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BioC 2.12: CHECK report for yaqcaffy on george2

This page was generated on 2013-10-09 09:37:26 -0700 (Wed, 09 Oct 2013).

Package 670/671HostnameOS / ArchBUILDCHECKBUILD BIN
yaqcaffy 1.20.0
Laurent Gatto
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/yaqcaffy
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: yaqcaffy
Version: 1.20.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings yaqcaffy_1.20.0.tar.gz
StartedAt: 2013-10-09 05:35:39 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 05:40:09 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 269.9 seconds
RetCode: 0
Status:  OK 
CheckDir: yaqcaffy.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/yaqcaffy.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘yaqcaffy/DESCRIPTION’ ... OK
* this is package ‘yaqcaffy’ version ‘1.20.0’
* 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 ‘yaqcaffy’ can be installed ... [21s/21s] 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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [107s/107s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
getOutliers 49.039  0.496  49.557
getAllInt   20.533  0.308  20.853
getQCRatios  9.401  0.132   9.533
yaqc.plot    8.476  0.044   8.523
yaqc.affy    8.357  0.036   8.391
* 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

yaqcaffy.Rcheck/00install.out:

* installing *source* package ‘yaqcaffy’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘summary’ from package ‘base’ in package ‘yaqcaffy’
Creating a generic function for ‘merge’ from package ‘base’ in package ‘yaqcaffy’
Creating a generic function for ‘identical’ from package ‘base’ in package ‘yaqcaffy’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (yaqcaffy)

yaqcaffy.Rcheck/yaqcaffy-Ex.timings:

nameusersystemelapsed
YaqcControlProbes-class0.3440.0040.350
getAllInt20.533 0.30820.853
getBioProbes0.5760.0160.592
getOutliers49.039 0.49649.557
getQCRatios9.4010.1329.533
getRatioProbes0.7200.0160.734
getSpikeProbes0.7360.0160.750
probeSelectionInterface0.0000.0000.003
reprodPlot0.0000.0000.004
yaqc.affy8.3570.0368.391
yaqc.plot8.4760.0448.523