Package: NormqPCR

Version: 1.26.0

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_1.26.0.tar.gz

StartedAt: 2018-10-16 22:58:32 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 23:00:52 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 140.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: NormqPCR.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running 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_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/NormqPCR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.26.0’
* 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-3.7-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
stabMeasureM: no visible global function definition for ‘sd’
ComputeNRQs,qPCRBatch: no visible global function definition for ‘effs’
ComputeNRQs,qPCRBatch: no visible global function definition for
  ‘se.effs’
CqValues,CyclesSet: no visible binding for global variable ‘l5’
CqValues,CyclesSet: no visible global function definition for ‘effs<-’
CqValues,CyclesSet: no visible global function definition for
  ‘se.effs<-’
combineTechReps,qPCRBatch: no visible binding for global variable
  ‘median’
combineTechRepsWithSD,qPCRBatch: no visible binding for global variable
  ‘sd’
combineTechRepsWithSD,qPCRBatch: no visible binding for global variable
  ‘median’
combineTechRepsWithSD,qPCRBatch: no visible binding for global variable
  ‘mad’
deltaDeltaCt,qPCRBatch: no visible global function definition for ‘sd’
selectHKs,matrix: no visible global function definition for ‘sd’
stabMeasureRho,matrix: no visible global function definition for
  ‘aggregate’
Undefined global functions or variables:
  aggregate effs effs<- l5 mad median sd se.effs se.effs<-
Consider adding
  importFrom("stats", "aggregate", "mad", "median", "sd")
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 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 48.766  0.711  49.903
* 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-3.7-bioc/meat/NormqPCR.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL NormqPCR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘NormqPCR’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare 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
   ‘NormqPCR.Rnw’ 
** 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 (NormqPCR)

name	user	system	elapsed
Bladder	0.025	0.004	0.028
BladderRepro	0.011	0.003	0.015
Colon	0.012	0.003	0.015
ComputeNRQs	0.443	0.005	0.453
CqValues	48.766	0.711	49.903
NormqPCR-package	0.001	0.001	0.002
combineTechReps	0.061	0.001	0.061
combineTechRepsSD	0.116	0.001	0.116
deltaCt	0.142	0.001	0.145
deltaDeltaCt	0.161	0.003	0.164
geNorm	0.009	0.002	0.013
geomMean	0.001	0.000	0.001
makeAllNAs	0.160	0.001	0.162
makeAllNewVal	0.152	0.002	0.156
replaceAboveCutOff	0.163	0.001	0.165
replaceNAs	0.129	0.001	0.130
selectHKs	0.047	0.003	0.050
stabMeasureM	0.177	0.002	0.180
stabMeasureRho	0.138	0.003	0.142