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This page was generated on 2023-10-20 09:38:01 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 527/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
deltaGseg 1.40.0  (landing page)
Diana Low
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/deltaGseg
git_branch: RELEASE_3_17
git_last_commit: 09128e9
git_last_commit_date: 2023-04-25 10:26:03 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for deltaGseg on kjohnson2


To the developers/maintainers of the deltaGseg package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: deltaGseg
Version: 1.40.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:deltaGseg.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings deltaGseg_1.40.0.tar.gz
StartedAt: 2023-10-17 15:03:10 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 15:09:38 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 387.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: deltaGseg.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:deltaGseg.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings deltaGseg_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/deltaGseg.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘deltaGseg/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘deltaGseg’ version ‘1.40.0’
* 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 ... 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 ... WARNING
checkRd: (5) SegSeriesTrajectories-class.Rd:40: \item in \describe must have non-empty label
checkRd: (5) SegSeriesTrajectories-class.Rd:41: \item in \describe must have non-empty label
checkRd: (5) SegSeriesTrajectories-class.Rd:42: \item in \describe must have non-empty label
checkRd: (5) SegSeriesTrajectories-class.Rd:43: \item in \describe must have non-empty label
checkRd: (5) SegSeriesTrajectories-class.Rd:44: \item in \describe must have non-empty label
checkRd: (5) SegSeriesTrajectories-class.Rd:50: \item in \describe must have non-empty label
checkRd: (5) SegSeriesTrajectories-class.Rd:51: \item in \describe must have non-empty label
checkRd: (5) SegSeriesTrajectories-class.Rd:52: \item in \describe must have non-empty label
checkRd: (5) SegSeriesTrajectories-class.Rd:53: \item in \describe must have non-empty label
checkRd: (5) SegTrajectories-class.Rd:37: \item in \describe must have non-empty label
checkRd: (5) SegTrajectories-class.Rd:38: \item in \describe must have non-empty label
checkRd: (5) SegTrajectories-class.Rd:39: \item in \describe must have non-empty label
checkRd: (5) SegTrajectories-class.Rd:40: \item in \describe must have non-empty label
checkRd: (5) SegTrajectories-class.Rd:41: \item in \describe must have non-empty label
checkRd: (5) SegTrajectories-class.Rd:47: \item in \describe must have non-empty label
checkRd: (5) SegTrajectories-class.Rd:48: \item in \describe must have non-empty label
checkRd: (5) SegTrajectories-class.Rd:49: \item in \describe must have non-empty label
checkRd: (5) SegTrajectories-class.Rd:50: \item in \describe must have non-empty label
checkRd: (5) Trajectories-class.Rd:25: \item in \describe must have non-empty label
checkRd: (5) Trajectories-class.Rd:26: \item in \describe must have non-empty label
checkRd: (5) Trajectories-class.Rd:27: \item in \describe must have non-empty label
checkRd: (5) Trajectories-class.Rd:28: \item in \describe must have non-empty label
checkRd: (5) Trajectories-class.Rd:35: \item in \describe must have non-empty label
checkRd: (5) Trajectories-class.Rd:36: \item in \describe must have non-empty label
checkRd: (5) Trajectories-class.Rd:37: \item in \describe must have non-empty label
checkRd: (5) Trajectories-class.Rd:38: \item in \describe must have non-empty label
checkRd: (5) TransTrajectories-class.Rd:34: \item in \describe must have non-empty label
checkRd: (5) TransTrajectories-class.Rd:35: \item in \describe must have non-empty label
checkRd: (5) TransTrajectories-class.Rd:36: \item in \describe must have non-empty label
checkRd: (5) TransTrajectories-class.Rd:37: \item in \describe must have non-empty label
checkRd: (5) TransTrajectories-class.Rd:44: \item in \describe must have non-empty label
checkRd: (5) TransTrajectories-class.Rd:45: \item in \describe must have non-empty label
checkRd: (5) TransTrajectories-class.Rd:46: \item in \describe must have non-empty label
checkRd: (5) TransTrajectories-class.Rd:47: \item in \describe must have non-empty label
* 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 (user + system) or elapsed time > 5s
             user system elapsed
clusterPV 172.568  14.12 277.683
* 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: 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/deltaGseg.Rcheck/00check.log’
for details.



Installation output

deltaGseg.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL deltaGseg
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘deltaGseg’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (deltaGseg)

Tests output


Example timings

deltaGseg.Rcheck/deltaGseg-Ex.timings

nameusersystemelapsed
SegSeriesTrajectories-class0.0020.0010.006
SegTrajectories-class0.0010.0010.004
Trajectories-class0.0000.0000.001
TransTrajectories-class0.0010.0000.002
chooseBreaks0.0740.0100.132
clusterPV-methods0.0010.0000.000
clusterPV172.568 14.120277.683
clusterSegments-methods0.0010.0000.000
clusterSegments0.0000.0010.000
denoiseSegments-methods000
denoiseSegments0.4660.0260.745
diagnosticPlots-methods000
diagnosticPlots0.6120.0190.975
getAVD0.0540.0050.089
getBreaks-methods0.0000.0000.001
getBreaks0.0550.0060.096
getIntervals-methods000
getIntervals0.0630.0050.102
getSegments-methods000
getSegments0.0540.0050.095
getTNames-methods000
getTNames0.0610.0050.100
getTraj0.0780.0060.127
parseTraj0.0830.0060.139
plotDiff-methods000
plotDiff0.3480.0110.553
splitTraj-methods000
splitTraj0.0580.0050.097
transformSeries-methods0.0010.0000.000
transformSeries0.0790.0060.129