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BioC 2.14: CHECK report for codelink on petty

This page was generated on 2014-10-08 08:57:33 -0700 (Wed, 08 Oct 2014).

Package 178/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
codelink 1.32.0
Diego Diez
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/codelink
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: codelink
Version: 1.32.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch codelink_1.32.0.tar.gz
StartedAt: 2014-10-07 21:27:40 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 21:31:42 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 241.9 seconds
RetCode: 0
Status:  OK 
CheckDir: codelink.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch codelink_1.32.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/codelink.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 ‘codelink/DESCRIPTION’ ... OK
* this is package ‘codelink’ version ‘1.32.0’
* 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 ‘codelink’ can be installed ... [31s/32s] 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 ... 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 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 ... [15s/15s] OK
* 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

codelink.Rcheck/00install.out:

* installing *source* package ‘codelink’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘createWeights’ with signature ‘"CodelinkSet"’: no definition for class “CodelinkSet”
in method for ‘createFlagWeights’ with signature ‘"CodelinkSet"’: no definition for class “CodelinkSet”
in method for ‘createTypeWeights’ with signature ‘"CodelinkSet"’: no definition for class “CodelinkSet”
Creating a generic function for ‘summary’ from package ‘base’ in package ‘codelink’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (codelink)

codelink.Rcheck/codelink-Ex.timings:

nameusersystemelapsed
Codelink-class0.0010.0000.001
CodelinkSet-class0.0010.0000.001
CodelinkSetUnique-class0.0010.0000.001
arrayNew0.0010.0000.001
as.matrix.Codelink0.0010.0000.001
averageProbes0.0010.0010.002
bkgdCorrect1.5140.0431.559
createWeights1.5170.0381.558
cutCV0.0010.0000.001
dim.Codelink0.0010.0000.001
imageCodelink0.0010.0000.001
logCodelink0.0010.0010.001
mergeArray0.0020.0000.001
na2false0.0010.0000.001
normalize2.3100.0852.407
plotCorrelation0.0010.0010.001
plotDensities0.0010.0000.001
plotMA0.0010.0010.002
readCodelink0.0010.0000.001
readHeader0.0010.0000.001
readHeaderXLS0.0000.0000.001
writeCodelink0.0010.0010.001