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CHECK report for flowDensity on merida1

This page was generated on 2019-04-16 11:57:45 -0400 (Tue, 16 Apr 2019).

Package 533/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowDensity 1.16.1
Mehrnoush Malek
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/flowDensity
Branch: RELEASE_3_8
Last Commit: e2655a2
Last Changed Date: 2019-01-04 13:32:14 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: flowDensity
Version: 1.16.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowDensity.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowDensity_1.16.1.tar.gz
StartedAt: 2019-04-15 23:58:03 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:59:49 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 106.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: flowDensity.Rcheck
Warnings: 5

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowDensity.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowDensity_1.16.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/flowDensity.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowDensity/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowDensity’ version ‘1.16.1’
* 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 ‘flowDensity’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘flowCore::plot’ by ‘graphics::plot’ when loading ‘flowDensity’
See ‘/Users/biocbuild/bbs-3.8-bioc/meat/flowDensity.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    extdata   4.3Mb
* 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 ... OK
* 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 ... WARNING
Rd files with duplicated alias 'flowDensity':
  ‘flowDensity-methods.Rd’ ‘flowDensity.Rd’
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'flowDensity' and siglist
    'CellPopulation,ANY,logical,missing'
  generic 'flowDensity' and siglist 'GatingHierarchy,ANY,logical,ANY'
  generic 'flowDensity' and siglist 'flowFrame,ANY,logical,missing'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'flowDensity-methods':
  ‘\S4method{flowDensity}{CellPopulation,ANY,logical,missing}’
  ‘\S4method{flowDensity}{flowFrame,ANY,logical,missing}’
  ‘\S4method{flowDensity}{GatingHierarchy,ANY,logical,ANY}’

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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... WARNING
Vignette sources in 'inst/doc' missing from the 'vignettes' directory:
  ‘flowDensity.Rnw’
* 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: 5 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/flowDensity.Rcheck/00check.log’
for details.



Installation output

flowDensity.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL flowDensity
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘flowDensity’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘flowCore::plot’ by ‘graphics::plot’ when loading ‘flowDensity’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘flowDensityVignette.Rnw’ 
** testing if installed package can be loaded
Warning: replacing previous import ‘flowCore::plot’ by ‘graphics::plot’ when loading ‘flowDensity’
* DONE (flowDensity)

Tests output


Example timings

flowDensity.Rcheck/flowDensity-Ex.timings

nameusersystemelapsed
CellPopulation-class0.0020.0010.002
deGate0.1690.0220.191
flowDensity0.0670.0070.074
getPeaks0.0240.0040.028
getflowFrame0.0580.0090.066
nmRemove0.2350.0190.256
notSubFrame0.1380.0130.154
plotDens0.1250.0150.140