Back to Build/check report for BioC 3.20 experimental data
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This page was generated on 2024-12-19 15:42 -0500 (Thu, 19 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4743
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 143/431HostnameOS / ArchINSTALLBUILDCHECK
gageData 2.44.0  (landing page)
Weijun Luo
Snapshot Date: 2024-12-19 07:30 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/gageData
git_branch: RELEASE_3_20
git_last_commit: fded3b2
git_last_commit_date: 2024-10-29 09:27:58 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published


CHECK results for gageData on nebbiolo2

To the developers/maintainers of the gageData 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.

raw results


Summary

Package: gageData
Version: 2.44.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:gageData.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings gageData_2.44.0.tar.gz
StartedAt: 2024-12-19 12:34:48 -0500 (Thu, 19 Dec 2024)
EndedAt: 2024-12-19 12:39:14 -0500 (Thu, 19 Dec 2024)
EllapsedTime: 265.8 seconds
RetCode: 0
Status:   OK  
CheckDir: gageData.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:gageData.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings gageData_2.44.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-data-experiment/meat/gageData.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘gageData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gageData’ version ‘2.44.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘gageData’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data  10.7Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
hnrnp.cnts 10.847  0.232   11.08
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-data-experiment/meat/gageData.Rcheck/00check.log’
for details.


Installation output

gageData.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL gageData
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘gageData’ ...
** using staged installation
** data
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (gageData)

Tests output


Example timings

gageData.Rcheck/gageData-Ex.timings

nameusersystemelapsed
bmp63.3910.1723.563
genesets2.6990.0552.754
gse16873.full1.4470.1011.550
hnrnp.cnts10.847 0.23211.080
sc.gene0.0240.0020.026