##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowBeads.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowBeads_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/flowBeads.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowBeads/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowBeads’ version ‘1.38.0’
* 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 ‘flowBeads’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘flowCore’ ‘rrcov’
A package should be listed in only one of these fields.
* 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 ... WARNING
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rrcov’ ‘xtable’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘Biobase’ ‘methods’ ‘rrcov’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Missing or unexported object: ‘flowCore::norm2Filter’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
BeadFlowFrame: no visible binding for global variable ‘filename’
BeadFlowFrame: no visible global function definition for ‘read.csv2’
BeadFlowFrame: no visible global function definition for ‘new’
mefTransform: no visible global function definition for ‘new’
absoluteNormalise,GatedBeadFlowFrame-data.frame: no visible global
  function definition for ‘lm’
gateBeads,BeadFlowFrame: no visible global function definition for ‘as’
gateBeads,BeadFlowFrame : <anonymous>: no visible global function
  definition for ‘quantile’
gateBeads,BeadFlowFrame : <anonymous>: no visible global function
  definition for ‘kmeans’
gateBeads,BeadFlowFrame : <anonymous>: no visible global function
  definition for ‘median’
gateBeads,BeadFlowFrame: no visible binding for global variable ‘sd’
gateBeads,BeadFlowFrame: no visible global function definition for ‘lm’
plot,BeadFlowFrame-character: no visible global function definition for
  ‘par’
plot,BeadFlowFrame-character: no visible global function definition for
  ‘hist’
plot,BeadFlowFrame-character: no visible global function definition for
  ‘segments’
plot,BeadFlowFrame-character: no visible global function definition for
  ‘title’
plot,GatedBeadFlowFrame-character: no visible global function
  definition for ‘par’
plot,GatedBeadFlowFrame-character: no visible global function
  definition for ‘hist’
plot,GatedBeadFlowFrame-character: no visible global function
  definition for ‘abline’
plot,GatedBeadFlowFrame-character: no visible global function
  definition for ‘segments’
plot,GatedBeadFlowFrame-character: no visible global function
  definition for ‘title’
relativeNormalise,GatedBeadFlowFrame-GatedBeadFlowFrame: no visible
  global function definition for ‘lm’
Undefined global functions or variables:
  abline as filename hist kmeans lm median new par quantile read.csv2
  sd segments title
Consider adding
  importFrom("graphics", "abline", "hist", "par", "segments", "title")
  importFrom("methods", "as", "new")
  importFrom("stats", "kmeans", "lm", "median", "quantile", "sd")
  importFrom("utils", "read.csv2")
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 ... OK
* checking Rd \usage sections ... OK
* 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.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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: 2 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/flowBeads.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL flowBeads
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘flowBeads’ ...
** 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 (flowBeads)