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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:flowClean.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings flowClean_1.44.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/flowClean.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘flowClean/DESCRIPTION’ ... OK
* this is package ‘flowClean’ version ‘1.44.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 code 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 loading without being on the library search path ... 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 Rd file 'clean.Rd':
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 Rd file 'clean.Rd':
  ‘announce’
Documented arguments not in \usage in Rd file 'clean.Rd':
  ‘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 ... WARNING
Found the following significant warnings:

  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.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 9.396  0.242   9.639
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/flowClean.Rcheck/00check.log’
for details.