BioC 3.4: CHECK report for EnrichmentBrowser on zin1

Package: EnrichmentBrowser

Version: 2.3.3

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings EnrichmentBrowser_2.3.3.tar.gz

StartedAt: 2016-09-20 06:03:04 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 06:09:20 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 375.4 seconds

RetCode: 0

Status:  OK

CheckDir: EnrichmentBrowser.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings EnrichmentBrowser_2.3.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/EnrichmentBrowser.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EnrichmentBrowser/DESCRIPTION’ ... OK
* this is package ‘EnrichmentBrowser’ version ‘2.3.3’
* 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 ... 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 ... NOTE
.clipper : <anonymous>: no visible global function definition for 'as'
.clipper : <anonymous>: no visible global function definition for 'is'
.degraph : <anonymous>: no visible global function definition for 'as'
.degraph : <anonymous>: no visible global function definition for 'is'
.topogsa : <anonymous>: no visible global function definition for 'as'
construct.ggea.graph: no visible global function definition for 'new'
de.ana: no visible global function definition for 'is'
ea.browse: no visible global function definition for 'is'
ebrowser: no visible global function definition for 'is'
global.GSA: no visible global function definition for 'getMethod'
global.PADOG: no visible global function definition for 'getMethod'
global.SAMGS: no visible global function definition for 'getMethod'
make.exmpl.eset: no visible global function definition for 'new'
make.kgraph.html: no visible global function definition for 'is'
normalize: no visible global function definition for 'new'
probe.2.gene.eset: no visible global function definition for 'new'
read.eset: no visible global function definition for 'new'
Undefined global functions or variables:
  as getMethod is new
Consider adding
  importFrom("methods", "as", "getMethod", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
ea.browse 7.332  0.492   7.979
* 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
  ‘/home/biocbuild/bbs-3.4-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	0.688	0.004	0.692
compile.grn.from.kegg	4.732	0.060	4.794
config.ebrowser	0.000	0.000	0.001
de.ana	0.984	0.004	0.990
download.kegg.pathways	0	0	0
ea.browse	7.332	0.492	7.979