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This page was generated on 2025-11-02 09:42 -0500 (Sun, 02 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-28 r88973) -- "Unsuffered Consequences" 917
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Package 179/230HostnameOS / ArchINSTALLBUILDCHECK
rhdf5 2.55.4  (landing page)
Hugo Gruson
Snapshot Date: 2025-11-02 06:00 -0500 (Sun, 02 Nov 2025)
git_url: https://git.bioconductor.org/packages/rhdf5
git_branch: devel
git_last_commit: 8cd8dc6
git_last_commit_date: 2025-10-31 04:46:45 -0500 (Fri, 31 Oct 2025)
teran2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  

CHECK results for rhdf5 on teran2

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: 2.55.4
Command: /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:rhdf5.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings rhdf5_2.55.4.tar.gz
StartedAt: 2025-11-02 09:00:59 -0500 (Sun, 02 Nov 2025)
EndedAt: 2025-11-02 09:05:39 -0500 (Sun, 02 Nov 2025)
EllapsedTime: 279.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: rhdf5.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:rhdf5.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings rhdf5_2.55.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5.Rcheck’
* using R Under development (unstable) (2025-10-28 r88973)
* 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
* checking for file ‘rhdf5/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rhdf5’ version ‘2.55.4’
* package encoding: UTF-8
* checking CRAN incoming feasibility ...Warning in parse_Rd(nfile, macros = macros) :
  /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/inst/NEWS.Rd:15: unexpected section header '\section'
Warning in parse_Rd(nfile, macros = macros) :
  /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/inst/NEWS.Rd:35: unexpected section header '\section'
Warning in parse_Rd(nfile, macros = macros) :
  /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/inst/NEWS.Rd:57: unexpected section header '\section'
Warning in parse_Rd(nfile, macros = macros) :
  /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/inst/NEWS.Rd:95: unexpected section header '\section'
Warning in parse_Rd(nfile, macros = macros) :
  /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/inst/NEWS.Rd:106: unexpected section header '\section'
Warning in parse_Rd(nfile, macros = macros) :
  /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/inst/NEWS.Rd:135: unexpected section header '\section'
Warning in parse_Rd(nfile, macros = macros) :
  /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/inst/NEWS.Rd:155: unexpected section header '\section'
Warning in parse_Rd(nfile, macros = macros) :
  /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/inst/NEWS.Rd:195: unexpected section header '\section'
Warning in parse_Rd(nfile, macros = macros) :
  /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/inst/NEWS.Rd:227: unexpected section header '\section'
Warning in parse_Rd(nfile, macros = macros) :
  /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/inst/NEWS.Rd:249: unexpected section header '\section'
Warning in parse_Rd(nfile, macros = macros) :
  /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/inst/NEWS.Rd:290: unexpected section header '\section'
Warning in parse_Rd(nfile, macros = macros) :
  /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/inst/NEWS.Rd:322: unexpected section header '\section'
Warning in parse_Rd(nfile, macros = macros) :
  /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/inst/NEWS.Rd:338: unexpected section header '\section'
Warning in parse_Rd(nfile, macros = macros) :
  /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/inst/NEWS.Rd:366: unexpected section header '\section'
Warning in parse_Rd(nfile, macros = macros) :
  /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/inst/NEWS.Rd:375: unexpected section header '\section'
Warning in parse_Rd(nfile, macros = macros) :
  /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/inst/NEWS.Rd:403: unexpected section header '\section'
Warning in parse_Rd(nfile, macros = macros) :
  /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/inst/NEWS.Rd:424: unexpected section header '\section'
Warning in parse_Rd(nfile, macros = macros) :
  /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/inst/NEWS.Rd:438: unexpected section header '\section'
Warning in parse_Rd(nfile, macros = macros) :
  /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/inst/NEWS.Rd:448: unexpected section header '\section'
Warning in parse_Rd(nfile, macros = macros) :
  /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/inst/NEWS.Rd:466: unexpected section header '\section'
Warning in parse_Rd(nfile, macros = macros) :
  /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/inst/NEWS.Rd:481: unexpected section header '\section'
Warning in parse_Rd(nfile, macros = macros) :
  /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/inst/NEWS.Rd:508: unexpected section header '\section'
Warning in parse_Rd(nfile, macros = macros) :
  /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/inst/NEWS.Rd:530: unexpected section header '\section'
Warning in parse_Rd(nfile, macros = macros) :
  /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/inst/NEWS.Rd:545: unexpected section header '\section'
Warning in parse_Rd(nfile, macros = macros) :
  /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/inst/NEWS.Rd:560: unexpected END_OF_INPUT '
'
 NOTE
Maintainer: ‘Hugo Gruson <hugo.gruson@embl.de>’

