Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2024-03-27 11:35:48 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
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

Package 534/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
deltaGseg 1.42.0  (landing page)
Diana Low
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/deltaGseg
git_branch: RELEASE_3_18
git_last_commit: fbbf108
git_last_commit_date: 2023-10-24 09:53:09 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for deltaGseg on nebbiolo2


To the developers/maintainers of the deltaGseg package:
- 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 Troubleshooting Build Report for more information.
- 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: 1.42.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:deltaGseg.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings deltaGseg_1.42.0.tar.gz
StartedAt: 2024-03-25 21:37:50 -0400 (Mon, 25 Mar 2024)
EndedAt: 2024-03-25 21:41:22 -0400 (Mon, 25 Mar 2024)
EllapsedTime: 212.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: deltaGseg.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:deltaGseg.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings deltaGseg_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/deltaGseg.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘deltaGseg/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘deltaGseg’ version ‘1.42.0’
* 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 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 ... 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 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 142.612  3.143 145.794
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘deltaGseg.Rnw’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/deltaGseg.Rcheck/00check.log’
for details.



Installation output

deltaGseg.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL deltaGseg
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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-class0.0000.0010.000
Trajectories-class0.0010.0000.001
TransTrajectories-class0.0010.0000.001
chooseBreaks0.0560.0240.080
clusterPV-methods0.0000.0000.001
clusterPV142.612 3.143145.794
clusterSegments-methods000
clusterSegments000
denoiseSegments-methods000
denoiseSegments0.4260.0110.436
diagnosticPlots-methods0.0000.0000.001
diagnosticPlots0.5110.0150.527
getAVD0.0530.0000.054
getBreaks-methods000
getBreaks0.0530.0000.053
getIntervals-methods0.0000.0000.001
getIntervals0.0460.0080.053
getSegments-methods0.0010.0000.000
getSegments0.0510.0040.055
getTNames-methods000
getTNames0.0520.0070.061
getTraj0.0450.0080.053
parseTraj0.0860.0000.087
plotDiff-methods0.0010.0000.000
plotDiff0.2650.0110.277
splitTraj-methods000
splitTraj0.0560.0000.056
transformSeries-methods000
transformSeries0.0630.0040.067