BioC 3.0: CHECK report for deltaGseg on oaxaca

Package: deltaGseg

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch deltaGseg_1.6.0.tar.gz

StartedAt: 2015-04-09 22:53:21 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 23:03:57 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 636.3 seconds

RetCode: 0

Status:  OK

CheckDir: deltaGseg.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch deltaGseg_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/deltaGseg.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘deltaGseg/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘deltaGseg’ version ‘1.6.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘ggplot2’ ‘changepoint’ ‘wavethresh’ ‘tseries’ ‘pvclust’ ‘fBasics’
  ‘grid’ ‘reshape’ ‘scales’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... [7s/8s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 loading without being on the library search path ... OK
* checking 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’ ... NOTE
The following files should probably not be installed:
  ‘diagplots.png’, ‘simclust.png’, ‘simtraj.png’, ‘simtrajtr.png’,
  ‘simtrajtr2.png’, ‘traj1.png’, ‘traj1break.png’, ‘traj1ss0.png’,
  ‘traj1ss1.png’, ‘traj1tr.png’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking files in ‘vignettes’ ... OK
* checking examples ... [548s/552s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
clusterPV 526.202 14.856 545.053
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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	0.003	0.000	0.002
SegTrajectories-class	0.002	0.000	0.001
Trajectories-class	0.001	0.000	0.001
TransTrajectories-class	0.001	0.000	0.001
chooseBreaks	0.235	0.022	0.272
clusterPV-methods	0.001	0.000	0.000
clusterPV	526.202	14.856	545.053
clusterSegments-methods	0.001	0.001	0.001
clusterSegments	0.001	0.000	0.001
denoiseSegments-methods	0.001	0.000	0.001
denoiseSegments	0.961	0.104	1.083
diagnosticPlots-methods	0.000	0.000	0.018
diagnosticPlots	0.73	0.03	0.76
getAVD	0.069	0.008	0.076
getBreaks-methods	0.000	0.000	0.001
getBreaks	0.067	0.008	0.075
getIntervals-methods	0	0	0
getIntervals	0.070	0.009	0.079
getSegments-methods	0	0	0
getSegments	0.072	0.011	0.083
getTNames-methods	0.001	0.000	0.001
getTNames	0.072	0.013	0.085
getTraj	0.067	0.007	0.075
parseTraj	0.184	0.012	0.214
plotDiff-methods	0.001	0.000	0.001
plotDiff	0.429	0.016	0.446
splitTraj-methods	0	0	0
splitTraj	0.075	0.010	0.087
transformSeries-methods	0.000	0.000	0.001
transformSeries	0.116	0.019	0.135