Package: flowcatchR

Version: 1.14.0

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_1.14.0.tar.gz

StartedAt: 2018-10-16 21:22:32 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 21:23:38 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 66.6 seconds

RetCode: 0

Status:  OK

CheckDir: flowcatchR.Rcheck

Warnings: 0

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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_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/flowcatchR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.14.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-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/3.5/Resources/library’
* installing *source* package ‘flowcatchR’ ...
** 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
* DONE (flowcatchR)

name	user	system	elapsed
Frames	0.425	0.098	0.525
add.contours	0.002	0.001	0.003
channel.Frames	0.395	0.091	0.487
crop.Frames	0.310	0.070	0.381
export.Frames	0.003	0.001	0.004
export.particles	0.002	0.001	0.003
inspect.Frames	0.002	0.001	0.003
kinematics	0.362	0.031	0.397
length.Frames	0.071	0.004	0.076
link.particles	0.154	0.003	0.157
matchTrajToParticles	0.299	0.017	0.316
normalizeFrames	2.516	1.560	4.101
particles	0.003	0.002	0.004
penaltyFunctionGenerator	0.001	0.000	0.001
plot.TrajectorySet	0.242	0.022	0.264
plot2D.TrajectorySet	0.340	0.019	0.359
preprocess.Frames	0.712	0.255	0.974
read.Frames	0.001	0.000	0.001
read.particles	0.001	0.001	0.001
rotate.Frames	0.289	0.099	0.388
select.Frames	1.385	1.055	2.444
select.particles	0.026	0.002	0.027
shinyFlow	0.002	0.000	0.002
show-Frames-method	0.17	0.07	0.24
show-KinematicsFeatures-method	0.256	0.020	0.278
show-KinematicsFeaturesSet-method	0.264	0.007	0.274
show-LinkedParticleSet-method	0.204	0.002	0.207
show-ParticleSet-method	0.009	0.001	0.010
show-TrajectorySet-method	0.242	0.015	0.258
snap	0.002	0.000	0.003
trajectories	0.209	0.001	0.212