Package: gCMAP

Version: 1.3.5

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings gCMAP_1.3.5.tar.gz

StartedAt: 2013-03-25 01:44:53 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:54:16 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 562.1 seconds

RetCode: 0

Status:  OK

CheckDir: gCMAP.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/gCMAP.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... [58s/59s] 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 ... [96s/83s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
romer_score-methods  19.877  0.240  20.997
mgsa_score-methods   17.949  0.528   8.400
CMAPResults-class     8.392  0.144   8.552
gsealm_score-methods  5.516  0.164   5.943
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [80s/75s]
 [80s/76s] 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
  ‘/home/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	1.872	0.352	1.935
CMAPResults-class	8.392	0.144	8.552
KEGG2cmap	0.012	0.008	0.018
SignedGeneSet-class	0.128	0.000	0.126
annotate_eset_list	0.248	0.000	0.244
camera_score-methods	1.044	0.212	1.360
center_eSet	0.036	0.000	0.038
connectivity_score-methods	1.112	0.972	1.638
eSetOnDisk	2.172	0.088	2.674
eset_instances	0.132	0.016	0.158
featureScores-methods	0.332	0.136	0.659
fisher_score-methods	1.109	0.732	1.055
gCMAPData-dataset	0.476	0.260	0.641
geneIndex-methods	0.536	0.296	0.723
generate_gCMAP_NChannelSet	0.364	0.016	0.382
gsealm_jg_score-methods	1.224	0.712	1.186
gsealm_score-methods	5.516	0.164	5.943
induceCMAPCollection-methods	0.876	0.388	0.655
mapNmerge	0.016	0.008	0.024
memorize	2.100	0.068	2.198
mergeCMAPs	0.196	0.004	0.219
mgsa_score-methods	17.949	0.528	8.400
minSetSize-methods	0.632	0.308	0.619
mroast_score-methods	2.016	0.448	1.923
romer_score-methods	19.877	0.240	20.997
signedRankSumTest	0.024	0.004	0.027
splitPerturbations	0.136	0.000	0.136
wilcox_score-methods	1.105	1.132	1.489