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BioC 3.1: CHECK report for NormqPCR on zin2

This page was generated on 2015-10-09 09:24:25 -0700 (Fri, 09 Oct 2015).

Package 663/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NormqPCR 1.14.0
James Perkins
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/NormqPCR
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: NormqPCR
Version: 1.14.0
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings NormqPCR_1.14.0.tar.gz
StartedAt: 2015-10-09 04:00:23 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 04:02:08 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 105.1 seconds
RetCode: 0
Status:  OK 
CheckDir: NormqPCR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings NormqPCR_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-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 ‘1.14.0’
* 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 ... [5s/5s] 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 sizes of PDF files under ‘inst/doc’ ... 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 49.955  0.068  50.099
* 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-3.1-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
** testing if installed package can be loaded
* DONE (NormqPCR)

NormqPCR.Rcheck/NormqPCR-Ex.timings:

nameusersystemelapsed
Bladder0.0260.0000.026
BladderRepro0.0060.0000.007
Colon0.0080.0000.008
ComputeNRQs0.1630.0000.186
CqValues49.955 0.06850.099
NormqPCR-package0.0010.0000.000
combineTechReps0.0550.0000.055
combineTechRepsSD0.0550.0000.055
deltaCt0.1080.0000.108
deltaDeltaCt0.1320.0000.132
geNorm0.0060.0000.006
geomMean0.0000.0000.001
makeAllNAs0.1240.0040.127
makeAllNewVal0.1240.0000.124
replaceAboveCutOff0.1190.0040.119
replaceNAs0.1200.0000.123
selectHKs0.0370.0000.037
stabMeasureM0.0340.0000.034
stabMeasureRho0.0170.0000.017