Unknown, possibly misspelled, fields in DESCRIPTION:
  ‘git_url’ ‘git_branch’ ‘git_last_commit’ ‘git_last_commit_date’

The Description field should not start with the package name,
  'This package' or similar.
* 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 ... NOTE
Found the following hidden files and directories:
  .git-blame-ignore-revs
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.

CRAN-pack does not know about
  .git-blame-ignore-revs
* 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 ‘build’ 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 ... NOTE
Problems with news in ‘inst/NEWS.Rd’:
  inst/NEWS.Rd:15: unexpected section header '\section'
  inst/NEWS.Rd:35: unexpected section header '\section'
  inst/NEWS.Rd:57: unexpected section header '\section'
  inst/NEWS.Rd:95: unexpected section header '\section'
  inst/NEWS.Rd:106: unexpected section header '\section'
  inst/NEWS.Rd:135: unexpected section header '\section'
  inst/NEWS.Rd:155: unexpected section header '\section'
  inst/NEWS.Rd:195: unexpected section header '\section'
  inst/NEWS.Rd:227: unexpected section header '\section'
  inst/NEWS.Rd:249: unexpected section header '\section'
  inst/NEWS.Rd:290: unexpected section header '\section'
  inst/NEWS.Rd:322: unexpected section header '\section'
  inst/NEWS.Rd:338: unexpected section header '\section'
  inst/NEWS.Rd:366: unexpected section header '\section'
  inst/NEWS.Rd:375: unexpected section header '\section'
  inst/NEWS.Rd:403: unexpected section header '\section'
  inst/NEWS.Rd:424: unexpected section header '\section'
  inst/NEWS.Rd:438: unexpected section header '\section'
  inst/NEWS.Rd:448: unexpected section header '\section'
  inst/NEWS.Rd:466: unexpected section header '\section'
  inst/NEWS.Rd:481: unexpected section header '\section'
  inst/NEWS.Rd:508: unexpected section header '\section'
  inst/NEWS.Rd:530: unexpected section header '\section'
  inst/NEWS.Rd:545: unexpected section header '\section'
  inst/NEWS.Rd:560: unexpected END_OF_INPUT '
  '
* 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 use of S3 registration ... 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 ... WARNING
prepare_Rd: ./inst/NEWS.Rd:15: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:35: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:57: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:95: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:106: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:135: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:155: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:195: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:227: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:249: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:290: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:322: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:338: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:366: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:375: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:403: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:424: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:438: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:448: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:466: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:481: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:508: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:530: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:545: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:560: unexpected END_OF_INPUT '
'
checkRd: (-1) NEWS.Rd:15: Lost braces; missing escapes or markup?
    15 | \section{Changes in version 2.54.0}{
       |         ^
checkRd: (-1) NEWS.Rd:15-33: Lost braces
    15 | \section{Changes in version 2.54.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:35: Lost braces; missing escapes or markup?
    35 | \section{Changes in version 2.52.0}{
       |         ^
checkRd: (-1) NEWS.Rd:35-55: Lost braces
    35 | \section{Changes in version 2.52.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:57: Lost braces; missing escapes or markup?
    57 | \section{Changes in version 2.48.0}{
       |         ^
checkRd: (-1) NEWS.Rd:57-92: Lost braces
    57 | \section{Changes in version 2.48.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:95: Lost braces; missing escapes or markup?
    95 | \section{Changes in version 2.46.0}{
       |         ^
checkRd: (-1) NEWS.Rd:95-104: Lost braces
    95 | \section{Changes in version 2.46.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:106: Lost braces; missing escapes or markup?
   106 | \section{Changes in version 2.44.0}{
       |         ^
checkRd: (-1) NEWS.Rd:106-133: Lost braces
   106 | \section{Changes in version 2.44.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:135: Lost braces; missing escapes or markup?
   135 | \section{Changes in version 2.42.0}{
