Package: NormqPCR

Version: 1.26.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:NormqPCR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings NormqPCR_1.26.0.tar.gz

StartedAt: 2018-10-16 02:23:26 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 02:25:06 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 100.2 seconds

RetCode: 0

Status:  OK

CheckDir: NormqPCR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:NormqPCR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings NormqPCR_1.26.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/NormqPCR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (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 ... 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 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 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 34.54  0.076  34.707
* 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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/NormqPCR.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL NormqPCR
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘NormqPCR’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘NormqPCR.Rnw’ 
** testing if installed package can be loaded
* DONE (NormqPCR)

name	user	system	elapsed
Bladder	0.016	0.000	0.015
BladderRepro	0.004	0.000	0.006
Colon	0.008	0.000	0.007
ComputeNRQs	0.488	0.004	0.620
CqValues	34.540	0.076	34.707
NormqPCR-package	0	0	0
combineTechReps	0.040	0.000	0.049
combineTechRepsSD	0.072	0.000	0.070
deltaCt	0.080	0.000	0.089
deltaDeltaCt	0.104	0.000	0.104
geNorm	0.004	0.000	0.007
geomMean	0	0	0
makeAllNAs	0.092	0.000	0.091
makeAllNewVal	0.084	0.000	0.085
replaceAboveCutOff	0.080	0.000	0.077
replaceNAs	0.076	0.000	0.077
selectHKs	0.028	0.000	0.026
stabMeasureM	0.108	0.000	0.110
stabMeasureRho	0.072	0.004	0.076