Package: deltaGseg

Version: 0.99.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch deltaGseg_0.99.2.tar.gz

StartedAt: 2013-03-25 02:04:25 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:29:12 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 1487.4 seconds

RetCode: 0

Status:  OK

CheckDir: deltaGseg.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/deltaGseg.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'deltaGseg/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'deltaGseg' 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 'deltaGseg' can be installed ... [12s/13s] 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 ... 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 ... NOTE
  WaveThresh: R wavelet software, release 4.6.1, installed
  
  Copyright Guy Nason and others 1993-2012
  
  Note: nlevels has been renamed to nlevelsWT
  
* 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 ... [23m/23m] OK
Examples with CPU or elapsed time > 5s
                   user  system elapsed
clusterPV       627.731 145.476 781.424
denoiseSegments 546.698  29.779 577.299
* 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/deltaGseg.Rcheck/00check.log'
for details.

* installing *source* package 'deltaGseg' ...
** R
** data
** inst
** preparing package for lazy loading
WaveThresh: R wavelet software, release 4.6.1, installed

Copyright Guy Nason and others 1993-2012

Note: nlevels has been renamed to nlevelsWT

** help
*** installing help indices
** building package indices
** installing vignettes
   'deltaGseg.Rnw' 
** testing if installed package can be loaded
WaveThresh: R wavelet software, release 4.6.1, installed

Copyright Guy Nason and others 1993-2012

Note: nlevels has been renamed to nlevelsWT

* DONE (deltaGseg)

name	user	system	elapsed
SegSeriesTrajectories-class	0.011	0.006	0.018
SegTrajectories-class	0.013	0.005	0.018
Trajectories-class	0.009	0.005	0.014
TransTrajectories-class	0.013	0.007	0.026
chooseBreaks	0.422	0.035	0.457
clusterPV-methods	0.006	0.006	0.012
clusterPV	627.731	145.476	781.424
clusterSegments-methods	0.005	0.006	0.010
clusterSegments	0.004	0.006	0.010
denoiseSegments-methods	0.004	0.006	0.010
denoiseSegments	546.698	29.779	577.299
diagnosticPlots-methods	0.004	0.017	0.022
diagnosticPlots	0.872	0.082	1.015
getAVD	0.092	0.024	0.118
getBreaks-methods	0.002	0.004	0.006
getBreaks	0.095	0.031	0.132
getIntervals-methods	0.002	0.004	0.006
getIntervals	0.099	0.029	0.127
getSegments-methods	0.002	0.005	0.009
getSegments	0.096	0.039	0.135
getTNames-methods	0.002	0.004	0.006
getTNames	0.093	0.027	0.120
getTraj	0.097	0.034	0.132
parseTraj	0.167	0.096	0.279
plotDiff-methods	0.005	0.012	0.017
plotDiff	0.474	0.039	0.516
splitTraj-methods	0.002	0.005	0.007
splitTraj	0.114	0.043	0.157
transformSeries-methods	0.002	0.004	0.006
transformSeries	0.129	0.041	0.171