Package: Clonality

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Clonality_1.7.0.tar.gz

StartedAt: 2013-03-24 03:48:12 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 03:52:46 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 274.4 seconds

RetCode: 0

Status:  OK

CheckDir: Clonality.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/Clonality.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'Clonality/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Clonality' version '1.7.0'
* 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 'Clonality' can be installed ... [2s/2s] OK
* checking installed package size ... OK
* checking package 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call with 'PACKAGE' argument in a different package:
  .Fortran("fndcpt", ..., PACKAGE = "DNAcopy")
See the chapter 'System and foreign language interfaces' of the
'Writing R Extensions' manual.
* 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 installed files from 'inst/doc' ... OK
* checking examples ... [226s/236s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
clonality.analysis  99.913  1.564 107.682
LOHclonality        52.902  1.589  55.096
LRtesting3or4tumors 44.040  0.178  46.610
ECMtesting          24.803  0.099  24.995
* 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
  '/Users/biocbuild/bbs-2.12-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
ECMtesting	24.803	0.099	24.995
LOHclonality	52.902	1.589	55.096
LRtesting3or4tumors	44.040	0.178	46.610
ave.adj.probes	0.025	0.002	0.035
chromosomePlots	0.088	0.005	0.160
clonality.analysis	99.913	1.564	107.682
genomewidePlots	0.069	0.002	0.072
histogramPlot	0.088	0.020	0.108
splitChromosomes	0.020	0.012	0.033