BioC 3.2: CHECK report for gCMAP on perceval

Package: gCMAP

Version: 1.13.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gCMAP_1.13.0.tar.gz

StartedAt: 2015-08-24 00:50:45 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 00:56:22 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 337.6 seconds

RetCode: 0

Status:  OK

CheckDir: gCMAP.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gCMAP_1.13.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/gCMAP.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.13.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘bigmemoryExtras’
* 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 ... [30s/30s] 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
'library' or 'require' calls in package code:
  ‘bigmemoryExtras’ ‘GO.db’ ‘KEGG.db’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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
camera_score,eSet-CMAPCollection : .local: no visible global function
  definition for ‘camera’
induceCMAPCollection,eSet : .local : <anonymous>: no visible global
  function definition for ‘mwhich’
mroast_score,eSet-CMAPCollection : .local: no visible global function
  definition for ‘mroast’
romer_score,eSet-CMAPCollection : .local: no visible global function
  definition for ‘romer’
* 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 files in ‘vignettes’ ... OK
* checking examples ... [79s/70s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
mgsa_score-methods  24.993  0.925  26.340
romer_score-methods  9.906  0.857  10.419
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [61s/54s]
 [61s/54s] 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
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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	1.268	0.652	1.328
CMAPResults-class	3.262	0.188	3.450
KEGG2cmap	0.001	0.000	0.000
SignedGeneSet-class	0.064	0.002	0.065
annotate_eset_list	0.107	0.012	0.152
camera_score-methods	0.555	0.207	1.354
center_eSet	0.039	0.008	0.046
connectivity_score-methods	1.886	1.560	1.429
eSetOnDisk	0.010	0.002	0.011
eset_instances	0.093	0.031	0.124
featureScores-methods	0.582	0.424	0.904
fisher_score-methods	1.309	0.941	0.966
gCMAPData-dataset	0.554	0.444	0.884
geneIndex-methods	0.916	0.677	1.063
generate_gCMAP_NChannelSet	0.240	0.051	0.291
gsealm_jg_score-methods	1.453	1.179	1.237
gsealm_score-methods	2.983	0.251	3.717
induceCMAPCollection-methods	0.814	0.559	0.741
mapNmerge	0.001	0.000	0.001
memorize	0.010	0.001	0.011
mergeCMAPs	0.115	0.034	0.149
mgsa_score-methods	24.993	0.925	26.340
minSetSize-methods	1.103	1.009	1.038
mroast_score-methods	2.414	1.397	2.249
romer_score-methods	9.906	0.857	10.419
signedRankSumTest	0.003	0.000	0.003
splitPerturbations	0.090	0.008	0.099
wilcox_score-methods	1.400	1.367	1.432