       |         ^
checkRd: (-1) NEWS.Rd:135-153: Lost braces
   135 | \section{Changes in version 2.42.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:155: Lost braces; missing escapes or markup?
   155 | \section{Changes in version 2.40.0}{
       |         ^
checkRd: (-1) NEWS.Rd:155-193: Lost braces
   155 | \section{Changes in version 2.40.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:195: Lost braces; missing escapes or markup?
   195 | \section{Changes in version 2.38.0}{
       |         ^
checkRd: (-1) NEWS.Rd:195-225: Lost braces
   195 | \section{Changes in version 2.38.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:227: Lost braces; missing escapes or markup?
   227 | \section{Changes in version 2.36.0}{
       |         ^
checkRd: (-1) NEWS.Rd:227-247: Lost braces
   227 | \section{Changes in version 2.36.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:249: Lost braces; missing escapes or markup?
   249 | \section{Changes in version 2.34.0}{
       |         ^
checkRd: (-1) NEWS.Rd:249-288: Lost braces
   249 | \section{Changes in version 2.34.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:290: Lost braces; missing escapes or markup?
   290 | \section{Changes in version 2.32.0}{
       |         ^
checkRd: (-1) NEWS.Rd:290-320: Lost braces
   290 | \section{Changes in version 2.32.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:322: Lost braces; missing escapes or markup?
   322 | \section{Changes in version 2.30.0}{
       |         ^
checkRd: (-1) NEWS.Rd:322-336: Lost braces
   322 | \section{Changes in version 2.30.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:338: Lost braces; missing escapes or markup?
   338 | \section{Changes in version 2.28.0}{
       |         ^
checkRd: (-1) NEWS.Rd:338-364: Lost braces
   338 | \section{Changes in version 2.28.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:366: Lost braces; missing escapes or markup?
   366 | \section{Changes in version 2.26.0}{
       |         ^
checkRd: (-1) NEWS.Rd:366-373: Lost braces
   366 | \section{Changes in version 2.26.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:375: Lost braces; missing escapes or markup?
   375 | \section{Changes in version 2.24.0}{
       |         ^
checkRd: (-1) NEWS.Rd:375-401: Lost braces
   375 | \section{Changes in version 2.24.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:403: Lost braces; missing escapes or markup?
   403 | \section{Changes in version 2.20.0}{
       |         ^
checkRd: (-1) NEWS.Rd:403-422: Lost braces
   403 | \section{Changes in version 2.20.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:424: Lost braces; missing escapes or markup?
   424 | \section{Changes in version 2.18.0}{
       |         ^
checkRd: (-1) NEWS.Rd:424-436: Lost braces
   424 | \section{Changes in version 2.18.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:438: Lost braces; missing escapes or markup?
   438 | \section{Changes in version 2.16.0}{
       |         ^
checkRd: (-1) NEWS.Rd:438-446: Lost braces
   438 | \section{Changes in version 2.16.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:448: Lost braces; missing escapes or markup?
   448 | \section{Changes in version 2.14.0}{
       |         ^
checkRd: (-1) NEWS.Rd:448-464: Lost braces
   448 | \section{Changes in version 2.14.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:466: Lost braces; missing escapes or markup?
   466 | \section{Changes in version 2.12.0}{
       |         ^
checkRd: (-1) NEWS.Rd:466-479: Lost braces
   466 | \section{Changes in version 2.12.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:481: Lost braces; missing escapes or markup?
   481 | \section{Changes in version 2.10.0}{
       |         ^
checkRd: (-1) NEWS.Rd:481-506: Lost braces
   481 | \section{Changes in version 2.10.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:508: Lost braces; missing escapes or markup?
   508 | \section{Changes in version 2.8.0}{
       |         ^
checkRd: (-1) NEWS.Rd:508-528: Lost braces
   508 | \section{Changes in version 2.8.0}{
       |                                   ^
checkRd: (-1) NEWS.Rd:530: Lost braces; missing escapes or markup?
   530 | \section{Changes in version 2.6.0}{
       |         ^
checkRd: (-1) NEWS.Rd:530-543: Lost braces
   530 | \section{Changes in version 2.6.0}{
       |                                   ^
checkRd: (-1) NEWS.Rd:545: Lost braces; missing escapes or markup?
   545 | \section{Changes in version 2.4.0}{
       |         ^
checkRd: (-1) NEWS.Rd:545-559: Lost braces
   545 | \section{Changes in version 2.4.0}{
       |                                   ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* 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 ... WARNING
Note: information on .o files is not available
File ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/rhdf5/libs/rhdf5.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5.Rcheck/00check.log’
for details.

