BioC 3.2: CHECK report for cogena on perceval

Package: cogena

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cogena_1.4.0.tar.gz

StartedAt: 2015-10-27 06:43:19 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 06:48:21 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 301.9 seconds

RetCode: 0

Status:  OK

CheckDir: cogena.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 cogena_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/cogena.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cogena/DESCRIPTION’ ... OK
* this is package ‘cogena’ version ‘1.4.0’
* package encoding: UTF-8
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘cogena’ can be installed ... [10s/11s] OK
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* 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 ... [37s/186s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
cogena_package 8.591  0.584 109.654
clEnrich_one   6.092  0.567  15.532
clEnrich       4.383  0.389  20.890
upDownGene     4.238  0.337  19.189
clusterMethods 2.571  0.015  11.798
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/cogena.Rcheck/00check.log’
for details.

* installing *source* package ‘cogena’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for ‘summary’ from package ‘base’ in package ‘cogena’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cogena)

name	user	system	elapsed
PEI	1.566	0.167	1.733
clEnrich	4.383	0.389	20.890
clEnrich_one	6.092	0.567	15.532
clusterMethods	2.571	0.015	11.798
coExp	0.004	0.001	0.004
cogena_package	8.591	0.584	109.654
corInCluster	0.003	0.000	0.003
enrichment	0.002	0.000	0.003
gene2set	0.081	0.002	0.082
geneExpInCluster	0.002	0.001	0.003
geneInCluster	0.002	0.000	0.003
geneclusters	0.001	0.001	0.001
gmt2list	0.047	0.000	0.048
heatmapCluster	0.003	0.001	0.004
heatmapCmap	0.003	0.001	0.003
heatmapPEI	0.003	0.000	0.003
mat	0.001	0.000	0.001
nClusters	0.001	0.000	0.001
show	0.000	0.000	0.001
sota	2.421	0.201	2.623
summary	0.000	0.000	0.001
upDownGene	4.238	0.337	19.189