Package: SomatiCA

Version: 0.99.2

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings SomatiCA_0.99.2.tar.gz

StartedAt: 2013-03-25 04:45:36 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:52:52 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 436.4 seconds

RetCode: 0

Status:  OK

CheckDir: SomatiCA.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/SomatiCA.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SomatiCA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SomatiCA’ version ‘0.99.2’
* 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 ‘SomatiCA’ can be installed ... [17s/18s] 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 ... NOTE
The following files look like leftovers:
  ‘SomatiCA/NEWS.Rd’
Please remove them from your package.
* 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 ... 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 examples ... [212s/245s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
SomatiCApipe         94.210  0.860 110.516
admixtureRate        83.133  0.160  97.893
GCbiasRemoval        11.105  0.144  12.028
segmentGCbiasRemoval  5.828  0.052   6.736
* 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
  ‘/home/biocbuild/bbs-2.12-bioc/meat/SomatiCA.Rcheck/00check.log’
for details.

* installing *source* package ‘SomatiCA’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘SomatiCA.Rnw’ 
** testing if installed package can be loaded
* DONE (SomatiCA)

name	user	system	elapsed
GCbiasRemoval	11.105	0.144	12.028
GCcount	0.052	0.000	0.052
MergeSegment	0.268	0.020	0.381
SomatiCA-package	1.576	0.024	1.823
SomatiCAUsersGuide	0.064	0.008	0.073
SomatiCApipe	94.210	0.860	110.516
admixtureRate	83.133	0.160	97.893
collapse	0.012	0.000	0.017
copynumberCorrected	0.068	0.000	0.098
denoise	0.152	0.004	0.208
larsCBSsegment	1.112	0.000	1.160
plotSegment	0.128	0.016	0.143
plotSubclonality	0.176	0.000	0.183
refineSegment	0.528	0.004	0.639
segmentGCbiasRemoval	5.828	0.052	6.736
somaticRatio	0.332	0.000	0.332
subclonality	3.121	0.036	3.611