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This page was generated on 2023-04-11 14:50:27 -0400 (Tue, 11 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
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 149/416HostnameOS / ArchINSTALLBUILDCHECK
GSBenchMark 1.18.0  (landing page)
Bahman Afsari
Snapshot Date: 2023-04-11 07:30:01 -0400 (Tue, 11 Apr 2023)
git_url: https://git.bioconductor.org/packages/GSBenchMark
git_branch: RELEASE_3_16
git_last_commit: ab3349f
git_last_commit_date: 2022-11-01 11:01:48 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GSBenchMark
Version: 1.18.0
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/site-library --timings GSBenchMark_1.18.0.tar.gz
StartedAt: 2023-04-11 11:49:15 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 11:49:45 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 30.3 seconds
RetCode: 0
Status:   OK  
CheckDir: GSBenchMark.Rcheck
Warnings: 0

Command output

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### Running 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/site-library --timings GSBenchMark_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-data-experiment/meat/GSBenchMark.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘GSBenchMark/DESCRIPTION’ ... OK
* this is package ‘GSBenchMark’ version ‘1.18.0’
* 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 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘GSBenchMark.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* 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/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
GSBenchMarkDatasets0.1570.0080.166
bipolar_GDS21900.1520.0040.157
breast_GDS8070.1540.0000.154
diracpathways0.0060.0000.006
exprsdata0.2220.0200.242
leukemia_GSEA0.1420.0120.154
logexprsdata0.2310.0200.250
marfan_GDS29600.0850.0000.085
melanoma_GDS27350.2010.0120.213
parkinsons_GDS25190.3700.0080.378
phenotypes0.2490.0080.257
prostate_GDS2545_m_nf0.1510.0040.155
prostate_GDS2545_m_p0.3250.0040.330
prostate_GDS2545_p_nf0.2550.0120.267
sarcoma_data0.4480.0360.484
squamous_GDS25200.1600.0040.164