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BioC 3.5: CHECK report for iCheck on oaxaca

This page was generated on 2017-03-04 16:50:43 -0500 (Sat, 04 Mar 2017).

Package 628/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iCheck 1.5.1
Weiliang Qiu
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/iCheck
Last Changed Rev: 124270 / Revision: 127142
Last Changed Date: 2016-11-18 15:13:05 -0500 (Fri, 18 Nov 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK 

Summary

Package: iCheck
Version: 1.5.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings iCheck_1.5.1.tar.gz
StartedAt: 2017-03-04 04:28:06 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 04:32:35 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 269.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: iCheck.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings iCheck_1.5.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/iCheck.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iCheck/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iCheck’ version ‘1.5.1’
* 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 ‘iCheck’ can be installed ... WARNING
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Users/biocbuild/bbs-3.5-bioc/meat/iCheck.Rcheck/00install.out’ for details.
* 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 ... OK
* 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 ... 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: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/iCheck.Rcheck/00check.log’
for details.


iCheck.Rcheck/00install.out:

* installing *source* package ‘iCheck’ ...
** R
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
* DONE (iCheck)

iCheck.Rcheck/iCheck-Ex.timings:

nameusersystemelapsed
LumiBatch2Table0.2610.0060.266
R2PlotFunc1.0110.0161.127
boxPlots0.2490.0110.263
densityPlots0.1020.0140.117
genSimData.BayesNormal0.0560.0030.057
getPCAFunc0.0650.0000.066
glmWrapper0.6620.0370.701
lkhrWrapper0.6470.0060.653
lmFitPaired0.6800.0040.683
lmFitWrapper0.1430.0020.145
pca2DPlot0.1820.0030.187
pca3DPlot0.0630.0010.064
plotCurves0.0450.0010.046
plotQCCurves0.1150.0020.117
plotSamplep95p050.1230.0010.126
quantilePlot0.1210.0100.136
scatterPlots0.1180.0090.129
sortExpressionSet0.0730.0010.074