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This page was generated on 2025-12-08 09:34 -0500 (Mon, 08 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-28 r88973) -- "Unsuffered Consequences" | 925 |
| 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 115/230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | |||||||
| GSVA 2.5.13 (landing page) Robert Castelo
| teran2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||
|
To the developers/maintainers of the GSVA 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. |
| Package: GSVA |
| Version: 2.5.13 |
| Command: /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:GSVA.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings GSVA_2.5.13.tar.gz |
| StartedAt: 2025-12-08 08:32:53 -0500 (Mon, 08 Dec 2025) |
| EndedAt: 2025-12-08 08:32:57 -0500 (Mon, 08 Dec 2025) |
| EllapsedTime: 4.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GSVA.Rcheck |
| Warnings: NA |
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### Running command:
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### /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:GSVA.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings GSVA_2.5.13.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/GSVA.Rcheck’
* using R Under development (unstable) (2025-10-28 r88973)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘GSVA/DESCRIPTION’ ... OK
* this is package ‘GSVA’ version ‘2.5.13’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Robert Castelo <robert.castelo@upf.edu>’
Unknown, possibly misspelled, fields in DESCRIPTION:
‘git_url’ ‘git_branch’ ‘git_last_commit’ ‘git_last_commit_date’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GSVA’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... OK
Warning in file.symlink(from, to) :
cannot symlink '/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/dbplyr' to '/tmp/RtmpBGYJrh/RLIBS_f16894a375626/dbplyr', reason 'No space left on device'
Error in flink(where, tmplib) :
cannot link from /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/dbplyr
Execution halted
GSVA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL GSVA ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library’ * installing *source* package ‘GSVA’ ... ** this is package ‘GSVA’ version ‘2.5.13’ ** 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-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/cli/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ecdfvals.c -o ecdfvals.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/cli/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c kcdfvals.c -o kcdfvals.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/cli/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c kernel_estimation.c -o kernel_estimation.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/cli/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ks_test.c -o ks_test.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/cli/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c register_cmethods.c -o register_cmethods.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/cli/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c row_rngs_nzrngs.c -o row_rngs_nzrngs.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/cli/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c utils.c -o utils.o gcc -std=gnu2x -shared -L/usr/local/lib -o GSVA.so ecdfvals.o kcdfvals.o kernel_estimation.o ks_test.o register_cmethods.o row_rngs_nzrngs.o utils.o installing to /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/00LOCK-GSVA/00new/GSVA/libs ** R ** 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 (GSVA)