Package: Clonality

Version: 1.4.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings Clonality_1.4.0.tar.gz

StartedAt: 2012-04-01 00:20:01 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 00:21:47 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 105.8 seconds

RetCode: 0

Status:  OK

CheckDir: Clonality.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/Clonality.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Clonality/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Clonality' version '1.4.0'
* 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 'Clonality' 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
ave.adj.probes: warning in CNA(as.matrix(all.ave[, -1]), chrom = chrs,
  maploc = as.numeric(all.ave[, 1]), sample = names(data)[-c(1, 2)]):
  partial argument match of 'sample' to 'sampleid'
* 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 installed files from '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

NOTE: There was 1 note.
See
  '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/Clonality.Rcheck/00check.log'
for details.

* installing *source* package 'Clonality' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'Clonality.Rnw' 
** testing if installed package can be loaded

* DONE (Clonality)

name	user	system	elapsed
LOHclonality	28.717	0.008	28.741
ave.adj.probes	0	0	0
chromosomePlots	0	0	0
clonality.analysis	55.707	0.348	60.244
genomewidePlots	0.000	0.000	0.001
histogramPlot	0.004	0.000	0.001
splitChromosomes	0	0	0