Package: deltaGseg

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings deltaGseg_1.18.0.tar.gz

StartedAt: 2018-04-12 02:42:01 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:47:29 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 327.9 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 deltaGseg_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/deltaGseg.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.18.0’
* 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 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 ... 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 248.211  7.833 260.424
* 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-3.6-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	0.002	0.001	0.003
SegTrajectories-class	0.002	0.000	0.002
Trajectories-class	0.001	0.001	0.001
TransTrajectories-class	0.001	0.000	0.001
chooseBreaks	0.550	0.025	0.594
clusterPV-methods	0.001	0.000	0.001
clusterPV	248.211	7.833	260.424
clusterSegments-methods	0	0	0
clusterSegments	0.000	0.000	0.001
denoiseSegments-methods	0.000	0.000	0.001
denoiseSegments	1.500	0.067	1.588
diagnosticPlots-methods	0.000	0.000	0.001
diagnosticPlots	2.210	0.040	2.284
getAVD	0.052	0.010	0.063
getBreaks-methods	0.000	0.000	0.001
getBreaks	0.055	0.010	0.065
getIntervals-methods	0.000	0.000	0.001
getIntervals	0.056	0.014	0.070
getSegments-methods	0.001	0.000	0.000
getSegments	0.059	0.013	0.079
getTNames-methods	0.000	0.000	0.001
getTNames	0.053	0.009	0.062
getTraj	0.056	0.009	0.066
parseTraj	0.203	0.013	0.222
plotDiff-methods	0	0	0
plotDiff	0.457	0.017	0.485
splitTraj-methods	0.001	0.000	0.001
splitTraj	0.073	0.007	0.080
transformSeries-methods	0	0	0
transformSeries	0.077	0.009	0.088