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CHECK report for GSBenchMark on malbec2

This page was generated on 2020-10-15 20:45:47 -0400 (Thu, 15 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE GSBenchMark PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 147/391HostnameOS / ArchINSTALLBUILDCHECK
GSBenchMark 1.8.0
Bahman Afsari
Snapshot Date: 2020-10-15 07:30:17 -0400 (Thu, 15 Oct 2020)
URL: https://git.bioconductor.org/packages/GSBenchMark
Branch: RELEASE_3_11
Last Commit: 78c4cd9
Last Changed Date: 2020-04-27 15:29:12 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: GSBenchMark
Version: 1.8.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:GSBenchMark.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings GSBenchMark_1.8.0.tar.gz
StartedAt: 2020-10-15 13:26:29 -0400 (Thu, 15 Oct 2020)
EndedAt: 2020-10-15 13:27:00 -0400 (Thu, 15 Oct 2020)
EllapsedTime: 30.9 seconds
RetCode: 0
Status:  OK 
CheckDir: GSBenchMark.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:GSBenchMark.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings GSBenchMark_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-data-experiment/meat/GSBenchMark.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.8.0’
* 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-3.11-data-experiment/meat/GSBenchMark.Rcheck/00check.log’
for details.



Installation output

GSBenchMark.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL GSBenchMark
###
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* installing to library ‘/home/biocbuild/bbs-3.11-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
GSBenchMarkDatasets0.2460.0080.255
bipolar_GDS21900.2110.0000.211
breast_GDS8070.1970.0040.201
diracpathways0.0240.0000.024
exprsdata0.2880.0040.292
leukemia_GSEA0.1820.0080.190
logexprsdata0.2820.0200.302
marfan_GDS29600.0940.0040.098
melanoma_GDS27350.2390.0080.247
parkinsons_GDS25190.420.020.44
phenotypes0.3090.0120.321
prostate_GDS2545_m_nf0.1530.0200.173
prostate_GDS2545_m_p0.3250.0080.333
prostate_GDS2545_p_nf0.2900.0120.302
sarcoma_data0.4940.0560.550
squamous_GDS25200.1920.0080.200