Package: EnrichmentBrowser

Version: 2.16.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:EnrichmentBrowser.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings EnrichmentBrowser_2.16.1.tar.gz

StartedAt: 2020-04-15 02:05:39 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 02:12:04 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 385.3 seconds

RetCode: 0

Status:  OK

CheckDir: EnrichmentBrowser.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:EnrichmentBrowser.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings EnrichmentBrowser_2.16.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/EnrichmentBrowser.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘2.16.1’
* 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 ‘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 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 ... NOTE
.netgsa: no visible global function definition for ‘write.csv’
.netgsa : .fitM: no visible global function definition for
  ‘bic.netEst.undir’
.netgsa : .fitM: no visible global function definition for
  ‘netEst.undir’
Undefined global functions or variables:
  bic.netEst.undir netEst.undir write.csv
Consider adding
  importFrom("utils", "write.csv")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
ebrowser    85.834 20.356 107.684
getGenesets 17.287  0.274  21.534
eaBrowse    10.319  0.612  11.243
deAna        5.734  0.161   6.012
compileGRN   4.736  0.537   5.315
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/EnrichmentBrowser.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL EnrichmentBrowser
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘EnrichmentBrowser’ ...
** using staged installation
** R
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (EnrichmentBrowser)

name	user	system	elapsed
combResults	0.714	0.056	0.788
compileGRN	4.736	0.537	5.315
configEBrowser	0.001	0.000	0.001
deAna	5.734	0.161	6.012
downloadPathways	0	0	0
eaBrowse	10.319	0.612	11.243
ebrowser	85.834	20.356	107.684
getGenesets	17.287	0.274	21.534
ggeaGraph	3.738	0.076	3.835
idMap	0.420	0.027	0.448
isAvailable	0	0	0
makeExampleData	0.029	0.000	0.029
nbea	0.464	0.006	0.473
normalize	2.428	0.136	2.599
plots	1.551	0.032	1.601
probe2gene	0.112	0.006	0.117
readSE	0.054	0.004	0.057
sbea	0.313	0.003	0.319