Package: codelink

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch codelink_1.22.0.tar.gz

StartedAt: 2012-03-24 00:28:04 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 00:31:03 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 179.6 seconds

RetCode: 0

Status:  OK

CheckDir: codelink.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/codelink.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'codelink/DESCRIPTION' ... OK
* this is package 'codelink' version '1.22.0'
* 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 whether package 'codelink' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated 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 ... NOTE
File 'codelink/R/Codelink-class.R':
  .onLoad calls:
    require(methods, quietly = TRUE)

Package startup functions should not change the search path.
See section 'Good practice' in ?.onAttach.

* 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                       old_size new_size compress
  codelink.example.rda    842Kb    522Kb       xz
  codelink.exprset.rda    2.5Mb    1.8Mb       xz
* checking sizes of PDF files under 'inst/doc' ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'codelink' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'summary' from package 'base' in package 'codelink'
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'CodelinkSet.Rnw' using 'latin1' 
   'codelink.Rnw' using 'latin1' 
** testing if installed package can be loaded

* DONE (codelink)

name	user	system	elapsed
Codelink-class	0	0	0
CodelinkSet-class	0.001	0.000	0.000
CodelinkSetUnique-class	0.001	0.001	0.000
arrayNew	0.001	0.000	0.001
as.matrix.Codelink	0	0	0
averageProbes	0.000	0.000	0.001
bkgdCorrect	0	0	0
createWeights	0	0	0
cutCV	0.000	0.000	0.001
dim.Codelink	0	0	0
imageCodelink	0	0	0
logCodelink	0	0	0
mergeArray	0.000	0.000	0.001
na2false	0.000	0.001	0.000
normalize	0	0	0
normalize.loess	0.000	0.000	0.001
plotCorrelation	0	0	0
plotDensities	0	0	0
plotMA	0	0	0
readCodelink	0	0	0
readHeader	0.000	0.000	0.001
readHeaderXLS	0.000	0.001	0.000
writeCodelink	0	0	0