Long Tests report for BioC 3.23 - CHECK results for rhdf5 on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	4821
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*

CHECK results for rhdf5 on nebbiolo1

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: 2.55.6

Command: /home/biocbuild/bbs-3.23-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_2.55.6.tar.gz

StartedAt: 2025-11-08 16:31:40 -0500 (Sat, 08 Nov 2025)

EndedAt: 2025-11-08 16:33:09 -0500 (Sat, 08 Nov 2025)

EllapsedTime: 89.0 seconds

RetCode: 0

Status: WARNINGS

CheckDir: rhdf5.Rcheck

Warnings: 1

Tests output

rhdf5.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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 
 22.620  35.833  58.507

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-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_2.55.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc-longtests/meat/rhdf5.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘2.55.6’
* 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 ... 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.
* 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  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
* 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 ... NOTE
Problems with news in ‘inst/NEWS.Rd’:
  inst/NEWS.Rd:26: unexpected section header '\section'
  inst/NEWS.Rd:46: unexpected section header '\section'
  inst/NEWS.Rd:68: unexpected section header '\section'
  inst/NEWS.Rd:106: unexpected section header '\section'
  inst/NEWS.Rd:117: unexpected section header '\section'
  inst/NEWS.Rd:146: unexpected section header '\section'
  inst/NEWS.Rd:166: unexpected section header '\section'
  inst/NEWS.Rd:206: unexpected section header '\section'
  inst/NEWS.Rd:238: unexpected section header '\section'
  inst/NEWS.Rd:260: unexpected section header '\section'
  inst/NEWS.Rd:301: unexpected section header '\section'
  inst/NEWS.Rd:333: unexpected section header '\section'
  inst/NEWS.Rd:349: unexpected section header '\section'
  inst/NEWS.Rd:377: unexpected section header '\section'
  inst/NEWS.Rd:386: unexpected section header '\section'
  inst/NEWS.Rd:414: unexpected section header '\section'
  inst/NEWS.Rd:435: unexpected section header '\section'
  inst/NEWS.Rd:449: unexpected section header '\section'
  inst/NEWS.Rd:459: unexpected section header '\section'
  inst/NEWS.Rd:477: unexpected section header '\section'
  inst/NEWS.Rd:492: unexpected section header '\section'
  inst/NEWS.Rd:519: unexpected section header '\section'
  inst/NEWS.Rd:541: unexpected section header '\section'
  inst/NEWS.Rd:556: unexpected section header '\section'
  inst/NEWS.Rd:571: 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 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:26: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:46: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:68: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:106: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:117: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:146: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:166: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:206: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:238: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:260: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:301: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:333: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:349: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:377: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:386: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:414: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:435: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:449: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:459: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:477: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:492: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:519: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:541: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:556: unexpected section header '\section'
prepare_Rd: ./inst/NEWS.Rd:571: unexpected END_OF_INPUT '
'
checkRd: (-1) NEWS.Rd:26: Lost braces; missing escapes or markup?
    26 | \section{Changes in version 2.54.0}{
       |         ^
checkRd: (-1) NEWS.Rd:26-44: Lost braces
    26 | \section{Changes in version 2.54.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:46: Lost braces; missing escapes or markup?
    46 | \section{Changes in version 2.52.0}{
       |         ^
checkRd: (-1) NEWS.Rd:46-66: Lost braces
    46 | \section{Changes in version 2.52.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:68: Lost braces; missing escapes or markup?
    68 | \section{Changes in version 2.48.0}{
       |         ^
checkRd: (-1) NEWS.Rd:68-103: Lost braces
    68 | \section{Changes in version 2.48.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:106: Lost braces; missing escapes or markup?
   106 | \section{Changes in version 2.46.0}{
       |         ^
checkRd: (-1) NEWS.Rd:106-115: Lost braces
   106 | \section{Changes in version 2.46.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:117: Lost braces; missing escapes or markup?
   117 | \section{Changes in version 2.44.0}{
       |         ^
checkRd: (-1) NEWS.Rd:117-144: Lost braces
