Package: flowcatchR

Version: 1.20.0

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_1.20.0.tar.gz

StartedAt: 2020-04-15 02:20:17 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 02:21:33 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 76.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: flowcatchR.Rcheck

Warnings: 1

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### Running command:
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###   /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_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/flowcatchR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.20.0’
* 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 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 ... 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 ... 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
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/flowcatchR.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL flowcatchR
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* 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)

name	user	system	elapsed
Frames	0.281	0.035	0.319
add.contours	0.002	0.001	0.002
channel.Frames	0.189	0.002	0.191
crop.Frames	0.195	0.010	0.206
export.Frames	0.001	0.001	0.001
export.particles	0.001	0.001	0.002
inspect.Frames	0.001	0.001	0.002
kinematics	0.366	0.035	0.402
length.Frames	0.052	0.001	0.054
link.particles	0.161	0.005	0.166
matchTrajToParticles	0.302	0.021	0.323
normalizeFrames	1.412	0.353	1.769
particles	0.001	0.001	0.003
penaltyFunctionGenerator	0.000	0.000	0.001
plot.TrajectorySet	0.277	0.016	0.296
plot2D.TrajectorySet	0.370	0.038	0.409
preprocess.Frames	0.700	0.141	0.846
read.Frames	0	0	0
read.particles	0	0	0
rotate.Frames	0.187	0.060	0.251
select.Frames	0.603	0.281	0.887
select.particles	0.039	0.002	0.041
shinyFlow	0.000	0.000	0.001
show-Frames-method	0.093	0.032	0.126
show-KinematicsFeatures-method	0.286	0.015	0.301
show-KinematicsFeaturesSet-method	0.455	0.040	0.497
show-LinkedParticleSet-method	0.189	0.004	0.194
show-ParticleSet-method	0.008	0.001	0.010
show-TrajectorySet-method	0.255	0.003	0.259
snap	0.001	0.000	0.001
trajectories	0.303	0.003	0.309