Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:06:05 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for deltaGseg on lconway


To the developers/maintainers of the deltaGseg package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/deltaGseg.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 509/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
deltaGseg 1.38.0  (landing page)
Diana Low
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/deltaGseg
git_branch: RELEASE_3_16
git_last_commit: 687e465
git_last_commit_date: 2022-11-01 11:07:57 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: deltaGseg
Version: 1.38.0
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_1.38.0.tar.gz
StartedAt: 2023-04-10 19:49:02 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 19:52:41 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 218.9 seconds
RetCode: 0
Status:   OK  
CheckDir: deltaGseg.Rcheck
Warnings: 0

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_1.38.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/deltaGseg.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.38.0’
* 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 ... 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 (user + system) or elapsed time > 5s
             user system elapsed
clusterPV 125.747 22.218 153.955
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.16-bioc/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/4.2/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-class0.0010.0000.002
SegTrajectories-class0.0010.0000.001
Trajectories-class0.0010.0000.001
TransTrajectories-class0.0010.0010.000
chooseBreaks0.0630.0110.074
clusterPV-methods000
clusterPV125.747 22.218153.955
clusterSegments-methods0.0010.0000.000
clusterSegments000
denoiseSegments-methods000
denoiseSegments0.4290.0590.490
diagnosticPlots-methods000
diagnosticPlots0.4270.0150.443
getAVD0.0380.0010.040
getBreaks-methods000
getBreaks0.0390.0010.040
getIntervals-methods000
getIntervals0.0440.0070.051
getSegments-methods000
getSegments0.0390.0010.041
getTNames-methods0.0010.0000.000
getTNames0.0440.0020.047
getTraj0.0580.0130.071
parseTraj0.0810.0090.091
plotDiff-methods0.0010.0000.000
plotDiff0.3260.0260.353
splitTraj-methods000
splitTraj0.0470.0030.049
transformSeries-methods000
transformSeries0.0730.0030.077