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CHECK report for furrowSeg on riesling1

This page was generated on 2021-01-21 16:01:28 -0500 (Thu, 21 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE furrowSeg PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 134/386HostnameOS / ArchINSTALLBUILDCHECK
furrowSeg 1.19.0
Joseph Barry
Snapshot Date: 2021-01-21 09:00:14 -0500 (Thu, 21 Jan 2021)
URL: https://git.bioconductor.org/packages/furrowSeg
Branch: master
Last Commit: dc5fff2
Last Changed Date: 2020-10-27 10:15:35 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ WARNINGS ]

Summary

Package: furrowSeg
Version: 1.19.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:furrowSeg.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings furrowSeg_1.19.0.tar.gz
StartedAt: 2021-01-21 11:23:47 -0500 (Thu, 21 Jan 2021)
EndedAt: 2021-01-21 11:26:28 -0500 (Thu, 21 Jan 2021)
EllapsedTime: 161.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: furrowSeg.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:furrowSeg.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings furrowSeg_1.19.0.tar.gz
###
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##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/furrowSeg.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'furrowSeg/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'furrowSeg' version '1.19.0'
* 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 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 'D:/biocbuild/bbs-3.13-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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
opto               22.92   0.33   23.25
exampleFurrowMovie  9.18   0.18    9.37
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
opto               18.02   0.37   18.39
exampleFurrowMovie  7.28   0.17    7.46
* 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
  'D:/biocbuild/bbs-3.13-data-experiment/meat/furrowSeg.Rcheck/00check.log'
for details.



Installation output

furrowSeg.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/furrowSeg_1.19.0.tar.gz && rm -rf furrowSeg.buildbin-libdir && mkdir furrowSeg.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=furrowSeg.buildbin-libdir furrowSeg_1.19.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL furrowSeg_1.19.0.zip && rm furrowSeg_1.19.0.tar.gz furrowSeg_1.19.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 11  348M   11 40.8M    0     0  69.1M      0  0:00:05 --:--:--  0:00:05 69.0M
 38  348M   38  134M    0     0  84.6M      0  0:00:04  0:00:01  0:00:03 84.5M
 68  348M   68  237M    0     0  91.7M      0  0:00:03  0:00:02  0:00:01 91.7M
 86  348M   86  301M    0     0  82.6M      0  0:00:04  0:00:03  0:00:01 82.5M
 98  348M   98  343M    0     0  72.2M      0  0:00:04  0:00:04 --:--:-- 72.2M
100  348M  100  348M    0     0  70.3M      0  0:00:04  0:00:04 --:--:-- 70.5M

install for i386

* 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
  converting help for package 'furrowSeg'
    finding HTML links ... done
    constructBox                            html  
REDIRECT:topic	 constructBox -> constructBox.html [ SUCCESS ]
    exampleFurrowMovie                      html  
REDIRECT:topic	 exampleFurrowMovie -> exampleFurrowMovie.html [ SUCCESS ]
    identifyFurrowPosition                  html  
REDIRECT:topic	 identifyFurrowPosition -> identifyFurrowPosition.html [ SUCCESS ]
    identifyTimeMinArea                     html  
REDIRECT:topic	 identifyTimeMinArea -> identifyTimeMinArea.html [ SUCCESS ]
    isOdd                                   html  
REDIRECT:topic	 isOdd -> isOdd.html [ SUCCESS ]
REDIRECT:topic	 makeOdd -> isOdd.html [ SUCCESS ]
    isolateBoxCells                         html  
REDIRECT:topic	 isolateBoxCells -> isolateBoxCells.html [ SUCCESS ]
    opto                                    html  
REDIRECT:topic	 opto -> opto.html [ SUCCESS ]
    plotFeatureEvolution                    html  
REDIRECT:topic	 plotFeatureEvolution -> plotFeatureEvolution.html [ SUCCESS ]
    px2area                                 html  
REDIRECT:topic	 px2area -> px2area.html [ SUCCESS ]
REDIRECT:topic	 area2px -> px2area.html [ SUCCESS ]
    px2microns                              html  
REDIRECT:topic	 px2microns -> px2microns.html [ SUCCESS ]
REDIRECT:topic	 microns2px -> px2microns.html [ SUCCESS ]
    sampleTable                             html  
REDIRECT:topic	 sampleTable -> sampleTable.html [ SUCCESS ]
    segmentFurrowAllStacks                  html  
REDIRECT:topic	 segmentFurrowAllStacks -> segmentFurrowAllStacks.html [ SUCCESS ]
** 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

install for x64

* installing *source* package 'furrowSeg' ...
** testing if installed package can be loaded
Warning: replacing previous import 'EBImage::abind' by 'abind::abind' when loading 'furrowSeg'
* MD5 sums
packaged installation of 'furrowSeg' as furrowSeg_1.19.0.zip
* DONE (furrowSeg)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'furrowSeg' successfully unpacked and MD5 sums checked

Tests output


Example timings

furrowSeg.Rcheck/examples_i386/furrowSeg-Ex.timings

nameusersystemelapsed
constructBox000
exampleFurrowMovie9.180.189.37
identifyFurrowPosition000
identifyTimeMinArea000
isOdd000
isolateBoxCells000
opto22.92 0.3323.25
plotFeatureEvolution000
px2area000
px2microns000
sampleTable0.000.020.01
segmentFurrowAllStacks000

furrowSeg.Rcheck/examples_x64/furrowSeg-Ex.timings

nameusersystemelapsed
constructBox000
exampleFurrowMovie7.280.177.46
identifyFurrowPosition000
identifyTimeMinArea000
isOdd000
isolateBoxCells000
opto18.02 0.3718.39
plotFeatureEvolution000
px2area000
px2microns000
sampleTable0.000.020.02
segmentFurrowAllStacks000