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 pwalign on teran2

To the developers/maintainers of the pwalign 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: pwalign

Version: 1.3.3

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

StartedAt: 2025-04-05 00:12:55 -0400 (Sat, 05 Apr 2025)

EndedAt: 2025-04-05 00:13:02 -0400 (Sat, 05 Apr 2025)

EllapsedTime: 6.5 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 pwalign
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* checking for file ‘pwalign/DESCRIPTION’ ... OK
* preparing ‘pwalign’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
      -----------------------------------
* installing *source* package ‘pwalign’ ...
** this is package ‘pwalign’ version ‘1.3.3’
** 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'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c Biostrings_stubs.c -o Biostrings_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'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c IRanges_stubs.c -o IRanges_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'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c R_init_pairwiseAlignment.c -o R_init_pairwiseAlignment.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'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/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'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c XVector_stubs.c -o XVector_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'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c align_pairwiseAlignment.c -o align_pairwiseAlignment.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'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c align_utils.c -o align_utils.o
align_utils.c: In function âalign_utils.c:234:78: warning: âindelStartPatternâ may be used uninitialized [-Wmaybe-uninitialized]
  234 |                                 if ((numberOfIndelPattern == 0) || (jPattern < indelStartPattern)) {
      |                                                                    ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
align_utils.c:223:21: note: ‘indelStartPattern’ was declared here
  223 |                 int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject;
      |                     ^~~~~~~~~~~~~~~~~
align_utils.c:240:55: warning: ‘indelWidthPattern’ may be used uninitialized [-Wmaybe-uninitialized]
  240 |                                         for (k = 0; k < indelWidthPattern; k++) {
      |                                                     ~~^~~~~~~~~~~~~~~~~~~
align_utils.c:223:40: note: ‘indelWidthPattern’ was declared here
  223 |                 int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject;
      |                                        ^~~~~~~~~~~~~~~~~
align_utils.c:233:63: warning: ‘indelStartSubject’ may be used uninitialized [-Wmaybe-uninitialized]
  233 |                         if ((numberOfIndelSubject == 0) || (j < indelStartSubject)) {
      |                                                            ~~~^~~~~~~~~~~~~~~~~~~~
align_utils.c:223:59: note: ‘indelStartSubject’ was declared here
  223 |                 int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject;
      |                                                           ^~~~~~~~~~~~~~~~~
align_utils.c:252:42: warning: ‘indelWidthSubject’ may be used uninitialized [-Wmaybe-uninitialized]
  252 |                                 jPattern += indelWidthSubject;
      |                                 ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
align_utils.c:223:78: note: ‘indelWidthSubject’ was declared here
  223 |                 int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject;
      |                                                                              ^~~~~~~~~~~~~~~~~
gcc -shared -L/usr/local/lib -o pwalign.so Biostrings_stubs.o IRanges_stubs.o R_init_pairwiseAlignment.o S4Vectors_stubs.o XVector_stubs.o align_pairwiseAlignment.o align_utils.o
installing to /tmp/Rtmpd4Yd97/Rinstfd4433570271f/00LOCK-pwalign/00new/pwalign/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘insertion’ in package ‘pwalign’
Creating a new generic function for ‘deletion’ in package ‘pwalign’
Creating a new generic function for ‘unaligned’ in package ‘pwalign’
Creating a new generic function for ‘aligned’ in package ‘pwalign’
Creating a new generic function for ‘indel’ in package ‘pwalign’
Creating a new generic function for ‘nindel’ in package ‘pwalign’
Creating a new generic function for ‘PairwiseAlignments’ in package ‘pwalign’
Creating a new generic function for ‘pattern’ in package ‘pwalign’
Creating a new generic function for ‘alignedPattern’ in package ‘pwalign’
Creating a new generic function for ‘alignedSubject’ in package ‘pwalign’
Creating a new generic function for ‘PairwiseAlignmentsSingleSubject’ in package ‘pwalign’
Creating a new generic function for ‘nedit’ in package ‘pwalign’
Creating a new generic function for ‘mismatchTable’ in package ‘pwalign’
Creating a new generic function for ‘mismatchSummary’ in package ‘pwalign’
Creating a new generic function for ‘compareStrings’ in package ‘pwalign’
Creating a new generic function for ‘pid’ in package ‘pwalign’
Creating a new generic function for ‘pairwiseAlignment’ in package ‘pwalign’
Creating a new generic function for ‘stringDist’ in package ‘pwalign’
Error in lazyLoadDBinsertValue(data, datafile, ascii, compress, envhook) : 
  write failed
Calls: <Anonymous> ... lazyLoadDBinsertValue -> <Anonymous> -> lazyLoadDBinsertValue
Execution halted
ERROR: lazy loading failed for package ‘pwalign’
* removing ‘/tmp/Rtmpd4Yd97/Rinstfd4433570271f/pwalign’
      -----------------------------------
ERROR: package installation failed