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This page was generated on 2025-03-22 18:56 -0400 (Sat, 22 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 869
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Package 181/217HostnameOS / ArchINSTALLBUILDCHECK
S4Arrays 1.7.3  (landing page)
Hervé Pagès
Snapshot Date: 2025-03-22 18:00 -0400 (Sat, 22 Mar 2025)
git_url: https://git.bioconductor.org/packages/S4Arrays
git_branch: devel
git_last_commit: 41a64ff
git_last_commit_date: 2025-02-07 21:02:59 -0400 (Fri, 07 Feb 2025)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  ERROR    OK    ERROR  

CHECK results for S4Arrays on teran2

To the developers/maintainers of the S4Arrays 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: S4Arrays
Version: 1.7.3
Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:S4Arrays.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings S4Arrays_1.7.3.tar.gz
StartedAt: 2025-03-22 18:46:31 -0400 (Sat, 22 Mar 2025)
EndedAt: 2025-03-22 18:46:34 -0400 (Sat, 22 Mar 2025)
EllapsedTime: 3.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: S4Arrays.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:S4Arrays.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings S4Arrays_1.7.3.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/S4Arrays.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* 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 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘S4Arrays/DESCRIPTION’ ... OK
* this is package ‘S4Arrays’ version ‘1.7.3’
* 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 ‘S4Arrays’ can be installed ... ERROR
Installation failed.
See ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/S4Arrays.Rcheck/00install.out’ for details.
* DONE

Status: 1 ERROR
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/S4Arrays.Rcheck/00check.log’
for details.

Installation output

S4Arrays.Rcheck/00install.out

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###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL S4Arrays
###
##############################################################################
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘S4Arrays’ ...
** this is package ‘S4Arrays’ version ‘1.7.3’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c R_init_S4Arrays.c -o R_init_S4Arrays.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c abind.c -o abind.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c array_selection.c -o array_selection.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c dim_tuning_utils.c -o dim_tuning_utils.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c rowsum.c -o rowsum.o
gcc -shared -L/usr/local/lib -o S4Arrays.so R_init_S4Arrays.o S4Vectors_stubs.o abind.o array_selection.o dim_tuning_utils.o rowsum.o
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/00LOCK-S4Arrays/00new/S4Arrays/libs
** R
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘rowsum’ in package ‘S4Arrays’
Creating a new generic function for ‘abind’ in package ‘S4Arrays’
** 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
Error in base::serialize(base::as.list(base::getNamespace("S4Arrays"),  : 
  error writing to connection
Calls: <Anonymous> -> withCallingHandlers -> <Anonymous>
Execution halted
ERROR: loading failed
* removing ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Arrays’
* restoring previous ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Arrays’

Tests output


Example timings