BioC 2.12: CHECK report for SomatiCA on petty

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: 2013-10-08 23:57:43 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-09 00:04:29 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 405.8 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 3.0.1 (2013-05-16)
* 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 ... 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 ... [16s/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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [238s/241s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
SomatiCApipe  101.227 10.921 113.354
admixtureRate  86.329 10.961  98.618
GCbiasRemoval   7.394  0.158   7.589
* 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/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	7.394	0.158	7.589
GCcount	0.044	0.012	0.057
MergeSegment	0.300	0.048	0.348
SomatiCA-package	1.644	0.089	1.750
SomatiCAUsersGuide	0.045	0.006	0.053
SomatiCApipe	101.227	10.921	113.354
admixtureRate	86.329	10.961	98.618
collapse	0.014	0.003	0.017
copynumberCorrected	0.094	0.009	0.104
denoise	0.216	0.010	0.227
larsCBSsegment	1.683	0.064	1.753
plotSegment	0.148	0.034	0.184
plotSubclonality	0.224	0.027	0.252
refineSegment	0.549	0.020	0.577
segmentGCbiasRemoval	4.598	0.117	4.730
somaticRatio	0.324	0.027	0.352
subclonality	2.769	0.098	2.947