BioC 3.5: CHECK report for gCMAP on toluca2

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: 2017-04-23 04:09:03 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 04:13:40 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 277.3 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_1.19.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/gCMAP.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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  16.321  0.460  16.663
romer_score-methods  6.685  0.727   7.404
* 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: 2 NOTEs
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	2.459	0.944	2.309
CMAPResults-class	2.592	0.131	2.776
KEGG2cmap	0.000	0.000	0.001
SignedGeneSet-class	0.025	0.001	0.026
annotate_eset_list	0.108	0.006	0.115
camera_score-methods	0.624	0.097	1.358
center_eSet	0.034	0.004	0.037
connectivity_score-methods	2.035	0.935	1.175
eSetOnDisk	1.462	0.115	1.600
eset_instances	0.075	0.005	0.094
featureScores-methods	0.296	0.100	0.842
fisher_score-methods	1.677	0.856	1.022
gCMAPData-dataset	0.152	0.081	0.738
geneIndex-methods	0.889	0.395	0.727
generate_gCMAP_NChannelSet	1.254	0.059	1.322
gsealm_jg_score-methods	1.600	0.773	0.947
gsealm_score-methods	2.829	0.158	3.322
induceCMAPCollection-methods	0.690	0.308	0.561
mapNmerge	0.001	0.000	0.001
memorize	0.845	0.106	0.959
mergeCMAPs	0.309	0.009	0.321
mgsa_score-methods	16.321	0.460	16.663
minSetSize-methods	0.741	0.361	0.762
mroast_score-methods	1.664	0.507	1.720
romer_score-methods	6.685	0.727	7.404
signedRankSumTest	0.002	0.000	0.003
splitPerturbations	0.082	0.006	0.091
wilcox_score-methods	1.574	0.939	1.050