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BioC 3.5: CHECK report for staRank on oaxaca

This page was generated on 2017-03-04 16:43:49 -0500 (Sat, 04 Mar 2017).

Package 1236/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
staRank 1.17.0
Juliane Siebourg
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/staRank
Last Changed Rev: 122712 / Revision: 127142
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
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
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: staRank
Version: 1.17.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings staRank_1.17.0.tar.gz
StartedAt: 2017-03-04 09:41:27 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 09:44:37 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 190.6 seconds
RetCode: 0
Status:  OK 
CheckDir: staRank.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings staRank_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/staRank.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘staRank/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘staRank’ version ‘1.17.0’
* 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 for sufficient/correct file permissions ... 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/staRank.Rcheck/00check.log’
for details.


staRank.Rcheck/00install.out:

* 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
* DONE (staRank)

staRank.Rcheck/staRank-Ex.timings:

nameusersystemelapsed
RankSummary-class0.1390.0090.148
aggregRank0.4940.0200.514
dataFormatRSA0.1340.0030.137
getRankmatrix0.0960.0010.097
getSampleScores-methods0.0720.0010.073
getStability0.1110.0030.113
mwTest2samp0.0010.0000.000
runRSA0.1080.0030.110
staRank-package0.1190.0020.122
stabilityRanking-methods0.1090.0020.111
summary-methods0.1200.0010.121
summaryStats-methods0.1200.0020.122
uniqueRSARanking0.1160.0020.118