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CHECK report for flowClean on tokay2

This page was generated on 2020-10-17 11:56:34 -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: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowClean.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings flowClean_1.26.0.tar.gz
StartedAt: 2020-10-17 04:05:26 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:07:28 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 121.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: flowClean.Rcheck
Warnings: 4

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowClean.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings flowClean_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/flowClean.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... 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 10.44   0.58   11.12
** running examples for arch 'x64' ... 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 14.37   0.54   16.82
* 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: 4 WARNINGs, 1 NOTE
See
  'C:/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:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/flowClean_1.26.0.tar.gz && rm -rf flowClean.buildbin-libdir && mkdir flowClean.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowClean.buildbin-libdir flowClean_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL flowClean_1.26.0.zip && rm flowClean_1.26.0.tar.gz flowClean_1.26.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 3823k  100 3823k    0     0  36.4M      0 --:--:-- --:--:-- --:--:-- 39.3M

install for i386

* installing *source* package 'flowClean' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'flowClean'
    finding HTML links ... done
    clean                                   html  
    synPerturbed                            html  
** 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

install for x64

* installing *source* package 'flowClean' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowClean' as flowClean_1.26.0.zip
* DONE (flowClean)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'flowClean' successfully unpacked and MD5 sums checked

Tests output


Example timings

flowClean.Rcheck/examples_i386/flowClean-Ex.timings

nameusersystemelapsed
clean10.44 0.5811.12
synPerturbed0.410.010.42

flowClean.Rcheck/examples_x64/flowClean-Ex.timings

nameusersystemelapsed
clean14.37 0.5416.82
synPerturbed0.420.020.43