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CHECK report for GSEABenchmarkeR on tokay1

This page was generated on 2021-05-06 12:31:42 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the GSEABenchmarkeR package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 795/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GSEABenchmarkeR 1.10.1  (landing page)
Ludwig Geistlinger
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/GSEABenchmarkeR
Branch: RELEASE_3_12
Last Commit: 4980161
Last Changed Date: 2020-12-09 16:49:51 -0400 (Wed, 09 Dec 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: GSEABenchmarkeR
Version: 1.10.1
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GSEABenchmarkeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings GSEABenchmarkeR_1.10.1.tar.gz
StartedAt: 2021-05-06 03:27:20 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 03:36:24 -0400 (Thu, 06 May 2021)
EllapsedTime: 543.6 seconds
RetCode: 0
Status:   OK   
CheckDir: GSEABenchmarkeR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GSEABenchmarkeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings GSEABenchmarkeR_1.10.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/GSEABenchmarkeR.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.10.1'
* 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 ... NOTE
evalRelevance: no visible binding for global variable 'REL.SCORE'
Undefined global functions or variables:
  REL.SCORE
* 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 (user + system) or elapsed time > 5s
                user system elapsed
loadEData      39.25   3.89   86.17
evalTypeIError 26.95   0.22   34.55
runEA          14.08   0.47   16.45
evalRandomGS    8.25   0.42   10.88
cacheResource   4.46   0.53    7.79
maPreproc       3.82   0.44    7.06
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
loadEData      36.57   2.71   51.56
evalTypeIError 32.67   0.34   37.50
runEA          14.91   0.44   17.83
evalRandomGS    9.63   0.35   13.49
cacheResource   4.73   0.23    5.03
maPreproc       3.53   0.40    6.32
* 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
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/GSEABenchmarkeR.Rcheck/00check.log'
for details.



Installation output

GSEABenchmarkeR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/GSEABenchmarkeR_1.10.1.tar.gz && rm -rf GSEABenchmarkeR.buildbin-libdir && mkdir GSEABenchmarkeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GSEABenchmarkeR.buildbin-libdir GSEABenchmarkeR_1.10.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL GSEABenchmarkeR_1.10.1.zip && rm GSEABenchmarkeR_1.10.1.tar.gz GSEABenchmarkeR_1.10.1.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  299k  100  299k    0     0  12.5M      0 --:--:-- --:--:-- --:--:-- 13.2M

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  
    evalRandomGS                            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_1.10.1.zip
* DONE (GSEABenchmarkeR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'GSEABenchmarkeR' successfully unpacked and MD5 sums checked

Tests output


Example timings

GSEABenchmarkeR.Rcheck/examples_i386/GSEABenchmarkeR-Ex.timings

nameusersystemelapsed
bpPlot0.040.000.03
cacheResource4.460.537.79
evalNrSigSets1.870.091.98
evalRandomGS 8.25 0.4210.88
evalRelevance0.770.001.17
evalTypeIError26.95 0.2234.55
loadEData39.25 3.8986.17
maPreproc3.820.447.06
readDataId2diseaseCodeMap000
readResults0.280.001.01
runDE2.140.313.66
runEA14.08 0.4716.45

GSEABenchmarkeR.Rcheck/examples_x64/GSEABenchmarkeR-Ex.timings

nameusersystemelapsed
bpPlot0.020.000.01
cacheResource4.730.235.03
evalNrSigSets3.000.033.33
evalRandomGS 9.63 0.3513.49
evalRelevance0.90.00.9
evalTypeIError32.67 0.3437.50
loadEData36.57 2.7151.56
maPreproc3.530.406.32
readDataId2diseaseCodeMap000
readResults0.30.00.3
runDE1.980.392.45
runEA14.91 0.4417.83