BioC 2.14: CHECK report for NormqPCR on zin2

Package: NormqPCR

Version: 1.10.2

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings NormqPCR_1.10.2.tar.gz

StartedAt: 2014-10-08 01:28:50 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 01:31:14 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 144.3 seconds

RetCode: 0

Status:  OK

CheckDir: NormqPCR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings NormqPCR_1.10.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/NormqPCR.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NormqPCR/DESCRIPTION’ ... OK
* this is package ‘NormqPCR’ version ‘1.10.2’
* 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 ... [7s/8s] 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 ... OK
* 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 ... [67s/68s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
CqValues 61.928  0.144  63.055
* 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

* 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	0.004	0.036
BladderRepro	0.012	0.000	0.013
Colon	0.012	0.000	0.010
ComputeNRQs	0.316	0.000	0.347
CqValues	61.928	0.144	63.055
NormqPCR-package	0	0	0
combineTechReps	0.076	0.000	0.077
combineTechRepsSD	0.08	0.00	0.08
deltaCt	0.152	0.000	0.154
deltaDeltaCt	0.180	0.004	0.186
geNorm	0.008	0.000	0.007
geomMean	0	0	0
makeAllNAs	0.164	0.000	0.168
makeAllNewVal	0.164	0.004	0.168
replaceAboveCutOff	0.148	0.004	0.153
replaceNAs	0.156	0.000	0.157
selectHKs	0.040	0.004	0.046
stabMeasureM	0.044	0.000	0.042
stabMeasureRho	0.020	0.000	0.019