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CHECK report for flowClean on merida1

This page was generated on 2021-05-06 12:34:58 -0400 (Thu, 06 May 2021).

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 615/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowClean 1.28.0  (landing page)
Kipper Fletez-Brant
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/flowClean
Branch: RELEASE_3_12
Last Commit: 49ca7e8
Last Changed Date: 2020-10-27 10:56:58 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: flowClean
Version: 1.28.0
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_1.28.0.tar.gz
StartedAt: 2021-05-06 01:48:13 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 01:49:41 -0400 (Thu, 06 May 2021)
EllapsedTime: 88.1 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_1.28.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/flowClean.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.28.0’
* 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 14.66  1.202  15.889
* 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-3.12-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
clean14.660 1.20215.889
synPerturbed0.4710.0140.489