Package: flowcatchR

Version: 1.20.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowcatchR.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings flowcatchR_1.20.0.tar.gz

StartedAt: 2020-04-15 03:11:46 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:13:29 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 102.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: flowcatchR.Rcheck

Warnings: 1

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowcatchR.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings flowcatchR_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/flowcatchR.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.20.0'
* 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 ... WARNING
Documented arguments not in \usage in documentation object 'show,Frames-method':
  '...'

Documented arguments not in \usage in documentation object 'show,KinematicsFeatures-method':
  '...'

Documented arguments not in \usage in documentation object 'show,KinematicsFeaturesSet-method':
  '...'

Documented arguments not in \usage in documentation object 'show,LinkedParticleSet-method':
  '...'

Documented arguments not in \usage in documentation object 'show,ParticleSet-method':
  '...'

Documented arguments not in \usage in documentation object 'show,TrajectorySet-method':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/flowcatchR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/flowcatchR_1.20.0.tar.gz && rm -rf flowcatchR.buildbin-libdir && mkdir flowcatchR.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowcatchR.buildbin-libdir flowcatchR_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL flowcatchR_1.20.0.zip && rm flowcatchR_1.20.0.tar.gz flowcatchR_1.20.0.zip
###
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  % 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  61.7M      0 --:--:-- --:--:-- --:--:-- 63.5M

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_1.20.0.zip
* DONE (flowcatchR)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'flowcatchR' successfully unpacked and MD5 sums checked