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BioC 3.2: CHECK report for pRolocGUI on zin1

This page was generated on 2015-08-24 10:50:00 -0700 (Mon, 24 Aug 2015).

Package 779/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pRolocGUI 1.3.2
Laurent Gatto , Thomas Naake
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pRolocGUI
Last Changed Rev: 106574 / Revision: 107696
Last Changed Date: 2015-07-20 06:53:59 -0700 (Mon, 20 Jul 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: pRolocGUI
Version: 1.3.2
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings pRolocGUI_1.3.2.tar.gz
StartedAt: 2015-08-24 02:43:07 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 02:46:56 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 229.1 seconds
RetCode: 0
Status:  OK 
CheckDir: pRolocGUI.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings pRolocGUI_1.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/pRolocGUI.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pRolocGUI/DESCRIPTION’ ... OK
* this is package ‘pRolocGUI’ version ‘1.3.2’
* 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 ... [20s/20s] 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’
.colourPCA: no visible global function definition for ‘fvarLabels’
.dTable: no visible global function definition for ‘exprs’
.dTable: no visible global function definition for ‘pData’
.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’
.minDistPlotDist: no visible global function definition for ‘exprs’
.plotPCA: no visible global function definition for ‘fvarLabels’
.plotPlotDist: no visible global function definition for ‘exprs’
.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’
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
  ‘.listSaseInd’
pRolocVis2: no visible global function definition for ‘fvarLabels’
pRolocVis2: no visible global function definition for ‘exprs’
pRolocVis2 : server: no visible binding for '<<-' assignment to ‘usr’
pRolocVis2 : server: no visible binding for global variable ‘usr’
* 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 ... [10s/10s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [22s/22s]
 [22s/22s] 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

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/pRolocGUI.Rcheck/00check.log’
for details.


pRolocGUI.Rcheck/00install.out:

* installing *source* package ‘pRolocGUI’ ...
** R
** inst
** preparing package for lazy loading
Note: the specification for S3 class “family” in package ‘MatrixModels’ seems equivalent to one from package ‘lme4’: 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 “family” in package ‘MatrixModels’ seems equivalent to one from package ‘lme4’: not turning on duplicate class definitions for this class.
* DONE (pRolocGUI)

pRolocGUI.Rcheck/pRolocGUI-Ex.timings:

nameusersystemelapsed
pRolocVis-pRolocComp0.0430.0000.043
pRolocVis20.120.000.12
plotMat2D0.0350.0000.035