Package: gCMAP

Version: 1.3.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch gCMAP_1.3.5.tar.gz

StartedAt: 2013-03-24 05:21:39 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 05:29:55 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 495.8 seconds

RetCode: 0

Status:  OK

CheckDir: gCMAP.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/gCMAP.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'gCMAP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gCMAP' version '1.3.5'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'gCMAP' can be installed ... [49s/51s] OK
* checking installed package size ... OK
* checking package 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 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 ... OK
* 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 examples ... [101s/89s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
mgsa_score-methods   26.156  0.744  16.722
romer_score-methods  18.490  1.783  21.273
CMAPResults-class     6.692  0.392   7.497
gsealm_score-methods  5.326  0.466   5.743
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'runTests.R' [75s/69s]
 [75s/70s] 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-2.12-bioc/meat/gCMAP.Rcheck/00check.log'
for details.

* 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' 
** testing if installed package can be loaded
* DONE (gCMAP)

name	user	system	elapsed
CMAPCollection-class	1.684	0.512	2.041
CMAPResults-class	6.692	0.392	7.497
KEGG2cmap	0.007	0.007	0.014
SignedGeneSet-class	0.091	0.008	0.101
annotate_eset_list	0.178	0.018	0.732
camera_score-methods	0.796	0.210	1.405
center_eSet	0.024	0.007	0.031
connectivity_score-methods	1.455	1.136	1.383
eSetOnDisk	1.325	0.264	1.721
eset_instances	0.122	0.023	0.146
featureScores-methods	0.583	0.389	0.819
fisher_score-methods	1.085	0.763	1.148
gCMAPData-dataset	0.488	0.357	0.860
geneIndex-methods	0.661	0.403	0.903
generate_gCMAP_NChannelSet	0.297	0.038	0.335
gsealm_jg_score-methods	1.273	0.945	1.494
gsealm_score-methods	5.326	0.466	5.743
induceCMAPCollection-methods	0.664	0.461	0.899
mapNmerge	0.012	0.009	0.021
memorize	1.388	0.223	1.622
mergeCMAPs	0.167	0.024	0.193
mgsa_score-methods	26.156	0.744	16.722
minSetSize-methods	0.418	0.255	1.013
mroast_score-methods	2.195	0.878	2.528
romer_score-methods	18.490	1.783	21.273
signedRankSumTest	0.016	0.015	0.032
splitPerturbations	0.138	0.027	0.167
wilcox_score-methods	1.145	1.059	1.462