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CHECK report for staRank on tokay2

This page was generated on 2019-10-16 12:26:31 -0400 (Wed, 16 Oct 2019).

Package 1593/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
staRank 1.26.0
Juliane Siebourg
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/staRank
Branch: RELEASE_3_9
Last Commit: eed8d7a
Last Changed Date: 2019-05-02 11:53:36 -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: staRank
Version: 1.26.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:staRank.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings staRank_1.26.0.tar.gz
StartedAt: 2019-10-16 07:22:39 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 07:26:06 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 207.3 seconds
RetCode: 0
Status:  OK  
CheckDir: staRank.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:staRank.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings staRank_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/staRank.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 'staRank/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'staRank' 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 'staRank' 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
OPIScore : : no visible global function definition for
  'phyper'
aggregRank : : no visible global function definition for
  'median'
mwTest2samp: no visible global function definition for 'pwilcox'
mwTest2samp: no visible global function definition for 'pnorm'
show,RankSummary: no visible global function definition for 'head'
stabilityRanking,cellHTS: no visible global function definition for
  'channelNames'
stabilityRanking,cellHTS: no visible global function definition for
  'sampleNames'
stabilityRanking,cellHTS: no visible global function definition for
  'featureNames'
stabilityRanking,numeric: no visible global function definition for
  'avrgRank<-'
stabilityRanking,numeric: no visible global function definition for
  'cor'
summaryStats,list : : no visible global function definition
  for 'median'
summaryStats,list : : no visible global function definition
  for 't.test'
summaryStats,matrix : : no visible global function
  definition for 'median'
summaryStats,matrix : : no visible global function
  definition for 't.test'
Undefined global functions or variables:
  avrgRank<- channelNames cor featureNames head median phyper pnorm
  pwilcox sampleNames t.test
Consider adding
  importFrom("stats", "cor", "median", "phyper", "pnorm", "pwilcox",
             "t.test")
  importFrom("utils", "head")
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 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 ...
** 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-3.9-bioc/meat/staRank.Rcheck/00check.log'
for details.



Installation output

staRank.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/staRank_1.26.0.tar.gz && rm -rf staRank.buildbin-libdir && mkdir staRank.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=staRank.buildbin-libdir staRank_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL staRank_1.26.0.zip && rm staRank_1.26.0.tar.gz staRank_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
  0  277k    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  277k  100  277k    0     0  4343k      0 --:--:-- --:--:-- --:--:-- 4789k

install for i386

* installing *source* package 'staRank' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'staRank'
    finding HTML links ... done
    Pi-methods                              html  
    RankSummary-class                       html  
    aggregRank                              html  
    avrgRank-methods                        html  
    baseRank-methods                        html  
    dataFormatRSA                           html  
    getRankmatrix                           html  
    getSampleScores-methods                 html  
    getStability                            html  
    method-methods                          html  
    mwTest2samp                             html  
    rankCor-methods                         html  
    runRSA                                  html  
    salmonellaInfection                     html  
    salmonellaStability                     html  
    show-methods                            html  
    staRank-package                         html  
    stabRank-methods                        html  
    stabilityRanking-methods                html  
    stableSetSize-methods                   html  
    summary-methods                         html  
    summaryStats-methods                    html  
    uniqueRSARanking                        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 'staRank' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'staRank' as staRank_1.26.0.zip
* DONE (staRank)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'staRank' successfully unpacked and MD5 sums checked

Tests output


Example timings

staRank.Rcheck/examples_i386/staRank-Ex.timings

nameusersystemelapsed
RankSummary-class0.070.000.08
aggregRank0.080.000.08
dataFormatRSA0.050.000.04
getRankmatrix0.060.000.07
getSampleScores-methods0.060.000.06
getStability0.010.070.08
mwTest2samp000
runRSA0.080.030.11
staRank-package0.090.060.16
stabilityRanking-methods0.080.050.12
summary-methods0.10.00.1
summaryStats-methods0.090.000.09
uniqueRSARanking0.090.000.09

staRank.Rcheck/examples_x64/staRank-Ex.timings

nameusersystemelapsed
RankSummary-class0.090.000.10
aggregRank0.160.000.15
dataFormatRSA0.130.000.12
getRankmatrix0.090.000.10
getSampleScores-methods0.110.010.12
getStability0.080.000.08
mwTest2samp000
runRSA0.060.000.06
staRank-package0.060.020.08
stabilityRanking-methods0.070.000.06
summary-methods0.060.000.07
summaryStats-methods0.070.000.07
uniqueRSARanking0.060.000.06