BioC 3.3: CHECK report for staRank on linux2.bioconductor.org
This page was generated on 2015-10-27 12:12:08 -0400 (Tue, 27 Oct 2015).
staRank 1.13.0 Juliane Siebourg
Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/staRank | Last Changed Rev: 109592 / Revision: 109948 | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |  |
Summary
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 |
Command output
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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.
staRank.Rcheck/00install.out:
* 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)
staRank.Rcheck/staRank-Ex.timings:
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 |
|