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"	869
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BUILD results for maftools on teran2

To the developers/maintainers of the maftools 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: maftools

Version: 2.23.0

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

StartedAt: 2025-03-20 12:43:38 -0400 (Thu, 20 Mar 2025)

EndedAt: 2025-03-20 12:43:52 -0400 (Thu, 20 Mar 2025)

EllapsedTime: 14.0 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 maftools
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* checking for file ‘maftools/DESCRIPTION’ ... OK
* preparing ‘maftools’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
      -----------------------------------
* installing *source* package ‘maftools’ ...
** this is package ‘maftools’ version ‘2.23.0’
** 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 -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/zlibbioc/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ntcounts.c -o ntcounts.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/zlibbioc/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c snpcounts.c -o snpcounts.o
snpcounts.c: In function ‘snpcounts’:
snpcounts.c:89:47: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=]
   89 |   fprintf(tsv_fp, "#idxstats_mapped_reads\t%llu\n", tot_mapped);
      |                                            ~~~^     ~~~~~~~~~~
      |                                               |     |
      |                                               |     uint64_t {aka long unsigned int}
      |                                               long long unsigned int
      |                                            %lu
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/zlibbioc/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c somaticfreq.c -o somaticfreq.o
gcc -shared -L/usr/local/lib -o maftools.so ntcounts.o snpcounts.o somaticfreq.o /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz
installing to /tmp/RtmpK11jF7/Rinstd9403719092c1/00LOCK-maftools/00new/maftools/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** 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("maftools"),  : 
  error writing to connection
Calls: <Anonymous> -> withCallingHandlers -> <Anonymous>
Execution halted
ERROR: loading failed
* removing ‘/tmp/RtmpK11jF7/Rinstd9403719092c1/maftools’
      -----------------------------------
ERROR: package installation failed