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BioC 2.14: CHECK report for yaqcaffy on petty

This page was generated on 2014-10-08 08:58:09 -0700 (Wed, 08 Oct 2014).

Package 823/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
yaqcaffy 1.24.0
Laurent Gatto
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/yaqcaffy
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: yaqcaffy
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch yaqcaffy_1.24.0.tar.gz
StartedAt: 2014-10-08 00:41:04 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 00:46:50 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 345.3 seconds
RetCode: 0
Status:  OK 
CheckDir: yaqcaffy.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch yaqcaffy_1.24.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/yaqcaffy.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 ‘yaqcaffy/DESCRIPTION’ ... OK
* this is package ‘yaqcaffy’ version ‘1.24.0’
* 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 ... [22s/25s] 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 dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘simpleaffy:::.bg.stats’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [138s/138s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
getOutliers 64.931  1.379  66.392
getAllInt   19.776  0.456  20.270
yaqc.affy   12.409  0.490  12.905
yaqc.plot   12.319  0.493  12.814
getQCRatios 12.063  0.505  12.569
* 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/yaqcaffy.Rcheck/00check.log’
for details.

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-class0.0030.0010.004
getAllInt19.776 0.45620.270
getBioProbes1.1610.0301.190
getOutliers64.931 1.37966.392
getQCRatios12.063 0.50512.569
getRatioProbes1.8010.0311.832
getSpikeProbes1.3540.0231.378
probeSelectionInterface0.0010.0000.001
reprodPlot0.0010.0000.001
yaqc.affy12.409 0.49012.905
yaqc.plot12.319 0.49312.814