BioC 2.13: CHECK report for codelink on perceval

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/codelink.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.30.9’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘codelink’ can be installed ... [23s/24s] 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 ... [14s/14s] 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

* 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)

name	user	system	elapsed
Codelink-class	0.008	0.002	0.010
CodelinkSet-class	0.014	0.001	0.015
CodelinkSetUnique-class	0.007	0.001	0.008
arrayNew	0.009	0.001	0.011
as.matrix.Codelink	0.009	0.001	0.010
averageProbes	0.009	0.002	0.010
bkgdCorrect	2.135	0.062	2.229
createWeights	0.811	0.067	0.878
cutCV	0.018	0.003	0.021
dim.Codelink	0.020	0.003	0.024
imageCodelink	0.021	0.002	0.023
logCodelink	0.019	0.003	0.022
mergeArray	0.313	0.007	0.325
na2false	0.006	0.006	0.012
normalize	2.151	0.173	2.389
plotCorrelation	0.010	0.004	0.014
plotDensities	0.011	0.004	0.014
plotMA	0.011	0.003	0.014
readCodelink	0.012	0.006	0.018
readHeader	0.010	0.004	0.013
readHeaderXLS	0.010	0.004	0.015
writeCodelink	0.013	0.004	0.017

BioC 2.13: CHECK report for codelink on perceval

Summary

Command output