BioC 3.1: CHECK report for NormqPCR on petty

Package: NormqPCR

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings NormqPCR_1.14.0.tar.gz

StartedAt: 2015-10-09 00:50:47 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 00:54:15 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 208.2 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 NormqPCR_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/NormqPCR.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.14.0’
* 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 ‘NormqPCR’ can be installed ... [10s/11s] 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 ... NOTE
ComputeNRQs,qPCRBatch : .local: no visible global function definition
  for ‘effs’
ComputeNRQs,qPCRBatch : .local: no visible global function definition
  for ‘se.effs’
CqValues,CyclesSet : .local: no visible binding for global variable
  ‘l5’
CqValues,CyclesSet : .local: no visible global function definition for
  ‘effs<-’
CqValues,CyclesSet : .local: no visible global function definition for
  ‘se.effs<-’
* 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 ... [95s/95s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
CqValues 86.707  0.851  87.736
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/NormqPCR.Rcheck/00check.log’
for details.

* 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	0.066	0.006	0.073
BladderRepro	0.013	0.002	0.015
Colon	0.013	0.003	0.015
ComputeNRQs	0.319	0.006	0.368
CqValues	86.707	0.851	87.736
NormqPCR-package	0.002	0.000	0.002
combineTechReps	0.117	0.001	0.118
combineTechRepsSD	0.122	0.001	0.124
deltaCt	0.299	0.002	0.304
deltaDeltaCt	0.345	0.002	0.347
geNorm	0.011	0.002	0.011
geomMean	0.001	0.000	0.001
makeAllNAs	0.300	0.003	0.330
makeAllNewVal	0.304	0.002	0.305
replaceAboveCutOff	0.289	0.002	0.291
replaceNAs	0.252	0.001	0.253
selectHKs	0.051	0.002	0.054
stabMeasureM	0.047	0.002	0.049
stabMeasureRho	0.025	0.002	0.027