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CHECK report for codelink on celaya2

This page was generated on 2019-04-09 12:51:15 -0400 (Tue, 09 Apr 2019).

Package 312/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
codelink 1.51.0
Diego Diez
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/codelink
Branch: master
Last Commit: 11f8037
Last Changed Date: 2018-10-30 11:54:27 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: codelink
Version: 1.51.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:codelink.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings codelink_1.51.0.tar.gz
StartedAt: 2019-04-09 00:51:54 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 00:54:38 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 163.8 seconds
RetCode: 0
Status:  OK 
CheckDir: codelink.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:codelink.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings codelink_1.51.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/codelink.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘codelink/DESCRIPTION’ ... OK
* this is package ‘codelink’ version ‘1.51.0’
* 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 ... 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 ... 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
* DONE

Status: OK


Installation output

codelink.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL codelink
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘codelink’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘Codelink_Introduction.Rnw’ using ‘UTF-8’ 
   ‘Codelink_Legacy.Rnw’ using ‘UTF-8’ 
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (codelink)

Tests output


Example timings

codelink.Rcheck/codelink-Ex.timings

nameusersystemelapsed
Codelink-class0.0000.0000.001
CodelinkSet-class0.0010.0000.001
CodelinkSetUnique-class0.0010.0000.001
arrayNew0.0000.0010.000
as.matrix.Codelink0.0010.0000.000
averageProbes0.0010.0000.001
bkgdCorrect0.5610.0640.626
createWeights0.8700.0610.932
cutCV0.0010.0000.000
dim.Codelink0.0000.0010.000
imageCodelink0.0010.0010.000
logCodelink0.0000.0000.001
mergeArray000
na2false0.0000.0000.001
normalize0.8060.1330.940
plotCorrelation0.0010.0010.001
plotDensities0.0000.0000.001
plotMA0.0000.0000.001
readCodelink0.0010.0000.000
readHeader000
readHeaderXLS0.0000.0000.001
writeCodelink0.0000.0000.001