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This page was generated on 2022-06-30 14:50:27 -0400 (Thu, 30 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4343
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

CHECK results for GSBenchMark on nebbiolo2


To the developers/maintainers of the GSBenchMark package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 147/407HostnameOS / ArchINSTALLBUILDCHECK
GSBenchMark 1.17.0  (landing page)
Bahman Afsari
Snapshot Date: 2022-06-30 07:30:01 -0400 (Thu, 30 Jun 2022)
git_url: https://git.bioconductor.org/packages/GSBenchMark
git_branch: master
git_last_commit: 6e18d67
git_last_commit_date: 2022-04-26 13:14:39 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GSBenchMark
Version: 1.17.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:GSBenchMark.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings GSBenchMark_1.17.0.tar.gz
StartedAt: 2022-06-30 11:24:03 -0400 (Thu, 30 Jun 2022)
EndedAt: 2022-06-30 11:24:26 -0400 (Thu, 30 Jun 2022)
EllapsedTime: 22.6 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-3.16-bioc/R/bin/R CMD check --install=check:GSBenchMark.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings GSBenchMark_1.17.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-data-experiment/meat/GSBenchMark.Rcheck’
* using R version 4.2.0 Patched (2022-06-02 r82447)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GSBenchMark/DESCRIPTION’ ... OK
* this is package ‘GSBenchMark’ version ‘1.17.0’
* 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 ‘GSBenchMark’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 41.9Mb
  sub-directories of 1Mb or more:
    data  41.8Mb
* 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 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.16-data-experiment/meat/GSBenchMark.Rcheck/00check.log’
for details.



Installation output

GSBenchMark.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL GSBenchMark
###
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/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
GSBenchMarkDatasets0.1590.0200.178
bipolar_GDS21900.1630.0090.172
breast_GDS8070.1520.0240.176
diracpathways0.0060.0000.006
exprsdata0.2820.0080.289
leukemia_GSEA0.1760.0120.188
logexprsdata0.2940.0160.310
marfan_GDS29600.0960.0120.108
melanoma_GDS27350.2450.0160.260
parkinsons_GDS25190.4140.0160.430
phenotypes0.2600.0160.276
prostate_GDS2545_m_nf0.1650.0080.172
prostate_GDS2545_m_p0.3560.0080.364
prostate_GDS2545_p_nf0.3040.0000.304
sarcoma_data0.4570.0600.517
squamous_GDS25200.1660.0180.184