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This page was generated on 2025-10-31 08:34 -0400 (Fri, 31 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" 4428
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Package 601/2321HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DNAcopy 1.85.0  (landing page)
Venkatraman E. Seshan
Snapshot Date: 2025-10-30 13:40 -0400 (Thu, 30 Oct 2025)
git_url: https://git.bioconductor.org/packages/DNAcopy
git_branch: devel
git_last_commit: a82e7ed
git_last_commit_date: 2025-10-29 09:54:58 -0400 (Wed, 29 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  YES

INSTALL results for DNAcopy on nebbiolo1

To the developers/maintainers of the DNAcopy package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DNAcopy.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: DNAcopy
Version: 1.85.0
Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL DNAcopy
StartedAt: 2025-10-30 15:01:44 -0400 (Thu, 30 Oct 2025)
EndedAt: 2025-10-30 15:01:53 -0400 (Thu, 30 Oct 2025)
EllapsedTime: 9.1 seconds
RetCode: 0
Status:   OK  

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL DNAcopy
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘DNAcopy’ ...
** this is package ‘DNAcopy’ version ‘1.85.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using Fortran compiler: ‘GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gfortran  -fpic  -g -O2  -Wall -Werror=format-security -c cbsWtstats.f -o cbsWtstats.o
f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran
cbsWtstats.f:282:72:

  282 |       iseg(1) = tmaxi
      |                                                                        ^
Warning: ‘tmaxi’ may be used uninitialized [-Wmaybe-uninitialized]
cbsWtstats.f:17:16:

   17 |      2     tmaxi, tmaxj, nal0
      |                ^
note: ‘tmaxi’ was declared here
cbsWtstats.f:283:72:

  283 |       iseg(2) = tmaxj
      |                                                                        ^
Warning: ‘tmaxj’ may be used uninitialized [-Wmaybe-uninitialized]
cbsWtstats.f:17:23:

   17 |      2     tmaxi, tmaxj, nal0
      |                       ^
note: ‘tmaxj’ was declared here
gfortran  -fpic  -g -O2  -Wall -Werror=format-security -c cbststats.f -o cbststats.o
f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran
cbststats.f:258:72:

  258 |                      tmaxj = sxmxi + i2j
      |                                                                        ^
Warning: ‘sxmxi’ may be used uninitialized [-Wmaybe-uninitialized]
cbststats.f:11:63:

   11 |      1     nb2, bi, bj, ilo, ihi, jlo, jhi, alenmax, i2j, sxmxi,
      |                                                               ^
note: ‘sxmxi’ was declared here
gfortran  -fpic  -g -O2  -Wall -Werror=format-security -c changepoints-wtd.f -o changepoints-wtd.o
f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran
gfortran  -fpic  -g -O2  -Wall -Werror=format-security -c changepoints.f -o changepoints.o
f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran
gfortran  -fpic  -g -O2  -Wall -Werror=format-security -c esegment.f -o esegment.o
f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c flchoose.c -o flchoose.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c fphyper.c -o fphyper.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c fpnorm.c -o fpnorm.o
gfortran  -fpic  -g -O2  -Wall -Werror=format-security -c getbdry.f -o getbdry.o
f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c init.c -o init.o
gfortran  -fpic  -g -O2  -Wall -Werror=format-security -c prune.f -o prune.o
f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c rshared.c -o rshared.o
gfortran  -fpic  -g -O2  -Wall -Werror=format-security -c segmentp.f -o segmentp.o
f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran
gfortran  -fpic  -g -O2  -Wall -Werror=format-security -c smoothCNA.f -o smoothCNA.o
f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran
gfortran  -fpic  -g -O2  -Wall -Werror=format-security -c tailprobs.f -o tailprobs.o
f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o DNAcopy.so cbsWtstats.o cbststats.o changepoints-wtd.o changepoints.o esegment.o flchoose.o fphyper.o fpnorm.o getbdry.o init.o prune.o rshared.o segmentp.o smoothCNA.o tailprobs.o -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-DNAcopy/00new/DNAcopy/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** 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
** testing if installed package keeps a record of temporary installation path
* DONE (DNAcopy)