BioC 3.2: CHECK report for gCMAP on linux1.bioconductor.org

Package: gCMAP

Version: 1.14.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings gCMAP_1.14.0.tar.gz

StartedAt: 2015-10-27 03:43:35 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:46:55 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 200.5 seconds

RetCode: 0

Status:  OK

CheckDir: gCMAP.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings gCMAP_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/gCMAP.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.14.0’
* 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 ... [20s/20s] 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 : .local: no visible global function
  definition for ‘camera’
induceCMAPCollection,eSet : .local : <anonymous>: no visible global
  function definition for ‘mwhich’
mroast_score,eSet-CMAPCollection : .local: no visible global function
  definition for ‘mroast’
romer_score,eSet-CMAPCollection : .local: no visible global function
  definition for ‘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 ... [54s/34s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
mgsa_score-methods  20.626  0.251   5.934
romer_score-methods  8.844  0.402   8.409
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [36s/28s]
 [36s/28s] 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-3.2-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	0.809	0.170	0.702
CMAPResults-class	2.653	0.052	2.712
KEGG2cmap	0.001	0.000	0.001
SignedGeneSet-class	0.056	0.000	0.056
annotate_eset_list	0.098	0.004	0.102
camera_score-methods	0.412	0.057	0.821
center_eSet	0.022	0.000	0.023
connectivity_score-methods	1.301	0.486	0.692
eSetOnDisk	0.003	0.000	0.003
eset_instances	0.051	0.000	0.052
featureScores-methods	0.348	0.099	0.474
fisher_score-methods	1.002	0.342	0.573
gCMAPData-dataset	0.344	0.100	0.484
geneIndex-methods	0.601	0.156	0.464
generate_gCMAP_NChannelSet	0.213	0.004	0.218
gsealm_jg_score-methods	1.083	0.330	0.577
gsealm_score-methods	2.057	0.053	2.319
induceCMAPCollection-methods	0.645	0.214	0.415
mapNmerge	0	0	0
memorize	0.003	0.000	0.003
mergeCMAPs	0.062	0.008	0.070
mgsa_score-methods	20.626	0.251	5.934
minSetSize-methods	0.469	0.104	0.538
mroast_score-methods	1.440	0.257	1.220
romer_score-methods	8.844	0.402	8.409
signedRankSumTest	0.002	0.000	0.001
splitPerturbations	0.059	0.000	0.060
wilcox_score-methods	0.845	0.394	0.526