BioC 3.2: CHECK report for EnrichmentBrowser on oaxaca

Package: EnrichmentBrowser

Version: 2.0.15

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EnrichmentBrowser_2.0.15.tar.gz

StartedAt: 2016-04-22 23:52:06 -0700 (Fri, 22 Apr 2016)

EndedAt: 2016-04-23 00:01:54 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 587.8 seconds

RetCode: 0

Status:  OK

CheckDir: EnrichmentBrowser.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 EnrichmentBrowser_2.0.15.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/EnrichmentBrowser.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EnrichmentBrowser/DESCRIPTION’ ... OK
* this is package ‘EnrichmentBrowser’ version ‘2.0.15’
* 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 ... [35s/60s] 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 ... [151s/183s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
ea.browse             9.263  0.429  10.064
compile.grn.from.kegg 8.241  0.104   8.352
* 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/EnrichmentBrowser.Rcheck/00check.log’
for details.

* installing *source* package ‘EnrichmentBrowser’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘ggbio’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘ggbio’
* DONE (EnrichmentBrowser)

name	user	system	elapsed
comb.ea.results	0.360	0.005	0.366
compile.grn.from.kegg	8.241	0.104	8.352
config.ebrowser	0.001	0.001	0.001
de.ana	1.438	0.011	1.451
download.kegg.pathways	0.000	0.000	0.001
ea.browse	9.263	0.429	10.064