Installation output

rhdf5.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL rhdf5
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library’
* installing *source* package ‘rhdf5’ ...
** this is package ‘rhdf5’ version ‘2.55.4’
** 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/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/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/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/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/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/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/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/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/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/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/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/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/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/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/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/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/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/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/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/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/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/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/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/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/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/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/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/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/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/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/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/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/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/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/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/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/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/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/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/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/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/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/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/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/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/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/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/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/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/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/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/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/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/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/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/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/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/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/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 /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/lib/libhdf5.a -L/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/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)

Tests output

rhdf5.Rcheck/tests/testthat.Rout


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> library(testthat)
> library(rhdf5)
> 
> test_check("rhdf5")
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 1121 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On Bioconductor (2): 'test_S3.R:20:5', 'test_S3.R:30:5'

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 1121 ]
> 
> proc.time()
   user  system elapsed 
  5.032   2.451   7.489

Example timings

rhdf5.Rcheck/rhdf5-Ex.timings

nameusersystemelapsed
H5Dget_num_chunks0.0130.0010.015
H5Dopen0.0050.0010.005
H5Fget_intent0.0020.0000.003
H5Fget_name0.0010.0010.002
H5Gget_info0.0050.0000.005
H5Iget_type0.0010.0000.002
H5Iis_valid0.0010.0000.001
H5Lcreate_external0.0030.0000.004
H5Ldelete0.0030.0010.003
H5Lmove0.0120.0020.014
H5Ocopy0.0070.0000.009
H5Oget_info0.0020.0020.003
H5Olink0.0020.0010.003
H5Oopen0.0090.0000.009
H5P_create_intermediate_group0.0010.0000.001
H5Pset_fapl_ros3000
H5R0.0080.0010.008
H5Scombine_hyperslab0.0010.0000.001
H5Scombine_select0.0010.0000.001
H5Sselect_hyperslab0.0000.0010.000
H5Sselect_index0.0010.0000.000
H5T_enum0.0000.0000.001
H5T_ops0.0010.0000.000
H5functions000
h5_FileLocking0.0010.0000.000
h5_createAttribute0.0060.0010.007
h5_createDataset0.0660.0020.078
h5_createFile0.0040.0000.004
h5_createGroup0.0030.0000.004
h5_dump0.0090.0000.009
h5_errorHandling000
h5_read0.0180.0000.018
h5_save0.0180.0000.018
h5_set_extent0.0080.0000.008
h5_write0.0110.0000.011
h5closeAll0.0030.0000.003
h5constants000
h5listObjects0.0020.0000.002
h5ls0.010.000.01
h5readTimestamps0.0020.0000.003
h5version0.0010.0000.001