BioC 2.12: CHECK report for gCMAP on petty

Package: gCMAP

Version: 1.4.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch gCMAP_1.4.1.tar.gz

StartedAt: 2013-10-08 22:26:27 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:35:44 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 556.9 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 3.0.1 (2013-05-16)
* 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 '1.4.1'
* 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 ... [55s/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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [108s/103s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
mgsa_score-methods   28.921  0.840  29.683
romer_score-methods  18.603  2.312  20.711
CMAPResults-class     6.872  0.214   7.255
gsealm_score-methods  5.143  0.485   5.667
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'runTests.R' [80s/76s]
 [81s/77s] 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	2.313	0.631	2.541
CMAPResults-class	6.872	0.214	7.255
KEGG2cmap	0.009	0.006	0.015
SignedGeneSet-class	0.147	0.007	0.155
annotate_eset_list	0.220	0.018	0.238
camera_score-methods	1.016	0.201	1.638
center_eSet	0.025	0.008	0.034
connectivity_score-methods	1.631	1.231	1.519
eSetOnDisk	1.373	0.273	1.653
eset_instances	0.154	0.026	0.180
featureScores-methods	0.660	0.380	0.884
fisher_score-methods	1.130	0.784	1.135
gCMAPData-dataset	0.331	0.243	0.746
geneIndex-methods	0.675	0.417	0.714
generate_gCMAP_NChannelSet	0.385	0.080	0.683
gsealm_jg_score-methods	1.443	0.953	1.431
gsealm_score-methods	5.143	0.485	5.667
induceCMAPCollection-methods	0.591	0.408	0.740
mapNmerge	0.011	0.008	0.019
memorize	1.333	0.235	1.579
mergeCMAPs	0.208	0.027	0.237
mgsa_score-methods	28.921	0.840	29.683
minSetSize-methods	0.752	0.476	0.740
mroast_score-methods	2.011	0.671	2.226
romer_score-methods	18.603	2.312	20.711
signedRankSumTest	0.013	0.010	0.023
splitPerturbations	0.176	0.020	0.197
wilcox_score-methods	1.513	1.407	1.462