BioC 2.12: CHECK report for SomatiCA on george2

Package: SomatiCA

Version: 1.0.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings SomatiCA_1.0.0.tar.gz

StartedAt: 2013-10-09 05:03:28 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 05:10:19 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 411.1 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 3.0.1 (2013-05-16)
* 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 ‘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 ... [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 ... [197s/231s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
SomatiCApipe         88.077  1.060 105.534
admixtureRate        76.553  0.080  86.546
GCbiasRemoval         9.821  0.124  12.966
segmentGCbiasRemoval  5.600  0.036   6.981
* 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
** testing if installed package can be loaded
* DONE (SomatiCA)

name	user	system	elapsed
GCbiasRemoval	9.821	0.124	12.966
GCcount	0.052	0.000	0.050
MergeSegment	0.300	0.008	0.404
SomatiCA-package	1.308	0.024	1.666
SomatiCAUsersGuide	0.008	0.004	0.018
SomatiCApipe	88.077	1.060	105.534
admixtureRate	76.553	0.080	86.546
collapse	0.012	0.000	0.012
copynumberCorrected	0.056	0.000	0.056
denoise	0.144	0.000	0.144
larsCBSsegment	1.108	0.016	1.450
plotSegment	0.116	0.008	0.125
plotSubclonality	0.168	0.004	0.174
refineSegment	0.44	0.00	0.57
segmentGCbiasRemoval	5.600	0.036	6.981
somaticRatio	0.305	0.004	0.321
subclonality	2.556	0.044	3.093