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This page was generated on 2025-07-24 09:37 -0400 (Thu, 24 Jul 2025).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 (2025-04-11) -- "How About a Twenty-Six" 914
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Package 56/229HostnameOS / ArchINSTALLBUILDCHECK
CNEr 1.45.0  (landing page)
Ge Tan
Snapshot Date: 2025-07-24 06:00 -0400 (Thu, 24 Jul 2025)
git_url: https://git.bioconductor.org/packages/CNEr
git_branch: devel
git_last_commit: 0622fa1
git_last_commit_date: 2025-04-15 10:28:43 -0400 (Tue, 15 Apr 2025)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  ERROR    ERROR  skipped

INSTALL results for CNEr on teran2

To the developers/maintainers of the CNEr 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: CNEr
Version: 1.45.0
Command: /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD INSTALL CNEr
StartedAt: 2025-07-24 06:20:30 -0400 (Thu, 24 Jul 2025)
EndedAt: 2025-07-24 06:20:34 -0400 (Thu, 24 Jul 2025)
EllapsedTime: 3.2 seconds
RetCode: 1
Status:   ERROR  

Command output

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### Running command:
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###   /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD INSTALL CNEr
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library’
* installing *source* package ‘CNEr’ ...
** this is package ‘CNEr’ version ‘1.45.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c R_init_CNEr.c -o R_init_CNEr.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c utils.c -o utils.o
utils.c: In function ‘bin_ranges_from_coord_range_standard’:
utils.c:50:7: warning: unused variable ‘_binNextShift’ [-Wunused-variable]
   50 |   int _binNextShift = binNextShift();
      |       ^~~~~~~~~~~~~
utils.c:49:7: warning: unused variable ‘_binFirstShift’ [-Wunused-variable]
   49 |   int _binFirstShift = binFirstShift();
      |       ^~~~~~~~~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c io.c -o io.o
io.c: In function ‘myReadAxt’:
io.c:94:26: warning: unused variable ‘curAxt’ [-Wunused-variable]
   94 |   struct axt *axt=NULL, *curAxt;
      |                          ^~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ceScan.c -o ceScan.o
ceScan.c: In function ‘ceScan’:
ceScan.c:615:8: warning: unused variable ‘rest’ [-Wunused-variable]
  615 |   char rest, path[PATH_LEN];
      |        ^~~~
ceScan.c:613:10: warning: unused variable ‘n’ [-Wunused-variable]
  613 |   int i, n;
      |          ^
ceScan.c: In function ‘freeSlThreshold’:
ceScan.c:674:17: warning: unused variable ‘CNE’ [-Wunused-variable]
  674 |   struct slCNE *CNE, *nextCNE, *el_CNE;
      |                 ^~~
ceScan.c:673:23: warning: unused variable ‘thresholds’ [-Wunused-variable]
  673 |   struct slThreshold *thresholds, *nextThreshold, *el_threshold;
      |                       ^~~~~~~~~~
ceScan.c: In function ‘myCeScan’:
ceScan.c:868:28: warning: unused variable ‘i’ [-Wunused-variable]
  868 |   int nrCNE[nrThresholds], i;
      |                            ^
ceScan.c:868:7: warning: unused variable ‘nrCNE’ [-Wunused-variable]
  868 |   int nrCNE[nrThresholds], i;
      |       ^~~~~
ceScan.c:865:17: warning: unused variable ‘CNE’ [-Wunused-variable]
  865 |   struct slCNE *CNE;
      |                 ^~~
ceScan.c: In function ‘myCeScanFile’:
ceScan.c:898:7: warning: unused variable ‘nrThresholds’ [-Wunused-variable]
  898 |   int nrThresholds = GET_LENGTH(winSize);
      |       ^~~~~~~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/axt.c -o ucsc/axt.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/base64.c -o ucsc/base64.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/binRange.c -o ucsc/binRange.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/bits.c -o ucsc/bits.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/chain.c -o ucsc/chain.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/cirTree.c -o ucsc/cirTree.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function ‘slUniqify’:
ucsc/common.c:360:9: error: too many arguments to function ‘free’
  360 |         free(el);
      |         ^~~~
make: *** [/home/rapidbuild/bbs-3.22-bioc-rapid/R/etc/Makeconf:202: ucsc/common.o] Error 1
ERROR: compilation failed for package ‘CNEr’
* removing ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/CNEr’