BioC 3.6: CHECK report for gCMAP on malbec1

Package: gCMAP

Version: 1.21.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings gCMAP_1.21.0.tar.gz

StartedAt: 2017-08-15 23:20:07 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 23:23:32 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 204.3 seconds

RetCode: 0

Status:  OK

CheckDir: gCMAP.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings gCMAP_1.21.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/gCMAP.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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 ‘1.21.0’
* 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 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  18.092  0.168  22.517
romer_score-methods  4.936  0.132   4.882
* 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
  ‘/home/biocbuild/bbs-3.6-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	1.768	0.444	1.410
CMAPResults-class	2.020	0.064	2.082
KEGG2cmap	0	0	0
SignedGeneSet-class	0.020	0.000	0.017
annotate_eset_list	0.096	0.008	0.242
camera_score-methods	0.700	0.108	0.824
center_eSet	0.032	0.004	0.034
connectivity_score-methods	0.932	0.392	0.629
eSetOnDisk	1.144	0.044	1.203
eset_instances	0.048	0.000	0.046
featureScores-methods	0.220	0.068	0.478
fisher_score-methods	0.852	0.328	0.447
gCMAPData-dataset	0.312	0.068	0.377
geneIndex-methods	0.460	0.128	0.351
generate_gCMAP_NChannelSet	0.708	0.012	0.723
gsealm_jg_score-methods	0.564	0.244	0.371
gsealm_score-methods	1.844	0.124	1.902
induceCMAPCollection-methods	0.200	0.052	0.197
mapNmerge	0.000	0.000	0.001
memorize	0.808	0.032	0.842
mergeCMAPs	0.176	0.000	0.179
mgsa_score-methods	18.092	0.168	22.517
minSetSize-methods	0.336	0.096	0.231
mroast_score-methods	0.956	0.112	0.784
romer_score-methods	4.936	0.132	4.882
signedRankSumTest	0.000	0.000	0.001
splitPerturbations	0.048	0.004	0.054
wilcox_score-methods	0.704	0.524	0.681