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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowDensity.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowDensity_1.41.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/flowDensity.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowDensity/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowDensity’ version ‘1.41.0’
* 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 ‘flowDensity’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 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 ... OK
* checking Rd files ... WARNING
checkRd: (7) deGate.Rd:126: Invalid email address: <mmalekes@bccrc.ca>
checkRd: (7) getPeaks.Rd:55: Invalid email address: <mmalekes@bccrc.ca>
checkRd: (7) getflowFrame.Rd:23: Invalid email address: <jtaghiyar@bccrc.ca>
checkRd: (7) nmRemove.Rd:37: Invalid email address: <jtaghiyar@bccrc.ca>
checkRd: (7) nmRemove.Rd:38: Invalid email address: <mmalekes@bccrc.ca>
checkRd: (7) notSubFrame.Rd:41: Invalid email address: <mmalekes@bccrc.ca>
checkRd: (7) plotDens.Rd:89: Invalid email address: <mmalekes@bccrc.ca>
checkRd: (7) plotDens.Rd:90: Invalid email address: <jtaghiyar@bccrc.ca>
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in Rd file 'deGate.Rd':
  ‘flowDensity’

Missing link(s) in Rd file 'getPeaks.Rd':
  ‘flowDensity’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  deGate.Rd: flowDensity
  getPeaks.Rd: flowDensity
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘flowDensity’
Undocumented S4 methods:
  generic 'flowDensity' and siglist 'CellPopulation,ANY,logical'
  generic 'flowDensity' and siglist 'flowFrame,ANY,logical'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/flowDensity.Rmd’
(Is a VignetteBuilder field missing?)
* checking examples ... OK
* checking package vignettes ... NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/flowDensity.Rcheck/00check.log’
for details.