BioC 3.2: CHECK report for NormqPCR on linux1.bioconductor.org

Package: NormqPCR

Version: 1.16.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings NormqPCR_1.16.0.tar.gz

StartedAt: 2015-10-27 06:20:14 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 06:22:06 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 111.9 seconds

RetCode: 0

Status:  OK

CheckDir: NormqPCR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings NormqPCR_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/NormqPCR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.16.0’
* 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 ... [6s/6s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [53s/54s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
CqValues 49.788  0.051  49.933
* 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-3.2-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
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (NormqPCR)

name	user	system	elapsed
Bladder	0.034	0.004	0.038
BladderRepro	0.009	0.000	0.008
Colon	0.01	0.00	0.01
ComputeNRQs	0.215	0.000	0.217
CqValues	49.788	0.051	49.933
NormqPCR-package	0	0	0
combineTechReps	0.05	0.00	0.05
combineTechRepsSD	0.084	0.000	0.084
deltaCt	0.152	0.000	0.152
deltaDeltaCt	0.146	0.000	0.146
geNorm	0.005	0.000	0.006
geomMean	0	0	0
makeAllNAs	0.103	0.000	0.103
makeAllNewVal	0.099	0.000	0.099
replaceAboveCutOff	0.098	0.000	0.098
replaceNAs	0.093	0.000	0.093
selectHKs	0.029	0.000	0.029
stabMeasureM	0.031	0.000	0.031
stabMeasureRho	0.012	0.000	0.012