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CHECK report for flowcatchR on merida1

This page was generated on 2019-04-16 11:58:04 -0400 (Tue, 16 Apr 2019).

Package 526/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowcatchR 1.16.0
Federico Marini
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/flowcatchR
Branch: RELEASE_3_8
Last Commit: 4cdcf2d
Last Changed Date: 2018-10-30 11:41:55 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: flowcatchR
Version: 1.16.0
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_1.16.0.tar.gz
StartedAt: 2019-04-15 23:56:50 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:58:07 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 77.7 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_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/flowcatchR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.16.0’
* 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-3.8-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/3.5/Resources/library’
* installing *source* package ‘flowcatchR’ ...
** 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
* DONE (flowcatchR)

Tests output


Example timings

flowcatchR.Rcheck/flowcatchR-Ex.timings

nameusersystemelapsed
Frames0.6100.1530.766
add.contours0.0020.0010.003
channel.Frames0.3380.1090.449
crop.Frames0.3930.0720.467
export.Frames0.0020.0020.003
export.particles0.0010.0010.002
inspect.Frames0.0010.0010.002
kinematics0.4110.0350.448
length.Frames0.0790.0030.083
link.particles0.2030.0090.213
matchTrajToParticles0.4050.0130.420
normalizeFrames2.5821.9304.540
particles0.0020.0010.002
penaltyFunctionGenerator0.0000.0000.001
plot.TrajectorySet0.2740.0180.293
plot2D.TrajectorySet0.4200.0130.437
preprocess.Frames0.8580.3451.205
read.Frames0.0000.0000.001
read.particles000
rotate.Frames0.3370.0950.434
select.Frames1.8611.2293.102
select.particles0.0350.0020.037
shinyFlow000
show-Frames-method0.0940.0440.139
show-KinematicsFeatures-method0.2440.0150.261
show-KinematicsFeaturesSet-method0.2530.0040.259
show-LinkedParticleSet-method0.1920.0060.199
show-ParticleSet-method0.0090.0020.011
show-TrajectorySet-method0.2490.0130.261
snap000
trajectories0.2520.0010.255