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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 182/217HostnameOS / ArchINSTALLBUILDCHECK
S4Vectors 0.45.4  (landing page)
Hervé Pagès
Snapshot Date: 2025-03-22 18:00 -0400 (Sat, 22 Mar 2025)
git_url: https://git.bioconductor.org/packages/S4Vectors
git_branch: devel
git_last_commit: 659194b
git_last_commit_date: 2025-02-10 18:56:58 -0400 (Mon, 10 Feb 2025)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  ERROR    OK    ERROR  

CHECK results for S4Vectors on teran2

To the developers/maintainers of the S4Vectors 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: S4Vectors
Version: 0.45.4
Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:S4Vectors.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings S4Vectors_0.45.4.tar.gz
StartedAt: 2025-03-22 18:46:35 -0400 (Sat, 22 Mar 2025)
EndedAt: 2025-03-22 18:46:38 -0400 (Sat, 22 Mar 2025)
EllapsedTime: 3.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: S4Vectors.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:S4Vectors.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings S4Vectors_0.45.4.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/S4Vectors.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 ‘S4Vectors/DESCRIPTION’ ... OK
* this is package ‘S4Vectors’ version ‘0.45.4’
* 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 ‘S4Vectors’ can be installed ... ERROR
Installation failed.
See ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/S4Vectors.Rcheck/00install.out’ for details.
* DONE

Status: 1 ERROR
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/S4Vectors.Rcheck/00check.log’
for details.

Installation output

S4Vectors.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL S4Vectors
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘S4Vectors’ ...
** this is package ‘S4Vectors’ version ‘0.45.4’
** 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/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c AEbufs.c -o AEbufs.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c DataFrame_class.c -o DataFrame_class.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c Hits_class.c -o Hits_class.o
In file included from /usr/include/string.h:548,
                 from /home/rapidbuild/bbs-3.21-bioc-rapid/R/include/R_ext/RS.h:34,
                 from /home/rapidbuild/bbs-3.21-bioc-rapid/R/include/Rdefines.h:38,
                 from ../inst/include/S4Vectors_defines.h:18,
                 from S4Vectors.h:1,
                 from Hits_class.c:4:
In function ‘memcpy’,
    inlined from ‘tsort_hits’ at Hits_class.c:113:3:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:10: warning: ‘__builtin_memcpy’ specified bound between 18446744065119617024 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=]
   29 |   return __builtin___memcpy_chk (__dest, __src, __len,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   30 |                                  __glibc_objsize0 (__dest));
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/rapidbuild/bbs-3.21-bioc-rapid/R/include/Rdefines.h:41:
Hits_class.c: In function ‘Hits_new’:
/home/rapidbuild/bbs-3.21-bioc-rapid/R/include/Rinternals.h:919:33: warning: ‘revmap’ may be used uninitialized [-Wmaybe-uninitialized]
  919 | #define defineVar               Rf_defineVar
Hits_class.c:244:9: note: in expansion of macro ‘defineVar’
  244 |         defineVar(install(translateChar(symbol)), revmap, revmap_envir);
      |         ^~~~~~~~~
Hits_class.c:219:19: note: ‘revmap’ was declared here
  219 |         SEXP ans, revmap, symbol;
      |                   ^~~~~~
Hits_class.c: In function ‘select_hits’:
Hits_class.c:348:48: warning: ‘is_used’ may be used uninitialized [-Wmaybe-uninitialized]
  348 |                                         is_used->elts[ans_elt - 1] = 1;
      |                                         ~~~~~~~^~~~~~
Hits_class.c:313:17: note: ‘is_used’ was declared here
  313 |         CharAE *is_used;
      |                 ^~~~~~~
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c LLint_class.c -o LLint_class.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c List_class.c -o List_class.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c R_init_S4Vectors.c -o R_init_S4Vectors.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c Rle_class.c -o Rle_class.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c Rle_utils.c -o Rle_utils.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c SEXP_utils.c -o SEXP_utils.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c SimpleList_class.c -o SimpleList_class.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c anyMissing.c -o anyMissing.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c character_utils.c -o character_utils.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c eval_utils.c -o eval_utils.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c hash_utils.c -o hash_utils.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c integer_utils.c -o integer_utils.o
integer_utils.c:909:1: fatal error: error writing to /tmp/cc5v7IwW.s: No space left on device
  909 | }
      | ^
compilation terminated.
make: *** [/home/rapidbuild/bbs-3.21-bioc-rapid/R/etc/Makeconf:195: integer_utils.o] Error 1
ERROR: compilation failed for package ‘S4Vectors’
* removing ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors’
* restoring previous ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors’

Tests output


Example timings