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CHECK report for flowClean on machv2

This page was generated on 2020-10-17 11:58:29 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE flowClean PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 608/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowClean 1.26.0
Kipper Fletez-Brant
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/flowClean
Branch: RELEASE_3_11
Last Commit: 9d58612
Last Changed Date: 2020-04-27 14:40:53 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: flowClean
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowClean.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowClean_1.26.0.tar.gz
StartedAt: 2020-10-17 01:11:32 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 01:12:57 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 85.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: flowClean.Rcheck
Warnings: 3

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowClean.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowClean_1.26.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/flowClean.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowClean/DESCRIPTION’ ... OK
* this is package ‘flowClean’ version ‘1.26.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘flowClean’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
clean: no visible global function definition for ‘runif’
clean: no visible global function definition for ‘png’
clean: no visible global function definition for ‘dev.off’
diagnosticPlot: no visible global function definition for ‘points’
diagnosticPlot: no visible global function definition for ‘abline’
makeFCS: no visible global function definition for ‘new’
make_pops : <anonymous>: no visible global function definition for
  ‘quantile’
make_pops : <anonymous>: no visible global function definition for
  ‘median’
Undefined global functions or variables:
  abline dev.off median new png points quantile runif
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "abline", "points")
  importFrom("methods", "new")
  importFrom("stats", "median", "quantile", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'clean':
clean
  Code: function(fF, vectMarkers, filePrefixWithDir, ext, binSize =
                 0.01, nCellCutoff = 500, announce = TRUE, cutoff =
                 "median", diagnostic = FALSE, fcMax = 1.3,
                 returnVector = FALSE, nstable = 5)
  Docs: function(fF, vectMarkers, filePrefixWithDir, ext, binSize =
                 0.01, nCellCutoff = 500, announce = TRUE, cutoff =
                 "median", diagnostic = FALSE, fcMax = 1.3)
  Argument names in code not in docs:
    returnVector nstable

* checking Rd \usage sections ... WARNING
Duplicated \argument entries in documentation object 'clean':
  ‘announce’
Documented arguments not in \usage in documentation object 'clean':
  ‘returnVector’ ‘nstable’

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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning: '.local' is deprecated.
  Warning: '.local' is deprecated.
  Warning: '.local' is deprecated.
  Warning: '.local' is deprecated.
  Warning: '.local' is deprecated.
  Warning: 'description<-' is deprecated.
  Warning: '.local' is deprecated.
  Warning: '.local' is deprecated.
  Warning: 'description<-' is deprecated.
  Warning: '.local' is deprecated.
  Warning: '.local' is deprecated.
  Warning: 'description<-' is deprecated.
  Warning: '.local' is deprecated.
  Warning: 'description<-' is deprecated.
  Warning: '.local' is deprecated.
  Warning: 'description<-' is deprecated.
  Warning: '.local' is deprecated.
  Warning: 'description<-' is deprecated.
  Warning: '.local' is deprecated.
  Warning: 'description<-' is deprecated.
  Warning: '.local' is deprecated.
  Warning: 'description<-' is deprecated.
  Warning: '.local' is deprecated.
  Warning: 'description<-' is deprecated.
  Warning: '.local' is deprecated.
  Warning: 'description<-' is deprecated.
  Warning: '.local' is deprecated.
  Warning: '.local' is deprecated.
  Warning: 'description<-' is deprecated.
  Warning: '.local' is deprecated.
  Warning: 'description<-' is deprecated.
  Warning: '.local' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
clean 18.771  1.443  20.248
* 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: 3 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/flowClean.Rcheck/00check.log’
for details.



Installation output

flowClean.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL flowClean
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘flowClean’ ...
** using staged installation
** R
** data
** 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 (flowClean)

Tests output


Example timings

flowClean.Rcheck/flowClean-Ex.timings

nameusersystemelapsed
clean18.771 1.44320.248
synPerturbed0.4910.0130.504