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This page was generated on 2021-10-16 15:51:46 -0400 (Sat, 16 Oct 2021).

CHECK results for furrowSeg on nebbiolo2

To the developers/maintainers of the furrowSeg package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 134/404HostnameOS / ArchINSTALLBUILDCHECK
furrowSeg 1.21.0  (landing page)
Joseph Barry
Snapshot Date: 2021-10-16 09:30:02 -0400 (Sat, 16 Oct 2021)
git_url: https://git.bioconductor.org/packages/furrowSeg
git_branch: master
git_last_commit: c96ff6e
git_last_commit_date: 2021-05-19 11:53:53 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published

Summary

Package: furrowSeg
Version: 1.21.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:furrowSeg.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings furrowSeg_1.21.0.tar.gz
StartedAt: 2021-10-16 12:16:06 -0400 (Sat, 16 Oct 2021)
EndedAt: 2021-10-16 12:18:18 -0400 (Sat, 16 Oct 2021)
EllapsedTime: 131.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: furrowSeg.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:furrowSeg.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings furrowSeg_1.21.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-data-experiment/meat/furrowSeg.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘furrowSeg/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘furrowSeg’ version ‘1.21.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘furrowSeg’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘EBImage::abind’ by ‘abind::abind’ when loading ‘furrowSeg’
See ‘/home/biocbuild/bbs-3.14-data-experiment/meat/furrowSeg.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 348.6Mb
  sub-directories of 1Mb or more:
    data  348.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
identifyFurrowPosition: no visible global function definition for
  ‘predict’
identifyFurrowPosition: no visible global function definition for ‘par’
identifyFurrowPosition: no visible global function definition for
  ‘points’
identifyFurrowPosition: no visible global function definition for
  ‘abline’
identifyTimeMinArea: no visible binding for global variable ‘median’
identifyTimeMinArea: no visible global function definition for
  ‘predict’
identifyTimeMinArea: no visible global function definition for ‘par’
identifyTimeMinArea: no visible global function definition for ‘points’
identifyTimeMinArea: no visible global function definition for ‘abline’
plotFeatureEvolution: no visible global function definition for ‘par’
plotFeatureEvolution: no visible binding for global variable ‘median’
plotFeatureEvolution: no visible binding for global variable ‘quantile’
plotFeatureEvolution: no visible global function definition for
  ‘polygon’
plotFeatureEvolution: no visible global function definition for ‘rgb’
plotFeatureEvolution: no visible global function definition for ‘axis’
plotFeatureEvolution: no visible global function definition for ‘mtext’
plotFeatureEvolution: no visible global function definition for ‘title’
Undefined global functions or variables:
  abline axis median mtext par points polygon predict quantile rgb
  title
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "abline", "axis", "mtext", "par", "points",
             "polygon", "title")
  importFrom("stats", "median", "predict", "quantile")
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
opto               21.119  0.396  21.515
exampleFurrowMovie  8.983  0.324   9.308
* 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-data-experiment/meat/furrowSeg.Rcheck/00check.log’
for details.



Installation output

furrowSeg.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL furrowSeg
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘furrowSeg’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘EBImage::abind’ by ‘abind::abind’ when loading ‘furrowSeg’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘EBImage::abind’ by ‘abind::abind’ when loading ‘furrowSeg’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘EBImage::abind’ by ‘abind::abind’ when loading ‘furrowSeg’
** testing if installed package keeps a record of temporary installation path
* DONE (furrowSeg)

Tests output


Example timings

furrowSeg.Rcheck/furrowSeg-Ex.timings

nameusersystemelapsed
constructBox000
exampleFurrowMovie8.9830.3249.308
identifyFurrowPosition000
identifyTimeMinArea000
isOdd0.0010.0000.002
isolateBoxCells000
opto21.119 0.39621.515
plotFeatureEvolution000
px2area000
px2microns000
sampleTable0.0020.0000.002
segmentFurrowAllStacks000