Package: EnrichmentBrowser

Version: 2.8.7

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EnrichmentBrowser_2.8.7.tar.gz

StartedAt: 2018-04-12 03:21:36 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:28:18 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 402.7 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 EnrichmentBrowser_2.8.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/EnrichmentBrowser.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EnrichmentBrowser/DESCRIPTION’ ... OK
* this is package ‘EnrichmentBrowser’ version ‘2.8.7’
* 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 ... 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 ... NOTE
Unexported object imported by a ':::' call: 'pathview:::parseKGML2Graph2'
  See the note in ?`:::` about the use of this operator.
* 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 ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
ebrowser        36.087  2.379  39.177
get.go.genesets 16.376  0.157  16.782
* 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-3.6-bioc/meat/EnrichmentBrowser.Rcheck/00check.log’
for details.

* 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	1.064	0.008	1.082
compile.grn.from.kegg	3.741	0.080	3.874
config.ebrowser	0.001	0.000	0.000
de.ana	2.582	0.016	2.620
download.kegg.pathways	0.001	0.000	0.000
ea.browse	1.599	0.152	1.773
ebrowser	36.087	2.379	39.177
get.go.genesets	16.376	0.157	16.782
get.kegg.genesets	3.669	0.034	3.742
ggea.graph	1.670	0.022	1.704
isAvailable	0	0	0
make.example.data	0.009	0.001	0.008
map.ids	0.143	0.009	0.152
nbea	0.298	0.006	0.308
normalize	1.177	0.021	1.212
parseGMT	0.024	0.001	0.024
plots	0.928	0.005	0.941
probe.2.gene.eset	0.083	0.005	0.088
read.eset	0.865	0.009	0.883
sbea	0.097	0.001	0.100