Multiple platform build/check report for BioC 3.20 - INSTALL results for oligo on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4670
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4355
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4446
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4439
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	4306
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*

INSTALL results for oligo on nebbiolo2

To the developers/maintainers of the oligo package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/oligo.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: oligo

Version: 1.70.1

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL oligo

StartedAt: 2025-03-06 15:21:41 -0500 (Thu, 06 Mar 2025)

EndedAt: 2025-03-06 15:22:12 -0500 (Thu, 06 Mar 2025)

EllapsedTime: 31.0 seconds

RetCode: 0

Status: OK

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL oligo
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘oligo’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c DABG.c -o DABG.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c ParserGzXYS.c -o ParserGzXYS.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c ParserXYS.c -o ParserXYS.o
ParserXYS.c: In function ‘xys_header_field’:
ParserXYS.c:148:5: warning: implicit declaration of function ‘error’; did you mean ‘perror’? [-Wimplicit-function-declaration]
  148 |     error("Error reading from %s.\n", currentFile);
      |     ^~~~~
      |     perror
ParserXYS.c: In function ‘R_read_xys_header’:
ParserXYS.c:324:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  324 |   fgets(buffer, LINEMAX, fp);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c baseProfile.c -o baseProfile.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c basecontent.c -o basecontent.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c chipbackground.c -o chipbackground.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c mas5calls.c -o mas5calls.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c rma2.c -o rma2.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c rma_common.c -o rma_common.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c trimmed.c -o trimmed.o
gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o oligo.so DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lz -lgfortran -lm -lquadmath -llapack -L/home/biocbuild/bbs-3.20-bioc/R/lib -lRblas -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-oligo/00new/oligo/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Note: in method for ‘pm<-’ with signature
‘object="TilingFeatureSet",subset="ANY",target="ANY",value="array"’:
expanding the signature to include omitted arguments in definition:
subset = "missing", target = "missing"
Note: in method for ‘mm<-’ with signature
‘object="TilingFeatureSet",subset="ANY",target="ANY",value="array"’:
expanding the signature to include omitted arguments in definition:
subset = "missing", target = "missing"
** 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
** testing if installed package keeps a record of temporary installation path
* DONE (oligo)