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CHECK report for flowcatchR on tokay2

This page was generated on 2020-10-17 11:56:34 -0400 (Sat, 17 Oct 2020).

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 605/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowcatchR 1.22.0
Federico Marini
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/flowcatchR
Branch: RELEASE_3_11
Last Commit: ffeb4d9
Last Changed Date: 2020-04-27 14:44:16 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: flowcatchR
Version: 1.22.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowcatchR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings flowcatchR_1.22.0.tar.gz
StartedAt: 2020-10-17 04:04:35 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:07:04 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 148.3 seconds
RetCode: 0
Status:  OK  
CheckDir: flowcatchR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowcatchR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings flowcatchR_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/flowcatchR.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowcatchR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowcatchR' version '1.22.0'
* 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 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
* 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 ... 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/flowcatchR.Rcheck/00check.log'
for details.



Installation output

flowcatchR.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/flowcatchR_1.22.0.tar.gz && rm -rf flowcatchR.buildbin-libdir && mkdir flowcatchR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowcatchR.buildbin-libdir flowcatchR_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL flowcatchR_1.22.0.zip && rm flowcatchR_1.22.0.tar.gz flowcatchR_1.22.0.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
100  9.9M  100  9.9M    0     0  59.8M      0 --:--:-- --:--:-- --:--:-- 61.9M

install for i386

* 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
  converting help for package 'flowcatchR'
    finding HTML links ... done
    Frames-class                            html  
    Frames                                  html  
    KinematicsFeatures-class                html  
    KinematicsFeaturesSet-class             html  
    LinkedParticleSet-class                 html  
    MesenteriumSubset                       html  
    ParticleSet-class                       html  
    TrajectorySet-class                     html  
    add.contours                            html  
    addParticles                            html  
    axesInfo                                html  
    candidate.platelets                     html  
    channel.Frames                          html  
    computeMSD                              html  
    crop.Frames                             html  
    finding level-2 HTML links ... done

    export.Frames                           html  
    export.particles                        html  
    extractKinematics.traj                  html  
    flowcatchR-pkg                          html  
    initialize.LinkedParticleSet            html  
    inspect.Frames                          html  
    kinematics                              html  
    length.Frames                           html  
    link.particles                          html  
    matchTrajToParticles                    html  
    normalizeFrames                         html  
    particles                               html  
    penaltyFunctionGenerator                html  
    plot.TrajectorySet                      html  
    plot2D.TrajectorySet                    html  
    preprocess.Frames                       html  
    read.Frames                             html  
    read.particles                          html  
    repmat                                  html  
    rotate.Frames                           html  
    select.Frames                           html  
    select.particles                        html  
    shinyFlow                               html  
    show-Frames-method                      html  
    show-KinematicsFeatures-method          html  
    show-KinematicsFeaturesSet-method       html  
    show-LinkedParticleSet-method           html  
    show-ParticleSet-method                 html  
    show-TrajectorySet-method               html  
    snap                                    html  
    toCartesianCoords                       html  
    toPolarCoords                           html  
    trajectories                            html  
** 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

install for x64

* installing *source* package 'flowcatchR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowcatchR' as flowcatchR_1.22.0.zip
* DONE (flowcatchR)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'flowcatchR' successfully unpacked and MD5 sums checked

Tests output


Example timings

flowcatchR.Rcheck/examples_i386/flowcatchR-Ex.timings

nameusersystemelapsed
Frames0.090.060.16
add.contours000
channel.Frames0.220.050.26
crop.Frames0.190.040.24
export.Frames000
export.particles0.020.000.01
inspect.Frames000
kinematics0.280.000.28
length.Frames0.080.030.11
link.particles0.120.000.13
matchTrajToParticles0.170.000.17
normalizeFrames1.130.291.41
particles000
penaltyFunctionGenerator000
plot.TrajectorySet0.170.000.17
plot2D.TrajectorySet0.290.030.32
preprocess.Frames0.640.090.73
read.Frames000
read.particles000
rotate.Frames0.180.030.22
select.Frames0.520.190.70
select.particles0.030.000.03
shinyFlow000
show-Frames-method0.080.030.11
show-KinematicsFeatures-method0.170.000.17
show-KinematicsFeaturesSet-method0.190.000.19
show-LinkedParticleSet-method0.140.010.15
show-ParticleSet-method0.010.000.02
show-TrajectorySet-method0.180.000.17
snap000
trajectories0.170.000.17

flowcatchR.Rcheck/examples_x64/flowcatchR-Ex.timings

nameusersystemelapsed
Frames0.230.060.30
add.contours0.000.010.01
channel.Frames0.300.040.33
crop.Frames0.250.040.29
export.Frames0.010.000.02
export.particles000
inspect.Frames000
kinematics0.350.000.34
length.Frames0.070.030.11
link.particles0.110.040.14
matchTrajToParticles0.240.000.24
normalizeFrames1.470.421.89
particles0.000.010.01
penaltyFunctionGenerator000
plot.TrajectorySet0.180.000.19
plot2D.TrajectorySet0.300.020.31
preprocess.Frames0.620.120.75
read.Frames000
read.particles000
rotate.Frames0.170.080.25
select.Frames0.550.270.81
select.particles0.020.010.03
shinyFlow000
show-Frames-method0.060.050.11
show-KinematicsFeatures-method0.170.000.18
show-KinematicsFeaturesSet-method0.310.020.32
show-LinkedParticleSet-method0.190.000.19
show-ParticleSet-method0.020.000.02
show-TrajectorySet-method0.20.00.2
snap000
trajectories0.210.000.20