BioC 2.14: CHECK report for gCMAP on petty

Package: gCMAP

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch gCMAP_1.8.0.tar.gz

StartedAt: 2014-10-07 22:04:14 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:13:46 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 571.7 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 --no-multiarch gCMAP_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/gCMAP.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.8.0’
* 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 ... [57s/58s] 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
Namespaces in Imports field not imported from:
  ‘annotate’ ‘Biobase’ ‘BiocGenerics’ ‘Category’ ‘methods’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘GSEABase’ ‘limma’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘GSEABase:::.showGeneSet’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘CMAPResults’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of 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
eSetOnDisk: no visible global function definition for ‘BigMatrix’
* 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 ... [111s/100s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
mgsa_score-methods   29.454  0.878  30.221
romer_score-methods  15.613  0.894  16.088
CMAPResults-class     7.099  0.238   7.427
gsealm_score-methods  5.981  0.270   6.911
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [80s/72s]
 [80s/73s] 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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	1.972	0.644	1.908
CMAPResults-class	7.099	0.238	7.427
KEGG2cmap	0.002	0.000	0.002
SignedGeneSet-class	0.149	0.002	0.155
annotate_eset_list	0.228	0.011	0.253
camera_score-methods	1.516	0.295	2.644
center_eSet	0.060	0.001	0.061
connectivity_score-methods	2.608	1.520	1.716
eSetOnDisk	0.018	0.004	0.022
eset_instances	0.171	0.044	0.216
featureScores-methods	0.375	0.198	1.129
fisher_score-methods	2.401	1.256	1.408
gCMAPData-dataset	0.333	0.179	1.213
geneIndex-methods	1.243	0.623	1.039
generate_gCMAP_NChannelSet	0.457	0.081	0.541
gsealm_jg_score-methods	2.682	1.409	1.773
gsealm_score-methods	5.981	0.270	6.911
induceCMAPCollection-methods	1.172	0.597	0.979
mapNmerge	0.002	0.000	0.002
memorize	0.020	0.002	0.022
mergeCMAPs	0.234	0.048	0.283
mgsa_score-methods	29.454	0.878	30.221
minSetSize-methods	1.254	0.596	1.158
mroast_score-methods	2.281	0.782	2.265
romer_score-methods	15.613	0.894	16.088
signedRankSumTest	0.005	0.001	0.005
splitPerturbations	0.159	0.010	0.173
wilcox_score-methods	2.595	1.599	1.857