BioC 2.13: CHECK report for gCMAP on perceval

Package: gCMAP

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch gCMAP_1.6.0.tar.gz

StartedAt: 2014-04-05 01:24:18 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:32:23 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 484.8 seconds

RetCode: 0

Status:  OK

CheckDir: gCMAP.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/gCMAP.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.6.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘gCMAP’ can be installed ... [45s/46s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘annotate’ ‘Biobase’ ‘BiocGenerics’ ‘Category’ ‘methods’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘GSEABase’ ‘limma’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ‘:::’ call: ‘GSEABase:::.showGeneSet’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘CMAPResults’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
eSetOnDisk: no visible global function definition for ‘BigMatrix’
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘diffExprAnalysis.Rnw’, ‘gCMAP.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [90s/85s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
mgsa_score-methods   18.462  0.784  19.729
romer_score-methods  14.662  0.978  15.329
CMAPResults-class     6.085  0.301   6.521
gsealm_score-methods  4.743  0.380   5.551
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [74s/70s]
 [75s/71s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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	1.277	0.603	1.393
CMAPResults-class	6.085	0.301	6.521
KEGG2cmap	0.003	0.004	0.008
SignedGeneSet-class	0.087	0.009	0.098
annotate_eset_list	0.156	0.017	0.172
camera_score-methods	0.614	0.188	1.451
center_eSet	0.054	0.009	0.063
connectivity_score-methods	1.989	1.845	1.941
eSetOnDisk	2.056	0.261	2.453
eset_instances	0.123	0.034	0.162
featureScores-methods	0.652	0.464	0.878
fisher_score-methods	1.099	0.827	1.139
gCMAPData-dataset	0.279	0.258	0.798
geneIndex-methods	0.756	0.519	0.789
generate_gCMAP_NChannelSet	0.343	0.073	0.419
gsealm_jg_score-methods	1.664	1.389	1.501
gsealm_score-methods	4.743	0.380	5.551
induceCMAPCollection-methods	0.643	0.484	0.644
mapNmerge	0.003	0.006	0.009
memorize	1.713	0.193	1.986
mergeCMAPs	0.174	0.023	0.205
mgsa_score-methods	18.462	0.784	19.729
minSetSize-methods	0.703	0.482	0.779
mroast_score-methods	1.578	0.651	1.775
romer_score-methods	14.662	0.978	15.329
signedRankSumTest	0.013	0.012	0.025
splitPerturbations	0.121	0.017	0.144
wilcox_score-methods	1.158	1.176	1.466