BioC 3.4: CHECK report for gCMAP on malbec1

Package: gCMAP

Version: 1.18.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings gCMAP_1.18.0.tar.gz

StartedAt: 2017-04-14 22:38:54 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 22:41:54 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 180.0 seconds

RetCode: 0

Status:  OK

CheckDir: gCMAP.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings gCMAP_1.18.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/gCMAP.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.18.0’
* 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 ... 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
'library' or 'require' calls in package code:
  ‘GO.db’ ‘KEGG.db’ ‘bigmemoryExtras’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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
camera_score,eSet-CMAPCollection: no visible global function definition
  for ‘camera’
induceCMAPCollection,eSet : <anonymous>: no visible global function
  definition for ‘mwhich’
mroast_score,eSet-CMAPCollection: no visible global function definition
  for ‘mroast’
romer_score,eSet-CMAPCollection: no visible global function definition
  for ‘romer’
Undefined global functions or variables:
  camera mroast mwhich romer
* 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  19.236  0.248    5.20
romer_score-methods  5.440  0.180    5.28
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-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	1.408	0.268	1.018
CMAPResults-class	2.812	0.056	2.874
KEGG2cmap	0.000	0.000	0.001
SignedGeneSet-class	0.028	0.000	0.026
annotate_eset_list	0.108	0.012	0.122
camera_score-methods	0.480	0.076	0.886
center_eSet	0.036	0.000	0.036
connectivity_score-methods	1.344	0.468	0.705
eSetOnDisk	0.004	0.000	0.005
eset_instances	0.052	0.004	0.055
featureScores-methods	0.328	0.136	0.392
fisher_score-methods	0.968	0.304	0.587
gCMAPData-dataset	0.396	0.076	0.491
geneIndex-methods	0.692	0.176	0.524
generate_gCMAP_NChannelSet	0.140	0.004	0.143
gsealm_jg_score-methods	1.120	0.344	0.631
gsealm_score-methods	1.980	0.088	2.351
induceCMAPCollection-methods	0.952	0.216	0.478
mapNmerge	0.000	0.000	0.001
memorize	0.004	0.000	0.005
mergeCMAPs	0.112	0.012	0.124
mgsa_score-methods	19.236	0.248	5.200
minSetSize-methods	0.712	0.144	0.448
mroast_score-methods	1.340	0.188	1.162
romer_score-methods	5.44	0.18	5.28
signedRankSumTest	0.004	0.000	0.002
splitPerturbations	0.048	0.004	0.051
wilcox_score-methods	0.828	0.472	0.687