BioC 3.2: CHECK report for staRank on zin1

Package: staRank

Version: 1.12.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings staRank_1.12.0.tar.gz

StartedAt: 2016-04-23 05:48:24 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 05:50:46 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 142.0 seconds

RetCode: 0

Status:  OK

CheckDir: staRank.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings staRank_1.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/staRank.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.12.0’
* 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 ... [13s/13s] 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 : .local: no visible global function
  definition for ‘channelNames’
stabilityRanking,cellHTS : .local: no visible global function
  definition for ‘sampleNames’
stabilityRanking,cellHTS : .local: no visible global function
  definition for ‘featureNames’
stabilityRanking,numeric : .local: no visible global function
  definition for ‘avrgRank<-’
* 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 ... [8s/8s] 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-3.2-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	0.069	0.000	0.069
aggregRank	0.102	0.000	0.103
dataFormatRSA	0.084	0.004	0.087
getRankmatrix	0.092	0.000	0.092
getSampleScores-methods	0.088	0.000	0.088
getStability	0.091	0.000	0.092
mwTest2samp	0.001	0.000	0.001
runRSA	0.090	0.000	0.106
staRank-package	0.084	0.004	0.093
stabilityRanking-methods	0.081	0.000	0.082
summary-methods	0.084	0.000	0.084
summaryStats-methods	0.082	0.000	0.082
uniqueRSARanking	0.085	0.000	0.087