Package: flowcatchR

Version: 1.20.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:flowcatchR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings flowcatchR_1.20.0.tar.gz

StartedAt: 2020-04-15 02:34:43 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 02:35:59 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 76.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: flowcatchR.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:flowcatchR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings flowcatchR_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/flowcatchR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.20.0’
* 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/flowcatchR.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL flowcatchR
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* installing to library ‘/home/biocbuild/bbs-3.10-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)

name	user	system	elapsed
Frames	0.188	0.036	0.224
add.contours	0.000	0.000	0.001
channel.Frames	0.256	0.032	0.291
crop.Frames	0.288	0.000	0.286
export.Frames	0.000	0.000	0.001
export.particles	0.004	0.000	0.001
inspect.Frames	0.000	0.000	0.001
kinematics	0.392	0.020	0.422
length.Frames	0.260	0.000	0.263
link.particles	0.176	0.000	0.174
matchTrajToParticles	0.288	0.000	0.291
normalizeFrames	1.532	0.096	1.631
particles	0.000	0.000	0.001
penaltyFunctionGenerator	0	0	0
plot.TrajectorySet	0.280	0.000	0.276
plot2D.TrajectorySet	0.408	0.004	0.414
preprocess.Frames	0.568	0.000	0.666
read.Frames	0	0	0
read.particles	0	0	0
rotate.Frames	0.176	0.016	0.192
select.Frames	0.536	0.012	0.548
select.particles	0.020	0.000	0.019
shinyFlow	0	0	0
show-Frames-method	0.184	0.000	0.184
show-KinematicsFeatures-method	0.192	0.000	0.192
show-KinematicsFeaturesSet-method	0.228	0.000	0.226
show-LinkedParticleSet-method	0.136	0.000	0.137
show-ParticleSet-method	0.004	0.000	0.006
show-TrajectorySet-method	0.164	0.000	0.167
snap	0	0	0
trajectories	0.188	0.000	0.189