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CHECK report for GSEABenchmarkeR on tokay2

This page was generated on 2019-10-16 12:40:56 -0400 (Wed, 16 Oct 2019).

Package 726/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GSEABenchmarkeR 1.4.0
Ludwig Geistlinger
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/GSEABenchmarkeR
Branch: RELEASE_3_9
Last Commit: 11383ab
Last Changed Date: 2019-05-02 11:54:11 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GSEABenchmarkeR
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GSEABenchmarkeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GSEABenchmarkeR_1.4.0.tar.gz
StartedAt: 2019-10-16 04:17:04 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:22:23 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 319.2 seconds
RetCode: 0
Status:  OK  
CheckDir: GSEABenchmarkeR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GSEABenchmarkeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GSEABenchmarkeR_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GSEABenchmarkeR.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GSEABenchmarkeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GSEABenchmarkeR' version '1.4.0'
* package encoding: UTF-8
* 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 whether package 'GSEABenchmarkeR' can be installed ... OK
* checking installed package size ... OK
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
loadEData      29.19   2.82   32.51
evalTypeIError 13.37   0.36   13.74
runEA           5.92   0.39    6.36
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
loadEData      26.37   2.29   29.08
evalTypeIError 14.05   0.25   14.32
runEA           5.60   0.46    6.06
* 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: OK


Installation output

GSEABenchmarkeR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/GSEABenchmarkeR_1.4.0.tar.gz && rm -rf GSEABenchmarkeR.buildbin-libdir && mkdir GSEABenchmarkeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GSEABenchmarkeR.buildbin-libdir GSEABenchmarkeR_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GSEABenchmarkeR_1.4.0.zip && rm GSEABenchmarkeR_1.4.0.tar.gz GSEABenchmarkeR_1.4.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  290k  100  290k    0     0  4929k      0 --:--:-- --:--:-- --:--:-- 5594k

install for i386

* installing *source* package 'GSEABenchmarkeR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GSEABenchmarkeR'
    finding HTML links ... done
    bpPlot                                  html  
    cacheResource                           html  
    finding level-2 HTML links ... done

    evalNrSigSets                           html  
    evalRelevance                           html  
    evalTypeIError                          html  
    loadEData                               html  
    maPreproc                               html  
    readDataId2diseaseCodeMap               html  
    readResults                             html  
    runDE                                   html  
    runEA                                   html  
** 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

install for x64

* installing *source* package 'GSEABenchmarkeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GSEABenchmarkeR' as GSEABenchmarkeR_1.4.0.zip
* DONE (GSEABenchmarkeR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'GSEABenchmarkeR' successfully unpacked and MD5 sums checked

Tests output


Example timings

GSEABenchmarkeR.Rcheck/examples_i386/GSEABenchmarkeR-Ex.timings

nameusersystemelapsed
bpPlot0.000.020.01
cacheResource2.030.363.36
evalNrSigSets1.470.051.52
evalRelevance0.600.000.59
evalTypeIError13.37 0.3613.74
loadEData29.19 2.8232.51
maPreproc3.370.603.97
readDataId2diseaseCodeMap0.020.000.03
readResults0.150.000.15
runDE1.00.51.5
runEA5.920.396.36

GSEABenchmarkeR.Rcheck/examples_x64/GSEABenchmarkeR-Ex.timings

nameusersystemelapsed
bpPlot0.020.000.01
cacheResource2.310.142.52
evalNrSigSets2.560.022.57
evalRelevance0.580.020.60
evalTypeIError14.05 0.2514.32
loadEData26.37 2.2929.08
maPreproc1.740.131.86
readDataId2diseaseCodeMap000
readResults0.110.010.12
runDE0.820.211.04
runEA5.600.466.06