BioC 3.4: CHECK report for NormqPCR on zin1

Package: NormqPCR

Version: 1.19.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings NormqPCR_1.19.0.tar.gz

StartedAt: 2016-08-18 09:40:16 -0700 (Thu, 18 Aug 2016)

EndedAt: 2016-08-18 09:42:03 -0700 (Thu, 18 Aug 2016)

EllapsedTime: 107.2 seconds

RetCode: 0

Status:  OK

CheckDir: NormqPCR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings NormqPCR_1.19.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/NormqPCR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.19.0’
* 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 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
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 51.284  0.048  51.383
* 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-3.4-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	0.032	0.000	0.031
BladderRepro	0.004	0.000	0.006
Colon	0.004	0.004	0.008
ComputeNRQs	0.148	0.004	0.165
CqValues	51.284	0.048	51.383
NormqPCR-package	0	0	0
combineTechReps	0.052	0.000	0.050
combineTechRepsSD	0.056	0.000	0.055
deltaCt	0.104	0.000	0.102
deltaDeltaCt	0.128	0.000	0.129
geNorm	0.012	0.000	0.011
geomMean	0	0	0
makeAllNAs	0.108	0.000	0.110
makeAllNewVal	0.108	0.000	0.108
replaceAboveCutOff	0.224	0.000	0.227
replaceNAs	0.096	0.000	0.098
selectHKs	0.028	0.004	0.031
stabMeasureM	0.028	0.000	0.028
stabMeasureRho	0.012	0.000	0.014