Package: gCMAP

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch gCMAP_1.4.0.tar.gz

StartedAt: 2013-05-01 05:35:07 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 05:44:26 -0700 (Wed, 01 May 2013)

EllapsedTime: 559.2 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 Patched (2013-04-08 r62531)
* 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 '1.4.0'
* 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 ... 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 ... [47s/52s] 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 ... [129s/132s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
mgsa_score-methods   55.658  1.008  61.833
romer_score-methods  18.563  1.977  20.595
CMAPResults-class     6.128  0.372   6.783
gsealm_score-methods  4.890  0.356   5.778
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'runTests.R' [85s/83s]
 [85s/84s] 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
** testing if installed package can be loaded
* DONE (gCMAP)

name	user	system	elapsed
CMAPCollection-class	1.659	0.501	1.945
CMAPResults-class	6.128	0.372	6.783
KEGG2cmap	0.003	0.005	0.010
SignedGeneSet-class	0.097	0.009	0.108
annotate_eset_list	0.192	0.023	0.252
camera_score-methods	0.778	0.202	1.600
center_eSet	0.027	0.008	0.035
connectivity_score-methods	1.547	1.297	1.524
eSetOnDisk	1.324	0.223	1.601
eset_instances	0.121	0.031	0.159
featureScores-methods	0.579	0.362	0.848
fisher_score-methods	1.031	0.724	1.072
gCMAPData-dataset	0.512	0.373	1.348
geneIndex-methods	0.399	0.267	0.675
generate_gCMAP_NChannelSet	0.306	0.052	0.359
gsealm_jg_score-methods	1.468	1.056	1.407
gsealm_score-methods	4.890	0.356	5.778
induceCMAPCollection-methods	0.875	0.572	0.827
mapNmerge	0.004	0.008	0.011
memorize	1.303	0.204	1.648
mergeCMAPs	0.163	0.021	0.187
mgsa_score-methods	55.658	1.008	61.833
minSetSize-methods	0.673	0.453	0.844
mroast_score-methods	2.086	0.545	2.777
romer_score-methods	18.563	1.977	20.595
signedRankSumTest	0.014	0.013	0.030
splitPerturbations	0.140	0.025	0.176
wilcox_score-methods	1.181	1.126	1.628