BioC 3.3: CHECK report for staRank on linux2.bioconductor.org

Package: staRank

Version: 1.13.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings staRank_1.13.0.tar.gz

StartedAt: 2015-10-27 08:23:40 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 08:25:53 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 133.1 seconds

RetCode: 0

Status:  OK

CheckDir: staRank.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings staRank_1.13.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/staRank.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (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 ‘1.13.0’
* 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 ... [11s/11s] 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
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<-’
Undefined global functions or variables:
  avrgRank<- channelNames featureNames sampleNames
* 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 ... [6s/6s] 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
  ‘/home/biocbuild/bbs-3.3-bioc/meat/staRank.Rcheck/00check.log’
for details.

* installing *source* package ‘staRank’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘summary’ from package ‘base’ in package ‘staRank’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (staRank)

name	user	system	elapsed
RankSummary-class	0.047	0.004	0.051
aggregRank	0.061	0.000	0.061
dataFormatRSA	0.065	0.000	0.065
getRankmatrix	0.067	0.000	0.067
getSampleScores-methods	0.066	0.000	0.066
getStability	0.063	0.000	0.063
mwTest2samp	0.028	0.000	0.029
runRSA	0.088	0.000	0.088
staRank-package	0.103	0.000	0.103
stabilityRanking-methods	0.077	0.000	0.077
summary-methods	0.066	0.000	0.066
summaryStats-methods	0.080	0.004	0.084
uniqueRSARanking	0.064	0.000	0.064