BioC 3.5: CHECK report for gCMAP on veracruz2

Package: gCMAP

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gCMAP_1.20.0.tar.gz

StartedAt: 2017-10-18 03:50:19 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 03:54:15 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 235.5 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_1.20.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/gCMAP.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.20.0’
* 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  20.086  0.435   6.941
romer_score-methods  6.062  0.407   6.460
* 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	1.994	0.931	1.852
CMAPResults-class	2.345	0.112	2.525
KEGG2cmap	0.001	0.000	0.001
SignedGeneSet-class	0.022	0.000	0.023
annotate_eset_list	0.091	0.008	0.100
camera_score-methods	0.514	0.099	1.001
center_eSet	0.024	0.004	0.027
connectivity_score-methods	1.351	0.767	0.861
eSetOnDisk	1.320	0.110	1.504
eset_instances	0.060	0.010	0.071
featureScores-methods	0.241	0.068	0.509
fisher_score-methods	0.905	0.497	0.598
gCMAPData-dataset	0.136	0.082	0.434
geneIndex-methods	0.471	0.251	0.448
generate_gCMAP_NChannelSet	0.976	0.046	1.046
gsealm_jg_score-methods	0.888	0.504	0.521
gsealm_score-methods	2.265	0.126	2.623
induceCMAPCollection-methods	0.337	0.186	0.300
mapNmerge	0.001	0.001	0.001
memorize	0.848	0.086	0.955
mergeCMAPs	0.248	0.008	0.262
mgsa_score-methods	20.086	0.435	6.941
minSetSize-methods	0.387	0.212	0.335
mroast_score-methods	1.111	0.261	1.142
romer_score-methods	6.062	0.407	6.460
signedRankSumTest	0.002	0.001	0.002
splitPerturbations	0.073	0.004	0.094
wilcox_score-methods	0.750	0.517	0.550