Package: staRank

Version: 1.28.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:staRank.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings staRank_1.28.0.tar.gz

StartedAt: 2020-04-15 05:59:16 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:02:29 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 193.2 seconds

RetCode: 0

Status:  OK

CheckDir: staRank.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:staRank.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings staRank_1.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/staRank.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.28.0’
* 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 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 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-3.10-bioc/meat/staRank.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL staRank
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘staRank’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (staRank)

name	user	system	elapsed
RankSummary-class	0.097	0.004	0.102
aggregRank	0.164	0.007	0.175
dataFormatRSA	0.114	0.001	0.117
getRankmatrix	0.113	0.002	0.119
getSampleScores-methods	0.123	0.017	0.142
getStability	0.127	0.012	0.140
mwTest2samp	0.001	0.000	0.001
runRSA	0.123	0.002	0.126
staRank-package	0.093	0.001	0.097
stabilityRanking-methods	0.099	0.003	0.103
summary-methods	0.101	0.002	0.104
summaryStats-methods	0.093	0.002	0.094
uniqueRSARanking	0.110	0.001	0.112