BioC 3.0: CHECK report for EnrichmentBrowser on perceval

Package: EnrichmentBrowser

Version: 1.0.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch EnrichmentBrowser_1.0.3.tar.gz

StartedAt: 2015-04-10 01:06:46 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 01:12:37 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 351.7 seconds

RetCode: 0

Status:  OK

CheckDir: EnrichmentBrowser.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch EnrichmentBrowser_1.0.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/EnrichmentBrowser.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EnrichmentBrowser/DESCRIPTION’ ... OK
* this is package ‘EnrichmentBrowser’ version ‘1.0.3’
* 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 ‘EnrichmentBrowser’ can be installed ... [23s/27s] 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [93s/110s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
ebrowser              19.490  0.524  24.624
ggea.graph            11.004  0.134  11.452
comb.ea.results       10.711  0.157  12.936
nbea                  10.067  0.141  10.963
get.kegg.genesets      8.804  0.084   9.185
compile.grn.from.kegg  7.879  0.075   8.644
plots                  7.078  0.281  13.152
* 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

* installing *source* package ‘EnrichmentBrowser’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (EnrichmentBrowser)

name	user	system	elapsed
comb.ea.results	10.711	0.157	12.936
compile.grn.from.kegg	7.879	0.075	8.644
de.ana	1.265	0.019	1.286
download.kegg.pathways	0.001	0.000	0.000
ea.browse	2.225	0.070	4.567
ebrowser	19.490	0.524	24.624
get.kegg.genesets	8.804	0.084	9.185
ggea.graph	11.004	0.134	11.452
nbea	10.067	0.141	10.963
plots	7.078	0.281	13.152
probe.2.gene.eset	0.955	0.035	0.993
read.eset	0.668	0.025	0.700
sbea	1.028	0.030	1.057