   117 | \section{Changes in version 2.44.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:146: Lost braces; missing escapes or markup?
   146 | \section{Changes in version 2.42.0}{
       |         ^
checkRd: (-1) NEWS.Rd:146-164: Lost braces
   146 | \section{Changes in version 2.42.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:166: Lost braces; missing escapes or markup?
   166 | \section{Changes in version 2.40.0}{
       |         ^
checkRd: (-1) NEWS.Rd:166-204: Lost braces
   166 | \section{Changes in version 2.40.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:206: Lost braces; missing escapes or markup?
   206 | \section{Changes in version 2.38.0}{
       |         ^
checkRd: (-1) NEWS.Rd:206-236: Lost braces
   206 | \section{Changes in version 2.38.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:238: Lost braces; missing escapes or markup?
   238 | \section{Changes in version 2.36.0}{
       |         ^
checkRd: (-1) NEWS.Rd:238-258: Lost braces
   238 | \section{Changes in version 2.36.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:260: Lost braces; missing escapes or markup?
   260 | \section{Changes in version 2.34.0}{
       |         ^
checkRd: (-1) NEWS.Rd:260-299: Lost braces
   260 | \section{Changes in version 2.34.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:301: Lost braces; missing escapes or markup?
   301 | \section{Changes in version 2.32.0}{
       |         ^
checkRd: (-1) NEWS.Rd:301-331: Lost braces
   301 | \section{Changes in version 2.32.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:333: Lost braces; missing escapes or markup?
   333 | \section{Changes in version 2.30.0}{
       |         ^
checkRd: (-1) NEWS.Rd:333-347: Lost braces
   333 | \section{Changes in version 2.30.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:349: Lost braces; missing escapes or markup?
   349 | \section{Changes in version 2.28.0}{
       |         ^
checkRd: (-1) NEWS.Rd:349-375: Lost braces
   349 | \section{Changes in version 2.28.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:377: Lost braces; missing escapes or markup?
   377 | \section{Changes in version 2.26.0}{
       |         ^
checkRd: (-1) NEWS.Rd:377-384: Lost braces
   377 | \section{Changes in version 2.26.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:386: Lost braces; missing escapes or markup?
   386 | \section{Changes in version 2.24.0}{
       |         ^
checkRd: (-1) NEWS.Rd:386-412: Lost braces
   386 | \section{Changes in version 2.24.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:414: Lost braces; missing escapes or markup?
   414 | \section{Changes in version 2.20.0}{
       |         ^
checkRd: (-1) NEWS.Rd:414-433: Lost braces
   414 | \section{Changes in version 2.20.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:435: Lost braces; missing escapes or markup?
   435 | \section{Changes in version 2.18.0}{
       |         ^
checkRd: (-1) NEWS.Rd:435-447: Lost braces
   435 | \section{Changes in version 2.18.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:449: Lost braces; missing escapes or markup?
   449 | \section{Changes in version 2.16.0}{
       |         ^
checkRd: (-1) NEWS.Rd:449-457: Lost braces
   449 | \section{Changes in version 2.16.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:459: Lost braces; missing escapes or markup?
   459 | \section{Changes in version 2.14.0}{
       |         ^
checkRd: (-1) NEWS.Rd:459-475: Lost braces
   459 | \section{Changes in version 2.14.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:477: Lost braces; missing escapes or markup?
   477 | \section{Changes in version 2.12.0}{
       |         ^
checkRd: (-1) NEWS.Rd:477-490: Lost braces
   477 | \section{Changes in version 2.12.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:492: Lost braces; missing escapes or markup?
   492 | \section{Changes in version 2.10.0}{
       |         ^
checkRd: (-1) NEWS.Rd:492-517: Lost braces
   492 | \section{Changes in version 2.10.0}{
       |                                    ^
checkRd: (-1) NEWS.Rd:519: Lost braces; missing escapes or markup?
   519 | \section{Changes in version 2.8.0}{
       |         ^
checkRd: (-1) NEWS.Rd:519-539: Lost braces
   519 | \section{Changes in version 2.8.0}{
       |                                   ^
checkRd: (-1) NEWS.Rd:541: Lost braces; missing escapes or markup?
   541 | \section{Changes in version 2.6.0}{
       |         ^
checkRd: (-1) NEWS.Rd:541-554: Lost braces
   541 | \section{Changes in version 2.6.0}{
       |                                   ^
checkRd: (-1) NEWS.Rd:556: Lost braces; missing escapes or markup?
   556 | \section{Changes in version 2.4.0}{
       |         ^
checkRd: (-1) NEWS.Rd:556-570: Lost braces
   556 | \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 ... SKIPPED
* 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 ... 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc-longtests/meat/rhdf5.Rcheck/00check.log’
for details.

Installation output

rhdf5.Rcheck/00install.out

* installing *source* package ‘rhdf5’ ...
** this is package ‘rhdf5’ version ‘2.55.6’
** 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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-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-3.23-bioc/R/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-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)