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Package 436/658HostnameOS / ArchBUILDCHECKBUILD BIN
NormqPCR 1.5.2
James Perkins
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/NormqPCR
Last Changed Rev: 74745 / Revision: 74774
Last Changed Date: 2013-03-23 09:12:53 -0700 (Sat, 23 Mar 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ WARNINGS ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: NormqPCR
Version: 1.5.2
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings NormqPCR_1.5.2.tar.gz
StartedAt: 2013-03-25 03:25:40 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 03:28:42 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 182.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: NormqPCR.Rcheck
Warnings: 1

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/NormqPCR.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ‘1.5.2’
* 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 ... [6s/7s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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 ... WARNING
Undocumented code objects:
  ‘ComputeNRQs’
Undocumented S4 methods:
  generic 'ComputeNRQs' and siglist 'qPCRBatch'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 examples ... [114s/118s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
CqValues 107.65   0.26 111.764
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/NormqPCR.Rcheck/00check.log’
for details.

NormqPCR.Rcheck/00install.out:

* 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
   ‘NormqPCR.Rnw’ 
** testing if installed package can be loaded
* DONE (NormqPCR)

NormqPCR.Rcheck/NormqPCR-Ex.timings:

nameusersystemelapsed
Bladder0.0640.0040.068
BladderRepro0.0200.0080.026
Colon0.0280.0000.031
CqValues107.650 0.260111.764
NormqPCR-package0.020.000.02
combineTechReps0.1440.0080.151
combineTechRepsSD0.1520.0040.157
deltaCt0.280.000.28
deltaDeltaCt0.3280.0080.339
geNorm0.0320.0000.034
geomMean0.0160.0000.017
makeAllNAs0.5330.0040.536
makeAllNewVal0.2760.0040.279
replaceAboveCutOff0.2640.0040.266
replaceNAs0.2440.0080.251
selectHKs0.0960.0080.103
stabMeasureM0.0960.0000.094
stabMeasureRho0.0640.0000.063