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CHECK report for flowcatchR on merida1

This page was generated on 2021-05-06 12:34:58 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the flowcatchR package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 612/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowcatchR 1.24.0  (landing page)
Federico Marini
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/flowcatchR
Branch: RELEASE_3_12
Last Commit: 2749cf4
Last Changed Date: 2020-10-27 10:59:52 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: flowcatchR
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowcatchR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowcatchR_1.24.0.tar.gz
StartedAt: 2021-05-06 01:47:30 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 01:49:02 -0400 (Thu, 06 May 2021)
EllapsedTime: 91.9 seconds
RetCode: 0
Status:   OK  
CheckDir: flowcatchR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowcatchR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowcatchR_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/flowcatchR.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowcatchR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowcatchR’ version ‘1.24.0’
* package encoding: UTF-8
* 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 ‘flowcatchR’ can be installed ... OK
* checking installed package size ... OK
* 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 ... NOTE
'library' or 'require' call to ‘EBImage’ which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/flowcatchR.Rcheck/00check.log’
for details.



Installation output

flowcatchR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL flowcatchR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘flowcatchR’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (flowcatchR)

Tests output


Example timings

flowcatchR.Rcheck/flowcatchR-Ex.timings

nameusersystemelapsed
Frames0.2930.0320.328
add.contours0.0010.0020.002
channel.Frames0.2540.0100.264
crop.Frames0.2190.0070.249
export.Frames0.0010.0010.002
export.particles0.0010.0020.003
inspect.Frames0.0010.0010.002
kinematics0.3260.0130.376
length.Frames0.0970.0030.099
link.particles0.1640.0060.172
matchTrajToParticles0.2550.0080.264
normalizeFrames1.4330.1271.561
particles0.0010.0010.002
penaltyFunctionGenerator000
plot.TrajectorySet0.2730.0140.288
plot2D.TrajectorySet0.4390.0140.453
preprocess.Frames0.6580.0790.739
read.Frames0.0000.0000.001
read.particles000
rotate.Frames0.1870.0340.221
select.Frames0.5690.0710.641
select.particles0.0380.0020.039
shinyFlow000
show-Frames-method0.2220.0330.255
show-KinematicsFeatures-method0.3030.0110.314
show-KinematicsFeaturesSet-method0.3420.0120.356
show-LinkedParticleSet-method0.2240.0030.228
show-ParticleSet-method0.0090.0020.011
show-TrajectorySet-method0.2470.0030.251
snap000
trajectories0.2820.0040.287