BioC 3.2: CHECK report for gCMAP on oaxaca

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: 2016-04-23 00:18:48 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 00:24:22 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 334.3 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 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (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 ... [27s/45s] 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:
  ‘GO.db’ ‘KEGG.db’ ‘bigmemoryExtras’
  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 ... [60s/103s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
mgsa_score-methods  15.46  0.549  66.809
romer_score-methods  7.49  0.999   7.705
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [40s/35s]
 [40s/36s] 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	1.332	0.431	1.321
CMAPResults-class	2.646	0.100	2.829
KEGG2cmap	0.001	0.000	0.001
SignedGeneSet-class	0.069	0.000	0.070
annotate_eset_list	0.120	0.007	0.255
camera_score-methods	0.551	0.105	1.301
center_eSet	0.033	0.002	0.035
connectivity_score-methods	1.850	0.838	1.012
eSetOnDisk	0.008	0.000	0.008
eset_instances	0.086	0.014	0.100
featureScores-methods	0.186	0.069	0.707
fisher_score-methods	1.784	0.796	0.886
gCMAPData-dataset	0.175	0.079	0.753
geneIndex-methods	0.959	0.394	0.696
generate_gCMAP_NChannelSet	0.211	0.020	0.231
gsealm_jg_score-methods	1.963	0.840	1.015
gsealm_score-methods	3.403	0.133	4.041
induceCMAPCollection-methods	1.290	0.566	0.652
mapNmerge	0.001	0.000	0.001
memorize	0.008	0.001	0.008
mergeCMAPs	0.109	0.016	0.125
mgsa_score-methods	15.460	0.549	66.809
minSetSize-methods	0.968	0.492	0.760
mroast_score-methods	1.689	0.562	1.637
romer_score-methods	7.490	0.999	7.705
signedRankSumTest	0.003	0.001	0.003
splitPerturbations	0.067	0.004	0.071
wilcox_score-methods	1.666	0.814	0.927