Rapid builds (Linux only) of a subset of BioC 3.23<BR>Report updated every 6 hours

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2026-03-12 r89611) -- "Unsuffered Consequences"	919
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 Rhdf5lib on teran2

To the developers/maintainers of the Rhdf5lib 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: Rhdf5lib

Version: 1.33.4

Command: /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:Rhdf5lib.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings Rhdf5lib_1.33.4.tar.gz

StartedAt: 2026-03-13 16:02:59 -0400 (Fri, 13 Mar 2026)

EndedAt: 2026-03-13 16:03:16 -0400 (Fri, 13 Mar 2026)

EllapsedTime: 17.0 seconds

RetCode: 0

Status: WARNINGS

CheckDir: Rhdf5lib.Rcheck

Warnings: 1

Command output

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###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:Rhdf5lib.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings Rhdf5lib_1.33.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rhdf5lib.Rcheck’
* using R Under development (unstable) (2026-03-12 r89611)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* current time: 2026-03-13 20:03:00 UTC
* checking for file ‘Rhdf5lib/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rhdf5lib’ version ‘1.33.4’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... 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 Title field should be in title case. Current version is:
  ‘hdf5 library as an R package’
In title case that is:
  ‘Hdf5 Library as an R Package’
* 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 ‘Rhdf5lib’ can be installed ... WARNING
Found the following significant warnings:
  /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rhdf5lib/vendor/hdf5/src/H5FDs3comms.c:1825:17: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-truncation]
  /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ destination unchanged after copying no bytes [-Wstringop-truncation]
  /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rhdf5lib/vendor/hdf5/c++/src/H5Location.cpp:2001:46: warning: argument 1 range [9223372036854775809, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
See ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rhdf5lib.Rcheck/00install.out’ for details.
* checking installed package size ... INFO
  installed size is 58.0Mb
  sub-directories of 1Mb or more:
    include   2.5Mb
    lib      55.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Authors@R field gives no person with name and author role
'LinkingTo' field is unused: package has no 'src' directory
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Found the following CITATION file in a non-standard place:
  vendor/hdf5/CITATION.cff
Most likely ‘inst/CITATION’ should be used instead.
* 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 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 ... OK
* 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 Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tinytest.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: 1 WARNING, 3 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rhdf5lib.Rcheck/00check.log’
for details.

