Package: deltaGseg

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch deltaGseg_1.0.0.tar.gz

StartedAt: 2013-05-01 04:28:43 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 04:56:29 -0700 (Wed, 01 May 2013)

EllapsedTime: 1665.5 seconds

RetCode: 0

Status:  OK

CheckDir: deltaGseg.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/deltaGseg.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 'deltaGseg/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'deltaGseg' 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 'deltaGseg' can be installed ... [10s/12s] 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 ... NOTE
clusterSegments,SegTrajectories: no visible global function definition
  for 'identify.hclust'
* 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 ... [23m/26m] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
clusterPV       898.033 48.870 970.585
denoiseSegments 434.524 15.671 569.842
* 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
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (deltaGseg)

name	user	system	elapsed
SegSeriesTrajectories-class	0.009	0.001	0.011
SegTrajectories-class	0.016	0.001	0.018
Trajectories-class	0.009	0.001	0.010
TransTrajectories-class	0.012	0.000	0.014
chooseBreaks	0.569	0.045	0.637
clusterPV-methods	0.007	0.001	0.008
clusterPV	898.033	48.870	970.585
clusterSegments-methods	0.005	0.005	0.009
clusterSegments	0.005	0.003	0.008
denoiseSegments-methods	0.005	0.005	0.009
denoiseSegments	434.524	15.671	569.842
diagnosticPlots-methods	0.003	0.005	0.021
diagnosticPlots	1.128	0.073	1.546
getAVD	0.093	0.027	0.121
getBreaks-methods	0.003	0.004	0.008
getBreaks	0.093	0.017	0.113
getIntervals-methods	0.007	0.020	0.027
getIntervals	0.098	0.027	0.127
getSegments-methods	0.003	0.006	0.027
getSegments	0.092	0.015	0.120
getTNames-methods	0.003	0.004	0.007
getTNames	0.093	0.026	0.143
getTraj	0.093	0.018	0.112
parseTraj	0.307	0.116	0.528
plotDiff-methods	0.002	0.004	0.006
plotDiff	0.599	0.037	0.638
splitTraj-methods	0.002	0.005	0.007
splitTraj	0.100	0.022	0.126
transformSeries-methods	0.010	0.015	0.024
transformSeries	0.143	0.036	0.182