Back to Long Tests report for BioC 3.22

This page was generated on 2025-10-18 23:55 -0400 (Sat, 18 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
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 27/31HostnameOS / ArchCHECK
rhdf5 2.53.6  (landing page)
Hugo Gruson
Snapshot Date: 2025-10-18 09:55 -0400 (Sat, 18 Oct 2025)
git_url: https://git.bioconductor.org/packages/rhdf5
git_branch: devel
git_last_commit: 919a739
git_last_commit_date: 2025-10-09 05:30:36 -0400 (Thu, 09 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  WARNINGS  
lconwaymacOS 12.7.6 Monterey / x86_64  WARNINGS  

CHECK results for rhdf5 on nebbiolo2

To the developers/maintainers of the rhdf5 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: rhdf5
Version: 2.53.6
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no rhdf5_2.53.6.tar.gz
StartedAt: 2025-10-18 16:23:22 -0400 (Sat, 18 Oct 2025)
EndedAt: 2025-10-18 16:24:55 -0400 (Sat, 18 Oct 2025)
EllapsedTime: 93.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: rhdf5.Rcheck
Warnings: 1

Tests output

rhdf5.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(rhdf5)
> 
> test_check("rhdf5")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ]
> 
> proc.time()
   user  system elapsed 
 30.076  33.694  63.765

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no rhdf5_2.53.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/rhdf5.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘rhdf5/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rhdf5’ version ‘2.53.6’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rhdf5’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'h5_createAttribute.Rd'
  ‘cset’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... INFO
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 OK
* DONE

Status: 1 WARNING
See
  ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/rhdf5.Rcheck/00check.log’
for details.

Installation output

rhdf5.Rcheck/00install.out

* installing *source* package ‘rhdf5’ ...
** this is package ‘rhdf5’ version ‘2.53.6’
** using staged installation
configure: creating ./config.status
config.status: creating src/external_filters.h
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c H5.c -o H5.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c H5A.c -o H5A.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c H5D.c -o H5D.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c H5E.c -o H5E.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c H5F.c -o H5F.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c H5G.c -o H5G.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c H5I.c -o H5I.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c H5L.c -o H5L.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c H5O.c -o H5O.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c H5P.c -o H5P.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c H5PL.c -o H5PL.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c H5R.c -o H5R.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c H5S.c -o H5S.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c H5S_extras.c -o H5S_extras.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c H5T.c -o H5T.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c H5T_extras.c -o H5T_extras.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c H5Z.c -o H5Z.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c H5constants.c -o H5constants.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c HandleList.cpp -o HandleList.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c HandleListWrap.c -o HandleListWrap.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c bit64conversion.c -o bit64conversion.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c external_filters.c -o external_filters.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c h5dump.c -o h5dump.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c h5ls.c -o h5ls.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c h5testLock.c -o h5testLock.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c h5writeDataFrame.c -o h5writeDataFrame.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c printdatatype.c -o printdatatype.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c utils.c -o utils.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c wrap.c -o wrap.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o rhdf5.so H5.o H5A.o H5D.o H5E.o H5F.o H5G.o H5I.o H5L.o H5O.o H5P.o H5PL.o H5R.o H5S.o H5S_extras.o H5T.o H5T_extras.o H5Z.o H5constants.o HandleList.o HandleListWrap.o bit64conversion.o external_filters.o h5dump.o h5ls.o h5testLock.o h5writeDataFrame.o printdatatype.o utils.o wrap.o /home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc-longtests/meat/rhdf5.Rcheck/00LOCK-rhdf5/00new/rhdf5/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (rhdf5)