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CHECK report for npGSEA on tokay1

This page was generated on 2021-05-06 12:32:34 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the npGSEA package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1236/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
npGSEA 1.26.0  (landing page)
Jessica Larson
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/npGSEA
Branch: RELEASE_3_12
Last Commit: 0231dd4
Last Changed Date: 2020-10-27 10:56:19 -0400 (Tue, 27 Oct 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: npGSEA
Version: 1.26.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:npGSEA.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings npGSEA_1.26.0.tar.gz
StartedAt: 2021-05-06 05:08:38 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 05:10:56 -0400 (Thu, 06 May 2021)
EllapsedTime: 138.5 seconds
RetCode: 0
Status:   OK   
CheckDir: npGSEA.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:npGSEA.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings npGSEA_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/npGSEA.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 'npGSEA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'npGSEA' version '1.26.0'
* 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 whether package 'npGSEA' 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
.prepXYZ: no visible global function definition for 'sd'
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
* 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
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/npGSEA.Rcheck/00check.log'
for details.



Installation output

npGSEA.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/npGSEA_1.26.0.tar.gz && rm -rf npGSEA.buildbin-libdir && mkdir npGSEA.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=npGSEA.buildbin-libdir npGSEA_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL npGSEA_1.26.0.zip && rm npGSEA_1.26.0.tar.gz npGSEA_1.26.0.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 20785  100 20785    0     0   815k      0 --:--:-- --:--:-- --:--:--  845k

install for i386

* installing *source* package 'npGSEA' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'npGSEA'
** help
*** installing help indices
  converting help for package 'npGSEA'
    finding HTML links ... done
    DF-methods                              html  
    alphaValue-methods                      html  
    betaHats-methods                        html  
    betaStat-methods                        html  
    betaValue-methods                       html  
    chiSqStat-methods                       html  
    geneSetName-methods                     html  
    getIncidence                            html  
    npGSEA                                  html  
    npGSEAPlot-methods                      html  
    npGSEAResultBeta-class                  html  
    npGSEAResultBetaCollection-class        html  
    npGSEAResultChiSq-class                 html  
    npGSEAResultChiSqCollection-class       html  
    npGSEAResultNorm-class                  html  
    npGSEAResultNormCollection-class        html  
    pLeft-methods                           html  
    pRight-methods                          html  
    pTwoSided-methods                       html  
    pValues-methods                         html  
    show-methods                            html  
    sigmaSq-methods                         html  
    stat-methods                            html  
    xSet-methods                            html  
    zStat-methods                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'npGSEA'
** testing if installed package can be loaded from final location
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'npGSEA'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'npGSEA' ...
** testing if installed package can be loaded
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'npGSEA'
* MD5 sums
packaged installation of 'npGSEA' as npGSEA_1.26.0.zip
* DONE (npGSEA)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'npGSEA' successfully unpacked and MD5 sums checked

Tests output


Example timings

npGSEA.Rcheck/examples_i386/npGSEA-Ex.timings

nameusersystemelapsed
DF-methods0.000.020.02
alphaValue-methods0.000.010.01
betaHats-methods000
betaStat-methods000
betaValue-methods000
chiSqStat-methods0.010.000.01
geneSetName-methods000
getIncidence000
npGSEA000
npGSEAPlot-methods0.000.020.02
npGSEAResultBeta-class000
npGSEAResultBetaCollection-class000
npGSEAResultChiSq-class000
npGSEAResultChiSqCollection-class000
npGSEAResultNorm-class000
npGSEAResultNormCollection-class000
pLeft-methods000
pRight-methods0.020.000.02
pTwoSided-methods000
pValues-methods000
show-methods000
sigmaSq-methods0.020.000.01
stat-methods000
xSet-methods000
zStat-methods000

npGSEA.Rcheck/examples_x64/npGSEA-Ex.timings

nameusersystemelapsed
DF-methods0.020.000.02
alphaValue-methods000
betaHats-methods000
betaStat-methods0.010.000.02
betaValue-methods000
chiSqStat-methods000
geneSetName-methods0.020.000.01
getIncidence000
npGSEA000
npGSEAPlot-methods000
npGSEAResultBeta-class000
npGSEAResultBetaCollection-class000
npGSEAResultChiSq-class000
npGSEAResultChiSqCollection-class000
npGSEAResultNorm-class000
npGSEAResultNormCollection-class000
pLeft-methods000
pRight-methods000
pTwoSided-methods000
pValues-methods000
show-methods0.000.020.01
sigmaSq-methods000
stat-methods000
xSet-methods000
zStat-methods000