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BioC 2.14: CHECK report for NormqPCR on petty

This page was generated on 2014-10-08 08:59:40 -0700 (Wed, 08 Oct 2014).

Package 538/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NormqPCR 1.10.2
James Perkins
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/NormqPCR
Last Changed Rev: 95013 / Revision: 95116
Last Changed Date: 2014-10-06 13:14:40 -0700 (Mon, 06 Oct 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: NormqPCR
Version: 1.10.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch NormqPCR_1.10.2.tar.gz
StartedAt: 2014-10-07 23:14:25 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 23:20:14 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 349.6 seconds
RetCode: 0
Status:  OK 
CheckDir: NormqPCR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch NormqPCR_1.10.2.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/NormqPCR.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [17s/29s] 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [129s/133s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
CqValues 116.379  0.932 121.076
* 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

NormqPCR.Rcheck/00install.out:

* installing *source* package ‘NormqPCR’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
* DONE (NormqPCR)

NormqPCR.Rcheck/NormqPCR-Ex.timings:

nameusersystemelapsed
Bladder0.2640.0070.270
BladderRepro0.0170.0020.020
Colon0.0210.0030.024
ComputeNRQs0.6290.0150.684
CqValues116.379 0.932121.076
NormqPCR-package0.0040.0010.004
combineTechReps0.1640.0020.169
combineTechRepsSD0.1880.0020.191
deltaCt0.3560.0030.361
deltaDeltaCt0.4300.0040.434
geNorm0.0140.0020.016
geomMean0.0020.0000.001
makeAllNAs0.3870.0030.397
makeAllNewVal0.3630.0020.372
replaceAboveCutOff0.3610.0030.367
replaceNAs0.3700.0030.377
selectHKs0.0900.0020.091
stabMeasureM0.0820.0020.085
stabMeasureRho0.0400.0020.041