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CHECK report for flowcatchR on merida2

This page was generated on 2018-10-17 08:53:45 -0400 (Wed, 17 Oct 2018).

Package 497/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowcatchR 1.14.0
Federico Marini
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/flowcatchR
Branch: RELEASE_3_7
Last Commit: 2df8ede
Last Changed Date: 2018-04-30 10:35:34 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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### Running 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
###
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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.



Installation output

flowcatchR.Rcheck/00install.out

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###
### Running command:
###
###   /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)

Tests output


Example timings

flowcatchR.Rcheck/flowcatchR-Ex.timings

nameusersystemelapsed
Frames0.4250.0980.525
add.contours0.0020.0010.003
channel.Frames0.3950.0910.487
crop.Frames0.3100.0700.381
export.Frames0.0030.0010.004
export.particles0.0020.0010.003
inspect.Frames0.0020.0010.003
kinematics0.3620.0310.397
length.Frames0.0710.0040.076
link.particles0.1540.0030.157
matchTrajToParticles0.2990.0170.316
normalizeFrames2.5161.5604.101
particles0.0030.0020.004
penaltyFunctionGenerator0.0010.0000.001
plot.TrajectorySet0.2420.0220.264
plot2D.TrajectorySet0.3400.0190.359
preprocess.Frames0.7120.2550.974
read.Frames0.0010.0000.001
read.particles0.0010.0010.001
rotate.Frames0.2890.0990.388
select.Frames1.3851.0552.444
select.particles0.0260.0020.027
shinyFlow0.0020.0000.002
show-Frames-method0.170.070.24
show-KinematicsFeatures-method0.2560.0200.278
show-KinematicsFeaturesSet-method0.2640.0070.274
show-LinkedParticleSet-method0.2040.0020.207
show-ParticleSet-method0.0090.0010.010
show-TrajectorySet-method0.2420.0150.258
snap0.0020.0000.003
trajectories0.2090.0010.212