BioC 2.12: CHECK report for deltaGseg on petty

Package: deltaGseg

Version: 1.0.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch deltaGseg_1.0.3.tar.gz

StartedAt: 2013-10-08 22:09:45 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:28:07 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 1101.3 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 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'deltaGseg/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'deltaGseg' version '1.0.3'
* 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 ... 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [16m/16m] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
clusterPV 907.526 34.238 956.348
* 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	0.010
SegTrajectories-class	0.013	0.001	0.013
Trajectories-class	0.010	0.000	0.011
TransTrajectories-class	0.011	0.000	0.011
chooseBreaks	0.647	0.031	0.684
clusterPV-methods	0.003	0.003	0.006
clusterPV	907.526	34.238	956.348
clusterSegments-methods	0.003	0.003	0.006
clusterSegments	0.005	0.024	0.029
denoiseSegments-methods	0.002	0.004	0.005
denoiseSegments	1.764	0.187	1.992
diagnosticPlots-methods	0.124	0.017	0.143
diagnosticPlots	1.310	0.039	1.402
getAVD	0.114	0.023	0.152
getBreaks-methods	0.006	0.003	0.011
getBreaks	0.259	0.026	0.286
getIntervals-methods	0.003	0.004	0.006
getIntervals	0.117	0.021	0.139
getSegments-methods	0.002	0.002	0.004
getSegments	0.118	0.027	0.145
getTNames-methods	0.002	0.004	0.006
getTNames	0.107	0.028	0.136
getTraj	0.108	0.028	0.136
parseTraj	0.308	0.034	0.371
plotDiff-methods	0.006	0.003	0.009
plotDiff	0.779	0.042	0.831
splitTraj-methods	0.003	0.003	0.005
splitTraj	0.118	0.024	0.142
transformSeries-methods	0.002	0.003	0.006
transformSeries	0.166	0.032	0.201