BioC 3.5: CHECK report for gCMAP on oaxaca

Package: gCMAP

Version: 1.19.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gCMAP_1.19.5.tar.gz

StartedAt: 2017-03-04 03:10:44 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 03:14:53 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 248.9 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_1.19.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/gCMAP.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.19.5’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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
Namespace in Imports field not imported from: ‘bigmemory’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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  15.313  0.314  15.610
romer_score-methods  6.373  0.888   6.714
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-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	2.725	1.041	2.398
CMAPResults-class	2.694	0.137	2.833
KEGG2cmap	0.001	0.000	0.001
SignedGeneSet-class	0.029	0.000	0.029
annotate_eset_list	0.120	0.005	0.169
camera_score-methods	0.622	0.098	1.343
center_eSet	0.036	0.004	0.040
connectivity_score-methods	2.197	1.003	1.163
eSetOnDisk	1.265	0.107	1.437
eset_instances	0.063	0.004	0.067
featureScores-methods	0.281	0.076	0.789
fisher_score-methods	1.666	0.719	0.870
gCMAPData-dataset	0.527	0.232	0.710
geneIndex-methods	0.518	0.217	0.732
generate_gCMAP_NChannelSet	1.107	0.044	1.152
gsealm_jg_score-methods	1.695	0.796	0.916
gsealm_score-methods	2.623	0.143	3.076
induceCMAPCollection-methods	1.026	0.446	0.553
mapNmerge	0.001	0.000	0.001
memorize	0.816	0.102	0.920
mergeCMAPs	0.278	0.005	0.282
mgsa_score-methods	15.313	0.314	15.610
minSetSize-methods	0.684	0.303	0.649
mroast_score-methods	1.637	0.492	1.496
romer_score-methods	6.373	0.888	6.714
signedRankSumTest	0.003	0.000	0.003
splitPerturbations	0.063	0.005	0.068
wilcox_score-methods	1.620	0.872	0.905