Benilton S Carvalho
| Snapshot Date: 2025-10-31 13:40 -0400 (Fri, 31 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/crlmm |
| git_branch: devel |
| git_last_commit: 51993cf |
| git_last_commit_date: 2025-10-29 10:02:32 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-01 11:32 -0400 (Sat, 01 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4774 |
| 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 | ||||
| Package 470/2321 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| crlmm 1.69.0 (landing page) Benilton S Carvalho
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
|
To the developers/maintainers of the crlmm package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/crlmm.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. |
| Package: crlmm |
| Version: 1.69.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL crlmm |
| StartedAt: 2025-10-31 15:40:37 -0400 (Fri, 31 Oct 2025) |
| EndedAt: 2025-10-31 15:41:22 -0400 (Fri, 31 Oct 2025) |
| EllapsedTime: 44.6 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL crlmm
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘crlmm’ ...
** this is package ‘crlmm’ version ‘1.69.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c gtypeCaller.c -o gtypeCaller.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c init.c -o init.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c trimmed.c -o trimmed.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c utils.c -o utils.o
utils.c: In function ‘countFileLines’:
utils.c:290:5: warning: argument 1 null where non-null expected [-Wnonnull]
290 | fclose(fInput);
| ^~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.23-bioc/R/include/R.h:44,
from utils.c:2:
/usr/include/stdio.h:184:12: note: in a call to function ‘fclose’ declared ‘nonnull’
184 | extern int fclose (FILE *__stream) __nonnull ((1));
| ^~~~~~
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o crlmm.so gtypeCaller.o init.o trimmed.o utils.o -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-crlmm/00new/crlmm/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’
** testing if installed package keeps a record of temporary installation path
* DONE (crlmm)