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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SingleMoleculeFootprinting.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings SingleMoleculeFootprinting_2.0.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/SingleMoleculeFootprinting.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SingleMoleculeFootprinting/DESCRIPTION' ... OK
* this is package 'SingleMoleculeFootprinting' version '2.0.0'
* package encoding: UTF-8
* 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 'SingleMoleculeFootprinting' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'Biostrings::setequal' by 'dplyr::setequal' when loading 'SingleMoleculeFootprinting'
  Warning: replacing previous import 'GenomicRanges::intersect' by 'dplyr::intersect' when loading 'SingleMoleculeFootprinting'
  Warning: replacing previous import 'GenomicRanges::union' by 'dplyr::union' when loading 'SingleMoleculeFootprinting'
  Warning: replacing previous import 'BiocGenerics::combine' by 'dplyr::combine' when loading 'SingleMoleculeFootprinting'
  Warning: replacing previous import 'Biostrings::collapse' by 'dplyr::collapse' when loading 'SingleMoleculeFootprinting'
  Warning: replacing previous import 'GenomicRanges::setdiff' by 'dplyr::setdiff' when loading 'SingleMoleculeFootprinting'
  Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'SingleMoleculeFootprinting'
  Warning: replacing previous import 'BiocGenerics::boxplot' by 'graphics::boxplot' when loading 'SingleMoleculeFootprinting'
  Warning: replacing previous import 'Matrix::image' by 'graphics::image' when loading 'SingleMoleculeFootprinting'
  Warning: replacing previous import 'dplyr::between' by 'plyranges::between' when loading 'SingleMoleculeFootprinting'
  Warning: replacing previous import 'dplyr::n_distinct' by 'plyranges::n_distinct' when loading 'SingleMoleculeFootprinting'
  Warning: replacing previous import 'dplyr::n' by 'plyranges::n' when loading 'SingleMoleculeFootprinting'
See 'F:/biocbuild/bbs-3.20-bioc/meat/SingleMoleculeFootprinting.Rcheck/00install.out' for details.
* 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 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
Create_MethylationCallingWindows: no visible binding for global
  variable 'idx'
GRanges_to_DF: no visible binding for global variable 'Sample'
GRanges_to_DF: no visible binding for global variable 'Score'
LowCoverageMethRate_RMSE: no visible binding for global variable
  'Sample'
PlotAvgSMF: no visible binding for global variable 'MethRate'
PlotSingleMoleculeStack : <anonymous>: no visible binding for global
  variable 'Coordinate'
PlotSingleMoleculeStack : <anonymous>: no visible binding for global
  variable 'Methylation'
PlotSingleMoleculeStack: no visible binding for global variable
  'Sample'
StateQuantificationPlot: no visible binding for global variable 'State'
StateQuantificationPlot: no visible binding for global variable
  'Pattern'
StateQuantificationPlot: no visible binding for global variable 'Bin'
StateQuantificationPlot: no visible binding for global variable
  'Methylation'
Undefined global functions or variables:
  Bin Coordinate MethRate Methylation Pattern Sample Score State idx
* 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 ... NOTE
S3 methods shown with full name in Rd file 'cbind.fill.Matrix.Rd':
  'cbind.fill.Matrix'

S3 methods shown with full name in Rd file 'rbind.fill.Matrix.Rd':
  'rbind.fill.Matrix'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
GetSingleMolMethMat 11.71   0.61   12.43
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/SingleMoleculeFootprinting.Rcheck/00check.log'
for details.