Multiple platform build/check report for BioC 3.21 - BUILD results for PICS on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4658
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4455
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4408
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

BUILD results for PICS on nebbiolo1

To the developers/maintainers of the PICS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PICS.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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: PICS

Version: 2.51.0

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data PICS

StartedAt: 2025-01-24 18:40:54 -0500 (Fri, 24 Jan 2025)

EndedAt: 2025-01-24 18:40:57 -0500 (Fri, 24 Jan 2025)

EllapsedTime: 3.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data PICS
###
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* checking for file ‘PICS/DESCRIPTION’ ... OK
* preparing ‘PICS’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* installing the package to build vignettes
      -----------------------------------
* installing *source* package ‘PICS’ ...
** this is package ‘PICS’ version ‘2.51.0’
** using staged installation
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c pics.c -o pics.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c segment.c -o segment.o
segment.c: In function ‘segReads’:
segment.c:147:22: warning: implicit declaration of function ‘Calloc’; did you mean ‘calloc’? [-Wimplicit-function-declaration]
  147 |   scoreRegionF=(int*)Calloc((M-m)/(2*INTEGER_VALUE(width)), int);
      |                      ^~~~~~
      |                      calloc
segment.c:147:61: error: expected expression before ‘int’
  147 |   scoreRegionF=(int*)Calloc((M-m)/(2*INTEGER_VALUE(width)), int);
      |                                                             ^~~
segment.c:148:61: error: expected expression before ‘int’
  148 |   scoreRegionR=(int*)Calloc((M-m)/(2*INTEGER_VALUE(width)), int);
      |                                                             ^~~
make: *** [/home/biocbuild/bbs-3.21-bioc/R/etc/Makeconf:195: segment.o] Error 1
ERROR: compilation failed for package ‘PICS’
* removing ‘/tmp/Rtmp2TiFhE/Rinst3ea05855b8153/PICS’
      -----------------------------------
ERROR: package installation failed