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CHECK report for furrowSeg on malbec1

This page was generated on 2019-04-16 15:26:14 -0400 (Tue, 16 Apr 2019).

Package 124/360HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
furrowSeg 1.10.0
Joseph Barry
Snapshot Date: 2019-04-16 11:00:05 -0400 (Tue, 16 Apr 2019)
URL: https://git.bioconductor.org/packages/furrowSeg
Branch: RELEASE_3_8
Last Commit: d7772b0
Last Changed Date: 2018-10-30 11:36:24 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository

Summary

Package: furrowSeg
Version: 1.10.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:furrowSeg.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings furrowSeg_1.10.0.tar.gz
StartedAt: 2019-04-16 13:42:39 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 13:44:37 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 117.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: furrowSeg.Rcheck
Warnings: 1

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:furrowSeg.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings furrowSeg_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-data-experiment/meat/furrowSeg.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.10.0’
* 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-3.8-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 ‘plot’
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 plot points polygon predict quantile rgb
  title
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "abline", "axis", "mtext", "par", "plot",
             "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 or elapsed time > 5s
                     user system elapsed
opto               27.500  0.412  27.941
exampleFurrowMovie 10.596  0.184  11.937
* 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-3.8-data-experiment/meat/furrowSeg.Rcheck/00check.log’
for details.



Installation output

furrowSeg.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL furrowSeg
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘furrowSeg’ ...
** 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
Warning: replacing previous import ‘EBImage::abind’ by ‘abind::abind’ when loading ‘furrowSeg’
* DONE (furrowSeg)

Tests output


Example timings

furrowSeg.Rcheck/furrowSeg-Ex.timings

nameusersystemelapsed
constructBox000
exampleFurrowMovie10.596 0.18411.937
identifyFurrowPosition000
identifyTimeMinArea0.0000.0000.001
isOdd000
isolateBoxCells000
opto27.500 0.41227.941
plotFeatureEvolution000
px2area000
px2microns000
sampleTable0.0040.0000.024
segmentFurrowAllStacks000