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BioC 3.5: CHECK report for staRank on tokay2

This page was generated on 2017-08-16 13:21:40 -0400 (Wed, 16 Aug 2017).

Package 1276/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
staRank 1.18.0
Juliane Siebourg
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/staRank
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: staRank
Version: 1.18.0
Command: rm -rf staRank.buildbin-libdir staRank.Rcheck && mkdir staRank.buildbin-libdir staRank.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=staRank.buildbin-libdir staRank_1.18.0.tar.gz >staRank.Rcheck\00install.out 2>&1 && cp staRank.Rcheck\00install.out staRank-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=staRank.buildbin-libdir --install="check:staRank-install.out" --force-multiarch --no-vignettes --timings staRank_1.18.0.tar.gz
StartedAt: 2017-08-16 03:09:05 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 03:13:15 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 249.7 seconds
RetCode: 0
Status:  OK  
CheckDir: staRank.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf staRank.buildbin-libdir staRank.Rcheck && mkdir staRank.buildbin-libdir staRank.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=staRank.buildbin-libdir staRank_1.18.0.tar.gz >staRank.Rcheck\00install.out 2>&1 && cp staRank.Rcheck\00install.out staRank-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=staRank.buildbin-libdir --install="check:staRank-install.out" --force-multiarch --no-vignettes --timings staRank_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/staRank.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.18.0'
* 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 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 : <anonymous>: no visible global function definition for
  'phyper'
aggregRank : <anonymous>: 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 : <anonymous>: no visible global function definition
  for 'median'
summaryStats,list : <anonymous>: no visible global function definition
  for 't.test'
summaryStats,matrix : <anonymous>: no visible global function
  definition for 'median'
summaryStats,matrix : <anonymous>: 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 installed files from 'inst/doc' ... 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-3.5-bioc/meat/staRank.Rcheck/00check.log'
for details.


staRank.Rcheck/00install.out:


install for i386

* installing *source* package 'staRank' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'staRank' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'staRank' as staRank_1.18.0.zip
* DONE (staRank)

staRank.Rcheck/examples_i386/staRank-Ex.timings:

nameusersystemelapsed
RankSummary-class0.070.030.11
aggregRank0.270.000.26
dataFormatRSA0.040.020.06
getRankmatrix0.040.000.04
getSampleScores-methods0.070.000.07
getStability0.060.000.06
mwTest2samp000
runRSA0.050.000.05
staRank-package0.040.000.04
stabilityRanking-methods0.050.000.05
summary-methods0.050.000.04
summaryStats-methods0.060.000.07
uniqueRSARanking0.050.000.04

staRank.Rcheck/examples_x64/staRank-Ex.timings:

nameusersystemelapsed
RankSummary-class0.090.000.09
aggregRank0.330.000.33
dataFormatRSA0.080.000.08
getRankmatrix0.080.000.08
getSampleScores-methods0.080.000.08
getStability0.070.000.08
mwTest2samp000
runRSA0.070.000.06
staRank-package0.070.000.08
stabilityRanking-methods0.080.000.07
summary-methods0.070.000.07
summaryStats-methods0.060.000.06
uniqueRSARanking0.060.000.06