Package: NormqPCR

Version: 1.32.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:NormqPCR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NormqPCR_1.32.0.tar.gz

StartedAt: 2020-04-15 04:15:57 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 04:18:15 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 137.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: NormqPCR.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:NormqPCR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NormqPCR_1.32.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/NormqPCR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NormqPCR/DESCRIPTION’ ... OK
* this is package ‘NormqPCR’ version ‘1.32.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Users/biocbuild/bbs-3.10-bioc/meat/NormqPCR.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 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
CqValues,CyclesSet: no visible binding for global variable ‘l5’
Undefined global functions or variables:
  l5
* 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 ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
CqValues 50.478  0.714  51.556
* 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-3.10-bioc/meat/NormqPCR.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL NormqPCR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘NormqPCR’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: GLX extension missing on server
2: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'. 
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘NormqPCR.Rnw’ 
** testing if installed package can be loaded from temporary location
Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
** testing if installed package can be loaded from final location
Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
** testing if installed package keeps a record of temporary installation path
* DONE (NormqPCR)

name	user	system	elapsed
Bladder	0.017	0.002	0.019
BladderRepro	0.007	0.002	0.008
Colon	0.008	0.002	0.011
ComputeNRQs	0.297	0.004	0.303
CqValues	50.478	0.714	51.556
NormqPCR-package	0	0	0
combineTechReps	0.063	0.000	0.064
combineTechRepsSD	0.106	0.000	0.109
deltaCt	0.128	0.001	0.130
deltaDeltaCt	0.160	0.002	0.163
geNorm	0.009	0.002	0.011
geomMean	0	0	0
makeAllNAs	0.124	0.001	0.126
makeAllNewVal	0.112	0.002	0.115
replaceAboveCutOff	0.106	0.001	0.108
replaceNAs	0.105	0.001	0.106
selectHKs	0.031	0.002	0.033
stabMeasureM	0.159	0.002	0.162
stabMeasureRho	0.126	0.003	0.130