BioC 2.13: CHECK report for codelink on moscato1

Package: codelink

Version: 1.30.9

Command: rm -rf codelink.buildbin-libdir && mkdir codelink.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=codelink.buildbin-libdir codelink_1.30.9.tar.gz >codelink-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=codelink.buildbin-libdir --install="check:codelink-install.out" --force-multiarch --no-vignettes --timings codelink_1.30.9.tar.gz && mv codelink.buildbin-libdir/* codelink.Rcheck/ && rmdir codelink.buildbin-libdir

StartedAt: 2014-04-05 03:14:56 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:18:05 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 188.9 seconds

RetCode: 0

Status:  OK

CheckDir: codelink.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/codelink.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'codelink/DESCRIPTION' ... OK
* this is package 'codelink' version '1.30.9'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [8s] OK
** running examples for arch 'x64' ... [9s] 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

install for i386

* 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

install for x64

* installing *source* package 'codelink' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'codelink' as codelink_1.30.9.zip
* DONE (codelink)

name	user	system	elapsed
Codelink-class	0.00	0.01	0.02
CodelinkSet-class	0	0	0
CodelinkSetUnique-class	0	0	0
arrayNew	0	0	0
as.matrix.Codelink	0.02	0.00	0.01
averageProbes	0	0	0
bkgdCorrect	1.06	0.00	1.06
createWeights	0.88	0.00	0.89
cutCV	0	0	0
dim.Codelink	0	0	0
imageCodelink	0.02	0.00	0.02
logCodelink	0	0	0
mergeArray	0.01	0.00	0.01
na2false	0	0	0
normalize	0.96	0.03	1.00
plotCorrelation	0	0	0
plotDensities	0.02	0.00	0.02
plotMA	0	0	0
readCodelink	0	0	0
readHeader	0.02	0.00	0.02
readHeaderXLS	0	0	0
writeCodelink	0.01	0.00	0.02

name	user	system	elapsed
Codelink-class	0	0	0
CodelinkSet-class	0.02	0.00	0.01
CodelinkSetUnique-class	0	0	0
arrayNew	0.01	0.00	0.02
as.matrix.Codelink	0	0	0
averageProbes	0.02	0.00	0.01
bkgdCorrect	1.12	0.02	1.14
createWeights	0.64	0.00	0.64
cutCV	0.02	0.00	0.02
dim.Codelink	0	0	0
imageCodelink	0	0	0
logCodelink	0.02	0.00	0.02
mergeArray	0.01	0.00	0.02
na2false	0	0	0
normalize	1.39	0.01	1.41
plotCorrelation	0	0	0
plotDensities	0.01	0.00	0.01
plotMA	0	0	0
readCodelink	0.14	0.00	0.14
readHeader	0	0	0
readHeaderXLS	0	0	0
writeCodelink	0	0	0