Rapid builds (Linux only) of a subset of BioC 3.21<BR>Report updated every 6 hours

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	871
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INSTALL 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 INSTALL S4Vectors

StartedAt: 2025-04-01 18:05:09 -0400 (Tue, 01 Apr 2025)

EndedAt: 2025-04-01 18:05:11 -0400 (Tue, 01 Apr 2025)

EllapsedTime: 1.9 seconds

RetCode: 1

Status: ERROR

Command output

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### Running command:
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###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL S4Vectors
###
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* 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
LLint_class.c:837:1: fatal error: error writing to /tmp/cckfbOfY.s: No space left on device
  837 | }
      | ^
compilation terminated.
make: *** [/home/rapidbuild/bbs-3.21-bioc-rapid/R/etc/Makeconf:195: LLint_class.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’