BioC 3.0: CHECK report for pRolocGUI on zin1

Package: pRolocGUI

Version: 1.0.2

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings pRolocGUI_1.0.2.tar.gz

StartedAt: 2015-04-10 03:10:48 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 03:16:31 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 342.4 seconds

RetCode: 0

Status:  OK

CheckDir: pRolocGUI.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings pRolocGUI_1.0.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/pRolocGUI.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pRolocGUI/DESCRIPTION’ ... OK
* this is package ‘pRolocGUI’ version ‘1.0.2’
* 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 ‘pRolocGUI’ can be installed ... [30s/31s] 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: ‘MSnbase:::getVariableName’
  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
.PC: no visible global function definition for ‘pData’
.checkFeatText: no visible global function definition for ‘fData’
.colourPCA: no visible global function definition for ‘fvarLabels’
.dTable: no visible global function definition for ‘exprs’
.dTable: no visible global function definition for ‘fData’
.dTable: no visible global function definition for ‘pData’
.fcex: no visible global function definition for ‘fData’
.fcex: no visible global function definition for ‘fvarLabels’
.featuresPlotDist: no visible global function definition for
  ‘fvarLabels’
.legendPCA: no visible global function definition for ‘fvarLabels’
.legendPosPCA: no visible global function definition for ‘fvarLabels’
.mC: no visible global function definition for ‘fData’
.minDistPlotDist: no visible global function definition for
  ‘featureNames’
.minDistPlotDist: no visible global function definition for ‘fData’
.minDistPlotDist: no visible global function definition for ‘exprs’
.obsNewFoI: no visible global function definition for ‘featureNames’
.obsProtText: no visible global function definition for ‘fData’
.orgName: no visible global function definition for ‘fData’
.plotPCA: no visible global function definition for ‘fvarLabels’
.plotPCA: no visible global function definition for ‘fData’
.plotPCA: no visible global function definition for ‘featureNames’
.plotPlotDist: no visible global function definition for ‘fData’
.plotPlotDist: no visible global function definition for ‘exprs’
.sRsubset: no visible global function definition for ‘fData’
.selVarText: no visible global function definition for ‘fvarLabels’
.symbolPCA: no visible global function definition for ‘fvarLabels’
pRolocComp : <anonymous>: no visible global function definition for
  ‘exprs’
pRolocComp : <anonymous>: no visible global function definition for
  ‘fData’
pRolocVis : <anonymous>: no visible global function definition for
  ‘exprs’
pRolocVis: no visible global function definition for ‘exprs’
pRolocVis : <anonymous>: no visible global function definition for
  ‘fData’
pRolocVis : <anonymous>: no visible global function definition for
  ‘featureNames’
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [15s/15s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [27s/28s]
 [27s/29s] OK
* 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/pRolocGUI.Rcheck/00check.log’
for details.

* installing *source* package ‘pRolocGUI’ ...
** R
** inst
** preparing package for lazy loading
Note: the specification for S3 class “AsIs” in package ‘RJSONIO’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class “AsIs” in package ‘RJSONIO’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
* DONE (pRolocGUI)

name	user	system	elapsed
pRolocVis-pRolocComp	0.004	0.000	0.001