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BioC 3.0: CHECK report for GeneExpressionSignature on perceval

This page was generated on 2015-04-10 09:56:13 -0700 (Fri, 10 Apr 2015).

Package 345/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneExpressionSignature 1.12.0
Yang Cao , Fei Li ,Lu Han
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/GeneExpressionSignature
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: GeneExpressionSignature
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneExpressionSignature_1.12.0.tar.gz
StartedAt: 2015-04-10 01:50:44 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 01:53:56 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 192.8 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneExpressionSignature.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneExpressionSignature_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/GeneExpressionSignature.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneExpressionSignature/DESCRIPTION’ ... OK
* this is package ‘GeneExpressionSignature’ 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 ‘GeneExpressionSignature’ can be installed ... [14s/15s] 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 ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘PGSEA’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
integratePRL: no visible global function definition for ‘phenoData’
integratePRL: no visible global function definition for ‘exprs’
RankMerging: no visible global function definition for ‘exprs’
RankMerging: no visible global function definition for ‘phenoData’
ScoreGSEA : PRL.Distance: no visible global function definition for
  ‘exprs’
ScoreGSEA: no visible global function definition for ‘exprs’
ScorePGSEA: no visible global function definition for ‘exprs’
ScorePGSEA: no visible global function definition for ‘PGSEA’
* 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 ... [56s/56s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
ScoreGSEA         12.535  1.613  14.194
SignatureDistance 12.377  1.537  13.953
ScorePGSEA        10.338  1.352  11.721
RankMerging        7.161  0.412   7.582
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/GeneExpressionSignature.Rcheck/00check.log’
for details.

GeneExpressionSignature.Rcheck/00install.out:

* installing *source* package ‘GeneExpressionSignature’ ...
** 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 (GeneExpressionSignature)

GeneExpressionSignature.Rcheck/GeneExpressionSignature-Ex.timings:

nameusersystemelapsed
RankMerging7.1610.4127.582
ScoreGSEA12.535 1.61314.194
ScorePGSEA10.338 1.35211.721
SignatureDistance12.377 1.53713.953
exampleSet0.2850.0210.307
getRLs1.1150.0521.228