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Package 436/436HostnameOS / ArchBUILDCHECKBUILD BIN
yaqcaffy 1.11.4
Laurent Gatto
Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/yaqcaffy
Last Changed Rev: 52675 / Revision: 53255
Last Changed Date: 2011-02-14 09:59:15 -0800 (Mon, 14 Feb 2011)
lamb2 Linux (openSUSE 11.2) / x86_64  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ WARNINGS ] OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.4) / i386  OK  WARNINGS  OK 

Summary

Package: yaqcaffy
Version: 1.11.4
Command: E:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings yaqcaffy_1.11.4.tar.gz
StartedAt: 2011-02-24 20:13:46 -0800 (Thu, 24 Feb 2011)
EndedAt: 2011-02-24 20:17:16 -0800 (Thu, 24 Feb 2011)
EllapsedTime: 209.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: yaqcaffy.Rcheck
Warnings: 1

Command output

* using log directory 'E:/biocbld/bbs-2.8-bioc/meat/yaqcaffy.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'yaqcaffy/DESCRIPTION' ... OK
* this is package 'yaqcaffy' version '1.11.4'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'yaqcaffy' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 S4 methods:
  generic 'merge' and siglist 'YAQCStats,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'E:/biocbld/bbs-2.8-bioc/meat/yaqcaffy.Rcheck/00check.log'
for details

yaqcaffy.Rcheck/00install.out:

* installing *source* package 'yaqcaffy' ...
** R
** inst
** preparing package for lazy loading
Loading required package: affy
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: genefilter
Loading required package: gcrma
Creating a new generic function for "summary" in "yaqcaffy"
Creating a new generic function for "merge" in "yaqcaffy"
Creating a new generic function for "identical" in "yaqcaffy"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (yaqcaffy)

yaqcaffy.Rcheck/yaqcaffy-Ex.timings:

nameusersystemelapsed
YaqcControlProbes-class000
getAllInt15.67 0.4016.14
getBioProbes1.240.001.26
getOutliers45.17 0.6546.89
getQCRatios 9.98 0.2110.22
getRatioProbes1.390.051.44
getSpikeProbes1.410.021.42
probeSelectionInterface000
reprodPlot000
yaqc.affy9.720.239.96
yaqc.plot9.530.179.71
yaqc.summary10.11 0.1710.30