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This page was generated on 2024-12-10 15:01 -0500 (Tue, 10 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4749
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 155/430HostnameOS / ArchINSTALLBUILDCHECK
GSBenchMark 1.27.0  (landing page)
Bahman Afsari
Snapshot Date: 2024-12-10 07:30 -0500 (Tue, 10 Dec 2024)
git_url: https://git.bioconductor.org/packages/GSBenchMark
git_branch: devel
git_last_commit: babaab4
git_last_commit_date: 2024-10-29 09:39:30 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published


CHECK results for GSBenchMark on nebbiolo1

To the developers/maintainers of the GSBenchMark 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: GSBenchMark
Version: 1.27.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:GSBenchMark.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings GSBenchMark_1.27.0.tar.gz
StartedAt: 2024-12-10 12:32:27 -0500 (Tue, 10 Dec 2024)
EndedAt: 2024-12-10 12:35:31 -0500 (Tue, 10 Dec 2024)
EllapsedTime: 184.5 seconds
RetCode: 0
Status:   OK  
CheckDir: GSBenchMark.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:GSBenchMark.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings GSBenchMark_1.27.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/GSBenchMark.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* 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 ‘GSBenchMark/DESCRIPTION’ ... OK
* this is package ‘GSBenchMark’ version ‘1.27.0’
* 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 ‘GSBenchMark’ can be installed ... OK
* checking installed package size ... INFO
  installed size is 42.0Mb
  sub-directories of 1Mb or more:
    data  41.9Mb
* checking package directory ... OK
* checking ‘build’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

GSBenchMark.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL GSBenchMark
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘GSBenchMark’ ...
** using staged installation
** data
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (GSBenchMark)

Tests output


Example timings

GSBenchMark.Rcheck/GSBenchMark-Ex.timings

nameusersystemelapsed
GSBenchMarkDatasets0.2060.0140.221
bipolar_GDS21900.1990.0110.210
breast_GDS8070.1930.0140.207
diracpathways0.0040.0030.007
exprsdata0.3150.0150.329
leukemia_GSEA0.1960.0100.206
logexprsdata0.3140.0170.331
marfan_GDS29600.1020.0110.113
melanoma_GDS27350.2640.0190.284
parkinsons_GDS25190.4410.0320.473
phenotypes0.3350.0190.354
prostate_GDS2545_m_nf0.1830.0110.194
prostate_GDS2545_m_p0.3320.0240.356
prostate_GDS2545_p_nf0.3090.0200.329
sarcoma_data0.5500.0440.594
squamous_GDS25200.2000.0070.207