Package: SomatiCA

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SomatiCA_1.0.0.tar.gz

StartedAt: 2013-05-01 11:09:52 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 11:15:43 -0700 (Wed, 01 May 2013)

EllapsedTime: 350.6 seconds

RetCode: 0

Status:  OK

CheckDir: SomatiCA.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/SomatiCA.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'SomatiCA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SomatiCA' version '1.0.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'SomatiCAData'
* 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 ... [14s/16s] 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 ... [202s/206s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
SomatiCApipe  80.943 12.769  96.076
admixtureRate 69.856 13.342  84.621
GCbiasRemoval  6.390  0.186   6.741
* 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 were 2 notes.
See
  '/Users/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
** testing if installed package can be loaded
* DONE (SomatiCA)

name	user	system	elapsed
GCbiasRemoval	6.390	0.186	6.741
GCcount	0.032	0.012	0.045
MergeSegment	0.225	0.043	0.270
SomatiCA-package	1.234	0.082	1.369
SomatiCAUsersGuide	0.035	0.005	0.041
SomatiCApipe	80.943	12.769	96.076
admixtureRate	69.856	13.342	84.621
collapse	0.011	0.004	0.014
copynumberCorrected	0.065	0.011	0.077
denoise	0.158	0.014	0.174
larsCBSsegment	1.097	0.058	1.156
plotSegment	0.103	0.036	0.148
plotSubclonality	0.157	0.025	0.186
refineSegment	0.417	0.020	0.458
segmentGCbiasRemoval	4.021	0.145	4.240
somaticRatio	0.254	0.023	0.278
subclonality	3.028	0.121	3.182