec_sexp) ? rdp[ib] : rip[ib]);
      |                                          ^
extract.c:90:11: note: ‘rdp’ was declared here
   90 |   double *rdp;
      |           ^~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o rhdf5client.so extract.o -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/site-library/00LOCK-rhdf5client/00new/rhdf5client/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 (rhdf5client)