Package: deltaGseg

Version: 1.23.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:deltaGseg.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings deltaGseg_1.23.0.tar.gz

StartedAt: 2019-04-09 00:23:02 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:27:51 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 288.6 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 --install=check:deltaGseg.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings deltaGseg_1.23.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/deltaGseg.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.23.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘deltaGseg’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 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
boot.hclust_new: no visible global function definition for ‘hclust’
dist.pvclust: no visible global function definition for ‘as.dist’
dist.pvclust: no visible global function definition for ‘cor’
dist.pvclust: no visible global function definition for ‘na.omit’
dist.pvclust: no visible global function definition for ‘dist’
distw.pvclust: no visible global function definition for ‘as.dist’
mydist: no visible global function definition for ‘dist’
mydist: no visible global function definition for ‘as.dist’
parseTraj: no visible global function definition for ‘read.table’
pvclust_new: no visible global function definition for ‘hclust’
segden1: no visible global function definition for ‘quantile’
text.pvclust: no visible global function definition for ‘par’
text.pvclust: no visible global function definition for ‘text’
clusterSegments,SegTrajectories: no visible global function definition
  for ‘hclust’
clusterSegments,SegTrajectories: no visible global function definition
  for ‘layout’
clusterSegments,SegTrajectories: no visible global function definition
  for ‘lines’
clusterSegments,SegTrajectories: no visible global function definition
  for ‘points’
clusterSegments,SegTrajectories: no visible global function definition
  for ‘abline’
clusterSegments,SegTrajectories: no visible global function definition
  for ‘text’
clusterSegments,SegTrajectories: no visible global function definition
  for ‘identify’
clusterSegments,SegTrajectories: no visible global function definition
  for ‘par’
clusterSegments,SegTrajectories: no visible global function definition
  for ‘locator’
clusterSegments,SegTrajectories: no visible global function definition
  for ‘cutree’
clusterSegments,SegTrajectories: no visible global function definition
  for ‘mtext’
clusterSegments,SegTrajectories: no visible global function definition
  for ‘median’
denoiseSegments,Trajectories: no visible global function definition for
  ‘txtProgressBar’
denoiseSegments,Trajectories: no visible global function definition for
  ‘setTxtProgressBar’
diagnosticPlots,SegSeriesTrajectories: no visible binding for global
  variable ‘residuals’
diagnosticPlots,SegSeriesTrajectories: no visible global function
  definition for ‘acf’
diagnosticPlots,SegSeriesTrajectories: no visible global function
  definition for ‘qnorm’
diagnosticPlots,SegSeriesTrajectories: no visible binding for global
  variable ‘lag’
Undefined global functions or variables:
  abline acf as.dist cor cutree dist hclust identify lag layout lines
  locator median mtext na.omit par points qnorm quantile read.table
  residuals setTxtProgressBar text txtProgressBar
Consider adding
  importFrom("graphics", "abline", "identify", "layout", "lines",
             "locator", "mtext", "par", "points", "text")
  importFrom("stats", "acf", "as.dist", "cor", "cutree", "dist",
             "hclust", "lag", "median", "na.omit", "qnorm", "quantile",
             "residuals")
  importFrom("utils", "read.table", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
clusterPV 208.727  8.261 221.578
* 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

Status: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/deltaGseg.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL deltaGseg
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘deltaGseg’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘deltaGseg.Rnw’ 
** testing if installed package can be loaded
* DONE (deltaGseg)

name	user	system	elapsed
SegSeriesTrajectories-class	0.003	0.000	0.003
SegTrajectories-class	0.001	0.001	0.001
Trajectories-class	0.001	0.000	0.001
TransTrajectories-class	0.001	0.001	0.002
chooseBreaks	0.098	0.022	0.120
clusterPV-methods	0.001	0.000	0.000
clusterPV	208.727	8.261	221.578
clusterSegments-methods	0.000	0.000	0.001
clusterSegments	0	0	0
denoiseSegments-methods	0	0	0
denoiseSegments	0.637	0.090	0.734
diagnosticPlots-methods	0	0	0
diagnosticPlots	0.745	0.025	0.777
getAVD	0.079	0.017	0.096
getBreaks-methods	0	0	0
getBreaks	0.066	0.012	0.079
getIntervals-methods	0.001	0.000	0.000
getIntervals	0.072	0.008	0.084
getSegments-methods	0	0	0
getSegments	0.065	0.012	0.078
getTNames-methods	0	0	0
getTNames	0.069	0.006	0.076
getTraj	0.100	0.022	0.122
parseTraj	0.094	0.008	0.105
plotDiff-methods	0	0	0
plotDiff	0.489	0.023	0.519
splitTraj-methods	0.000	0.001	0.000
splitTraj	0.061	0.013	0.075
transformSeries-methods	0	0	0
transformSeries	0.081	0.014	0.094