BioC 3.3: CHECK report for gCMAP on morelia

Package: gCMAP

Version: 1.15.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gCMAP_1.15.0.tar.gz

StartedAt: 2015-10-22 06:13:57 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 06:17:22 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 205.1 seconds

RetCode: 0

Status:  OK

CheckDir: gCMAP.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gCMAP_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/gCMAP.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘1.15.0’
* 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 ... [18s/19s] 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 ... [44s/49s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
mgsa_score-methods  12.493  0.332  24.360
romer_score-methods  5.381  0.740   5.228
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [30s/26s]
 [30s/26s] 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-3.3-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	0.850	0.301	0.857
CMAPResults-class	1.918	0.077	1.996
KEGG2cmap	0	0	0
SignedGeneSet-class	0.066	0.000	0.066
annotate_eset_list	0.098	0.006	0.149
camera_score-methods	0.575	0.177	0.758
center_eSet	0.024	0.002	0.026
connectivity_score-methods	1.050	0.534	0.774
eSetOnDisk	0.009	0.001	0.010
eset_instances	0.089	0.015	0.104
featureScores-methods	0.433	0.196	0.556
fisher_score-methods	1.039	0.499	0.683
gCMAPData-dataset	0.134	0.086	0.497
geneIndex-methods	0.622	0.263	0.518
generate_gCMAP_NChannelSet	0.172	0.021	0.194
gsealm_jg_score-methods	1.497	0.657	0.786
gsealm_score-methods	2.109	0.103	2.638
induceCMAPCollection-methods	1.032	0.468	0.535
mapNmerge	0	0	0
memorize	0.005	0.000	0.006
mergeCMAPs	0.069	0.011	0.080
mgsa_score-methods	12.493	0.332	24.360
minSetSize-methods	1.025	0.532	0.572
mroast_score-methods	0.996	0.297	1.250
romer_score-methods	5.381	0.740	5.228
signedRankSumTest	0.002	0.000	0.002
splitPerturbations	0.052	0.003	0.056
wilcox_score-methods	0.937	0.486	0.658