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Package 224/609HostnameOS / ArchBUILDCHECKBUILD BIN
gCMAP 1.1.7
Thomas Sandmann
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/gCMAP
Last Changed Rev: 73292 / Revision: 74773
Last Changed Date: 2013-02-08 13:35:36 -0800 (Fri, 08 Feb 2013)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 N O T   S U P P O R T E D
perceval Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: gCMAP
Version: 1.1.7
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch gCMAP_1.1.7.tar.gz
StartedAt: 2013-03-24 23:35:23 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 23:41:13 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 349.5 seconds
RetCode: 0
Status:  OK 
CheckDir: gCMAP.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/gCMAP.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'gCMAP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gCMAP' version '1.1.7'
* 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 whether package 'gCMAP' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 for unstated 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
plot,CMAPResults-ANY: no visible binding for global variable 'y'
romer_score,eSet-GeneSetCollection: no visible binding for global
  variable 'predictor'
* 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 examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
romer_score-methods 12.478  0.083  12.745
CMAPResults-class    5.523  0.238   5.876
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'runTests.R'
 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/gCMAP.Rcheck/00check.log'
for details.

gCMAP.Rcheck/00install.out:

* installing *source* package 'gCMAP' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'diffExprAnalysis.Rnw' 
   'gCMAP.Rnw' 
   'keggReactome.Rnw' 
** testing if installed package can be loaded

* DONE (gCMAP)

gCMAP.Rcheck/gCMAP-Ex.timings:

nameusersystemelapsed
CMAPCollection-class1.2240.0691.355
CMAPResults-class5.5230.2385.876
SignedGeneSet-class0.0700.0010.071
camera_score-methods0.5570.0220.591
center_eSet0.0230.0020.026
connectivity_score-methods0.3180.4060.728
eSetOnDisk0.9370.1681.122
featureScores-methods0.4000.0300.441
fisher_score-methods0.2770.2240.452
gCMAPData-dataset0.1120.0350.149
geneIndex-methods0.1070.0230.132
generate_gCMAP_NChannelSet0.2640.0290.304
gsealm_jg_score-methods0.4670.3700.733
gsealm_score-methods4.0310.2204.353
induceCMAPCollection-methods0.0730.0020.077
mapNmerge0.0000.0000.001
memorize0.9330.1111.064
minSetSize-methods0.0970.0020.101
mroast_score-methods0.8710.1161.006
romer_score-methods12.478 0.08312.745
signedRankSumTest0.0010.0000.002
wilcox_score-methods0.4000.5370.788