BioC 3.4: CHECK report for gCMAP on morelia

Package: gCMAP

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gCMAP_1.18.0.tar.gz

StartedAt: 2017-04-15 02:25:40 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 02:29:48 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 247.3 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_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/gCMAP.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.18.0’
* 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 ... 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: no visible global function definition
  for ‘camera’
induceCMAPCollection,eSet : <anonymous>: no visible global function
  definition for ‘mwhich’
mroast_score,eSet-CMAPCollection: no visible global function definition
  for ‘mroast’
romer_score,eSet-CMAPCollection: no visible global function definition
  for ‘romer’
Undefined global functions or variables:
  camera mroast mwhich 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 ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
mgsa_score-methods  16.095  0.468  30.880
romer_score-methods  5.369  0.557   5.829
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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-3.4-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	1.653	0.805	1.594
CMAPResults-class	2.358	0.103	2.468
KEGG2cmap	0.001	0.000	0.001
SignedGeneSet-class	0.024	0.001	0.025
annotate_eset_list	0.117	0.013	0.169
camera_score-methods	0.477	0.080	0.953
center_eSet	0.031	0.002	0.034
connectivity_score-methods	1.494	0.735	0.883
eSetOnDisk	0.008	0.002	0.009
eset_instances	0.085	0.016	0.102
featureScores-methods	0.154	0.066	0.611
fisher_score-methods	1.387	0.794	0.742
gCMAPData-dataset	0.125	0.059	0.571
geneIndex-methods	0.722	0.358	0.607
generate_gCMAP_NChannelSet	0.170	0.016	0.185
gsealm_jg_score-methods	1.470	0.722	0.796
gsealm_score-methods	2.667	0.109	3.114
induceCMAPCollection-methods	0.635	0.302	0.532
mapNmerge	0.001	0.000	0.001
memorize	0.008	0.001	0.009
mergeCMAPs	0.143	0.021	0.165
mgsa_score-methods	16.095	0.468	30.880
minSetSize-methods	0.732	0.370	0.544
mroast_score-methods	1.679	0.560	1.334
romer_score-methods	5.369	0.557	5.829
signedRankSumTest	0.002	0.001	0.003
splitPerturbations	0.071	0.006	0.077
wilcox_score-methods	1.207	0.592	0.702