Installation output

Rhdf5lib.Rcheck/00install.out

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###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL Rhdf5lib
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library’
* installing *source* package ‘Rhdf5lib’ ...
** this is package ‘Rhdf5lib’ version ‘1.33.4’
** using staged installation
-- The C compiler identification is GNU 13.3.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Performing Test HAVE_DECL___BUILTIN_CLZLL
-- Performing Test HAVE_DECL___BUILTIN_CLZLL - Success
-- Looking for snprintf
-- Looking for snprintf - found
-- Configuring done (0.5s)
-- Generating done (0.0s)
-- Build files have been written to: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rhdf5lib/_build_libaec
[ 11%] Building C object src/CMakeFiles/aec-static-objects.dir/encode.c.o
[ 22%] Building C object src/CMakeFiles/aec-static-objects.dir/encode_accessors.c.o
[ 33%] Building C object src/CMakeFiles/aec-static-objects.dir/decode.c.o
[ 44%] Building C object src/CMakeFiles/aec-static-objects.dir/vector.c.o
[ 44%] Built target aec-static-objects
[ 55%] Linking C static library libaec.a
[ 55%] Built target aec-static
[ 66%] Building C object src/CMakeFiles/sz-static-objects.dir/sz_compat.c.o
[ 66%] Built target sz-static-objects
[ 77%] Linking C static library libsz.a
[ 77%] Built target sz-static
[ 88%] Building C object src/CMakeFiles/graec.dir/graec.c.o
[100%] Linking C executable graec
[100%] Built target graec
-- Install configuration: "Release"
-- Installing: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rhdf5lib/inst/lib/cmake/libaec/libaec-config.cmake
-- Installing: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rhdf5lib/inst/lib/cmake/libaec/libaec-config-version.cmake
-- Installing: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rhdf5lib/inst/include/libaec.h
-- Installing: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rhdf5lib/inst/include/szlib.h
-- Installing: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rhdf5lib/inst/lib/libaec.a
-- Installing: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rhdf5lib/inst/lib/libsz.a
-- Installing: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rhdf5lib/inst/lib/cmake/libaec/libaec-targets.cmake
-- Installing: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rhdf5lib/inst/lib/cmake/libaec/libaec-targets-release.cmake
-- The C compiler identification is GNU 13.3.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Final: share
-- Looking for include file sys/file.h
-- Looking for include file sys/file.h - found
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-- Looking for include files sys/file.h, sys/ioctl.h - found
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-- Looking for 3 include files sys/file.h, ..., sys/resource.h - found
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-- Looking for 4 include files sys/file.h, ..., sys/socket.h - found
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-- Looking for 16 include files sys/file.h, ..., arpa/inet.h - found
-- Looking for include file quadmath.h
-- Looking for include file quadmath.h - found
-- Looking for ceil in m;
-- Looking for ceil in m; - found
-- Looking for dlopen in dl;m
-- Looking for dlopen in dl;m - found
-- Looking for WSAStartup in ws2_32;m;dl
-- Looking for WSAStartup in ws2_32;m;dl - not found
-- Looking for gethostbyname in wsock32;m;dl
-- Looking for gethostbyname in wsock32;m;dl - not found
-- Looking for gethostname in ucb;m;dl
-- Looking for gethostname in ucb;m;dl - not found
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of char
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-- Check size of _Bool
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-- Looking for CLOCK_MONOTONIC
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-- Performing Test H5_HAVE_TM_GMTOFF
-- Performing Test H5_HAVE_TM_GMTOFF - Success
-- Performing Test H5_HAVE___TM_GMTOFF
-- Performing Test H5_HAVE___TM_GMTOFF - Failed
-- Performing Test H5_HAVE_STRUCT_TIMEZONE
-- Performing Test H5_HAVE_STRUCT_TIMEZONE - Failed
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-- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "8.5.0")  
-- Found OpenSSL: /usr/lib/x86_64-linux-gnu/libcrypto.so (found version "3.0.13")  
-- Checking if _Float16 support is available
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-- Found Perl: /usr/bin/perl (found version "5.38.2") 
-- ... disable color and URL extended diagnostic messages
-- ....All Warnings are enabled
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3")  
-- The CXX compiler identification is GNU 13.3.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- ... disable color and URL extended diagnostic messages
-- ....All Warnings are enabled
-- Configuring done (14.5s)
-- Generating done (0.1s)
-- Build files have been written to: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rhdf5lib/_build_hdf5
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/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rhdf5lib/vendor/hdf5/src/H5FDs3comms.c: In function ‘H5FD__s3comms_load_aws_creds_from_file’:
/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rhdf5lib/vendor/hdf5/src/H5FDs3comms.c:1825:17: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-truncation]
 1825 |                 strncpy(setting_pointers[setting_i], (const char *)line_buffer, strlen(line_buffer));
      |                 ^
/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rhdf5lib/vendor/hdf5/src/H5FDs3comms.c:1825:17: note: length computed here
 1825 |                 strncpy(setting_pointers[setting_i], (const char *)line_buffer, strlen(line_buffer));
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:548,
                 from /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rhdf5lib/vendor/hdf5/src/H5private.h:34,
                 from /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rhdf5lib/vendor/hdf5/src/H5FDs3comms.c:38:
In function ‘strncpy’,
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/usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ destination unchanged after copying no bytes [-Wstringop-truncation]
   95 |   return __builtin___strncpy_chk (__dest, __src, __len,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   96 |                                   __glibc_objsize (__dest));
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~
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/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rhdf5lib/vendor/hdf5/c++/src/H5Location.cpp: In member function ‘std::string H5::H5Location::getObjnameByIdx(hsize_t) const’:
/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rhdf5lib/vendor/hdf5/c++/src/H5Location.cpp:2001:46: warning: argument 1 range [9223372036854775809, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
 2001 |     char *name_C = new char[actual_name_len]();
      |                                              ^
In file included from /usr/include/c++/13/bits/exception_ptr.h:38,
                 from /usr/include/c++/13/exception:164,
                 from /usr/include/c++/13/ios:41,
                 from /usr/include/c++/13/ostream:40,
                 from /usr/include/c++/13/iostream:41,
                 from /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rhdf5lib/vendor/hdf5/c++/src/H5Location.cpp:13:
/usr/include/c++/13/new:128:26: note: in a call to allocation function ‘void* operator new [](std::size_t)’ declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^~~~~~~~
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-- Install configuration: "Release"
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-- Installing: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rhdf5lib/inst/include/H5CppDoc.h
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-- Installing: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rhdf5lib/inst/cmake/hdf5-targets.cmake
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-- Installing: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rhdf5lib/inst/cmake/hdf5-config-version.cmake
-- Installing: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rhdf5lib/inst/lib/libhdf5.settings
-- Installing: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rhdf5lib/inst/share/COPYING
[1] TRUE TRUE TRUE
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rhdf5lib)

Tests output

Rhdf5lib.Rcheck/tests/tinytest.Rout


R Under development (unstable) (2026-03-12 r89611) -- "Unsuffered Consequences"
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Platform: x86_64-pc-linux-gnu

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> if ( requireNamespace("tinytest", quietly=TRUE) ) {
+   tinytest::test_package("Rhdf5lib")
+ }

test_library_version.R........    1 tests [0;32mOK[0m 
test_library_version.R........    2 tests [0;32mOK[0m [0;36m35ms[0m

test_link_flags.R.............    0 tests    
test_link_flags.R.............    0 tests    
test_link_flags.R.............    0 tests    
test_link_flags.R.............    0 tests    
test_link_flags.R.............    0 tests    
test_link_flags.R.............    1 tests [0;32mOK[0m 
test_link_flags.R.............    2 tests [0;32mOK[0m 
test_link_flags.R.............    3 tests [0;32mOK[0m 
test_link_flags.R.............    4 tests [0;32mOK[0m 
test_link_flags.R.............    5 tests [0;32mOK[0m 
test_link_flags.R.............    6 tests [0;32mOK[0m 
test_link_flags.R.............    7 tests [0;32mOK[0m 
test_link_flags.R.............    8 tests [0;32mOK[0m [0;34m0.2s[0m
All ok, 10 results (0.2s)
> 
> proc.time()
   user  system elapsed 
  0.284   0.065   0.348

Example timings

Rhdf5lib.Rcheck/Rhdf5lib-Ex.timings

name	user	system	elapsed
getHdf5Version	0.001	0.000	0.002
pkgconfig	0.003	0.000	0.004