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CHECK report for flowcatchR on malbec2

This page was generated on 2019-10-16 12:05:33 -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: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:flowcatchR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings flowcatchR_1.18.0.tar.gz
StartedAt: 2019-10-16 01:39:20 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 01:40:24 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 64.3 seconds
RetCode: 0
Status:  OK 
CheckDir: flowcatchR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:flowcatchR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings flowcatchR_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/flowcatchR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/flowcatchR.Rcheck/00check.log’
for details.



Installation output

flowcatchR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL flowcatchR
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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
Frames0.3180.0280.346
add.contours0.0020.0000.002
channel.Frames0.2430.0080.251
crop.Frames0.2630.0040.267
export.Frames0.0010.0000.001
export.particles0.0000.0010.001
inspect.Frames0.0000.0010.001
kinematics0.3630.0000.364
length.Frames0.1070.0080.114
link.particles0.1480.0000.148
matchTrajToParticles0.3020.0040.306
normalizeFrames1.4070.0721.478
particles0.0000.0010.002
penaltyFunctionGenerator0.0000.0010.001
plot.TrajectorySet0.2530.0050.258
plot2D.TrajectorySet0.4220.0000.422
preprocess.Frames0.7090.0000.709
read.Frames000
read.particles000
rotate.Frames0.2430.0080.251
select.Frames0.5930.0080.601
select.particles0.0210.0000.021
shinyFlow000
show-Frames-method0.0660.0040.069
show-KinematicsFeatures-method0.1510.0000.150
show-KinematicsFeaturesSet-method0.1820.0000.183
show-LinkedParticleSet-method0.1200.0000.121
show-ParticleSet-method0.0050.0000.005
show-TrajectorySet-method0.1580.0000.158
snap0.0010.0000.000
trajectories0.1640.0000.164