BioC 3.2: CHECK report for gCMAP on perceval

Package: gCMAP

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gCMAP_1.14.0.tar.gz

StartedAt: 2015-10-27 07:59:50 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 08:05:06 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 316.3 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_1.14.0.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 (2015-10-08 r69496)
* 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 ‘1.14.0’
* 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 ... [28s/28s] 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 ... [78s/73s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
mgsa_score-methods  30.251  0.726  34.657
romer_score-methods  9.183  0.431   9.478
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [53s/47s]
 [53s/47s] 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	1.166	0.434	1.172
CMAPResults-class	2.839	0.159	3.000
KEGG2cmap	0.001	0.000	0.001
SignedGeneSet-class	0.054	0.001	0.055
annotate_eset_list	0.114	0.012	0.138
camera_score-methods	0.561	0.162	1.206
center_eSet	0.038	0.006	0.043
connectivity_score-methods	1.646	0.989	1.048
eSetOnDisk	0.010	0.001	0.010
eset_instances	0.089	0.020	0.109
featureScores-methods	0.201	0.115	0.732
fisher_score-methods	1.554	0.836	0.860
gCMAPData-dataset	0.174	0.122	0.678
geneIndex-methods	0.795	0.377	0.708
generate_gCMAP_NChannelSet	0.248	0.044	0.292
gsealm_jg_score-methods	1.815	1.004	1.100
gsealm_score-methods	3.271	0.230	3.872
induceCMAPCollection-methods	0.776	0.360	0.626
mapNmerge	0.001	0.000	0.001
memorize	0.010	0.000	0.011
mergeCMAPs	0.136	0.029	0.165
mgsa_score-methods	30.251	0.726	34.657
minSetSize-methods	1.812	1.228	0.842
mroast_score-methods	1.399	0.476	1.886
romer_score-methods	9.183	0.431	9.478
signedRankSumTest	0.003	0.000	0.003
splitPerturbations	0.089	0.012	0.100
wilcox_score-methods	1.676	1.072	1.173