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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BUILD results for biovizBase on teran2

To the developers/maintainers of the biovizBase 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: biovizBase

Version: 1.55.0

Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data biovizBase

StartedAt: 2025-04-05 00:10:46 -0400 (Sat, 05 Apr 2025)

EndedAt: 2025-04-05 00:10:47 -0400 (Sat, 05 Apr 2025)

EllapsedTime: 1.2 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data biovizBase
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* checking for file ‘biovizBase/DESCRIPTION’ ... OK
* preparing ‘biovizBase’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
      -----------------------------------
* installing *source* package ‘biovizBase’ ...
** this is package ‘biovizBase’ version ‘1.55.0’
** 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 R_init_biovizBase.c -o R_init_biovizBase.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 bin_offsets.c -o bin_offsets.o
bin_offsets.c: In function ‘scan_bam_bin_offsets’:
bin_offsets.c:57:15: warning: pointer targets in passing argument 1 of ‘strncmp’ differ in signedness [-Wpointer-sign]
   57 |   if (strncmp(b, "BAI\1", 4))
      |               ^
      |               |
      |               Rbyte * {aka unsigned char *}
In file included 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 bin_offsets.h:1,
                 from bin_offsets.c:3:
/usr/include/string.h:159:33: note: expected ‘const char *’ but argument is of type ‘Rbyte *’ {aka ‘unsigned char *’}
  159 | extern int strncmp (const char *__s1, const char *__s2, size_t __n)
      |                     ~~~~~~~~~~~~^~~~
/tmp/cceQwSP9.s: Assembler messages:
/tmp/cceQwSP9.s: Fatal error: bin_offsets.o: No space left on device
make: *** [/home/rapidbuild/bbs-3.21-bioc-rapid/R/etc/Makeconf:195: bin_offsets.o] Error 1
ERROR: compilation failed for package ‘biovizBase’
* removing ‘/tmp/Rtmpyl98FO/Rinstfb8db64a1fbf6/biovizBase’
      -----------------------------------
ERROR: package installation failed