BioC 3.3: CHECK report for iCheck on morelia

Package: iCheck

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings iCheck_1.1.0.tar.gz

StartedAt: 2016-04-21 04:00:35 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 04:05:39 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 304.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: iCheck.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings iCheck_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/iCheck.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.1.0’
* 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 ... [28s/30s] WARNING
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Users/biocbuild/bbs-3.3-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 ... NOTE
LumiBatch2Table: no visible global function definition for
  ‘write.table’
myCombineIntersect: no visible global function definition for
  ‘capture.output’
myCombineIntersect: no visible global function definition for
  ‘packageDescription’
myCombineUnion: no visible global function definition for
  ‘capture.output’
myCombineUnion: no visible global function definition for
  ‘packageDescription’
readbgx: no visible global function definition for ‘read.delim’
readbgx2: no visible global function definition for ‘read.delim’
Undefined global functions or variables:
  capture.output packageDescription read.delim write.table
Consider adding
  importFrom("utils", "capture.output", "packageDescription",
             "read.delim", "write.table")
to your NAMESPACE file.
* 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 ... [18s/18s] 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/iCheck.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
LumiBatch2Table	0.180	0.003	0.185
R2PlotFunc	0.415	0.012	0.470
genSimData.BayesNormal	0.064	0.000	0.065
getPCAFunc	0.093	0.000	0.094
glmWrapper	1.146	0.028	1.211
lkhrWrapper	1.052	0.027	1.086
lmFitPaired	0.085	0.002	0.089
lmFitWrapper	0.081	0.002	0.089
pca2DPlot	0.082	0.001	0.090
pca3DPlot	0.089	0.002	0.094
plotCurves	0.069	0.001	0.079
plotQCCurves	0.113	0.002	0.138
plotSamplep95p05	0.122	0.002	0.153
quantilePlot	0.188	0.010	0.232
sortExpressionSet	0.104	0.001	0.108