BioC 2.14: CHECK report for NormqPCR on petty

Package: NormqPCR

Version: 1.10.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch NormqPCR_1.10.2.tar.gz

StartedAt: 2014-10-07 23:14:25 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:20:14 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 349.6 seconds

RetCode: 0

Status:  OK

CheckDir: NormqPCR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch NormqPCR_1.10.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/NormqPCR.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NormqPCR/DESCRIPTION’ ... OK
* this is package ‘NormqPCR’ version ‘1.10.2’
* 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 ‘NormqPCR’ can be installed ... [17s/29s] 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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [129s/133s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
CqValues 116.379  0.932 121.076
* 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

* installing *source* package ‘NormqPCR’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
** 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 in fun(libname, pkgname) : error in rgl_init
* DONE (NormqPCR)

name	user	system	elapsed
Bladder	0.264	0.007	0.270
BladderRepro	0.017	0.002	0.020
Colon	0.021	0.003	0.024
ComputeNRQs	0.629	0.015	0.684
CqValues	116.379	0.932	121.076
NormqPCR-package	0.004	0.001	0.004
combineTechReps	0.164	0.002	0.169
combineTechRepsSD	0.188	0.002	0.191
deltaCt	0.356	0.003	0.361
deltaDeltaCt	0.430	0.004	0.434
geNorm	0.014	0.002	0.016
geomMean	0.002	0.000	0.001
makeAllNAs	0.387	0.003	0.397
makeAllNewVal	0.363	0.002	0.372
replaceAboveCutOff	0.361	0.003	0.367
replaceNAs	0.370	0.003	0.377
selectHKs	0.090	0.002	0.091
stabMeasureM	0.082	0.002	0.085
stabMeasureRho	0.040	0.002	0.041