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CHECK report for flowcatchR on celaya2

This page was generated on 2019-10-16 12:54:17 -0400 (Wed, 16 Oct 2019).

Package 558/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowcatchR 1.18.0
Federico Marini
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/flowcatchR
Branch: RELEASE_3_9
Last Commit: 3be93a4
Last Changed Date: 2019-05-02 11:53:50 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: flowcatchR
Version: 1.18.0
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_1.18.0.tar.gz
StartedAt: 2019-10-16 02:49:37 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:51:23 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 106.0 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_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/flowcatchR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.18.0’
* 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-3.9-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/3.6/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
Frames0.3440.0720.415
add.contours0.0020.0020.003
channel.Frames0.2560.0030.260
crop.Frames0.2580.0320.297
export.Frames0.0020.0020.004
export.particles0.0020.0030.004
inspect.Frames0.0020.0020.004
kinematics0.5850.0960.680
length.Frames0.0840.0020.086
link.particles0.2200.0060.225
matchTrajToParticles0.4600.0310.491
normalizeFrames1.8710.8362.751
particles0.0020.0010.003
penaltyFunctionGenerator0.0000.0010.001
plot.TrajectorySet0.4230.0650.502
plot2D.TrajectorySet0.6060.1250.758
preprocess.Frames0.7880.2491.037
read.Frames0.0000.0010.001
read.particles0.0010.0000.001
rotate.Frames0.2240.1190.343
select.Frames0.7570.5051.268
select.particles0.0380.0050.043
shinyFlow000
show-Frames-method0.1040.0520.156
show-KinematicsFeatures-method0.4310.0520.482
show-KinematicsFeaturesSet-method0.4310.0420.474
show-LinkedParticleSet-method0.2750.0060.281
show-ParticleSet-method0.0100.0030.012
show-TrajectorySet-method0.4290.0320.461
snap0.0010.0010.001
trajectories0.4590.0410.538