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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SingleMoleculeFootprinting.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SingleMoleculeFootprinting_2.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/SingleMoleculeFootprinting.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SingleMoleculeFootprinting/DESCRIPTION’ ... OK
* this is package ‘SingleMoleculeFootprinting’ version ‘2.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘SingleMoleculeFootprinting’ 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 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
.detect.footprints: no visible binding for global variable ‘occupancy’
.detect.footprints: no visible binding for global variable
  ‘biological.state’
AggregateFootprints : <anonymous>: no visible binding for global
  variable ‘TF’
AggregateFootprints : <anonymous>: no visible binding for global
  variable ‘biological.state’
AnnotateFootprints: no visible binding for global variable
  ‘biological.state’
Create_MethylationCallingWindows: no visible binding for global
  variable ‘.’
Create_MethylationCallingWindows: no visible binding for global
  variable ‘idx’
DetectFootprints: no visible binding for global variable ‘partition.nr’
DetectFootprints: no visible binding for global variable
  ‘partition.coverage’
DetectFootprints: no visible binding for global variable ‘nr.cytosines’
DetectFootprints: no visible binding for global variable
  ‘biological.state’
FootprintCharter: no visible binding for global variable
  ‘partition.coverage’
FootprintCharter: no visible binding for global variable ‘partition.nr’
FootprintCharter: no visible binding for global variable ‘.’
GRanges_to_DF: no visible global function definition for ‘matches’
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’
MethSM.to.dense: no visible binding for global variable ‘.’
PlotAvgSMF: no visible binding for global variable ‘MethRate’
PlotFootprints: no visible binding for global variable ‘partition.nr’
PlotFootprints: no visible binding for global variable
  ‘biological.state’
PlotFootprints: no visible binding for global variable
  ‘partition.coverage’
PlotFootprints: no visible binding for global variable ‘TF’
PlotFootprints: no visible binding for global variable ‘coordinate’
PlotFootprints: no visible binding for global variable ‘bulk.SMF’
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’
Plot_FootprintCharter_SM: no visible binding for global variable
  ‘biological.state’
Plot_FootprintCharter_SM: no visible binding for global variable
  ‘partition.nr’
Plot_FootprintCharter_SM: no visible binding for global variable
  ‘partition.coverage’
Plot_FootprintCharter_SM: no visible binding for global variable
  ‘partition.coverage.cumsum’
Plot_FootprintCharter_SM: no visible binding for global variable ‘d’
Plot_FootprintCharter_SM: no visible binding for global variable
  ‘read.idx’
StateQuantificationPlot: no visible binding for global variable ‘State’
StateQuantificationPlot: no visible binding for global variable
  ‘Pattern’
StateQuantificationPlot: no visible binding for global variable ‘.’
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 TF
  biological.state bulk.SMF coordinate d idx matches nr.cytosines
  occupancy partition.coverage partition.coverage.cumsum partition.nr
  read.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 ... OK
* 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
PlotFootprints           10.309  0.133  10.606
GetSingleMolMethMat       6.659  1.800   8.497
Plot_FootprintCharter_SM  7.375  0.080   7.475
FootprintCharter          6.113  0.171   6.491
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/SingleMoleculeFootprinting.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SingleMoleculeFootprinting
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘SingleMoleculeFootprinting’ ...
** this is package ‘SingleMoleculeFootprinting’ version ‘2.2.0’
** using staged installation
** R
** 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 (SingleMoleculeFootprinting)

R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(SingleMoleculeFootprinting)
> 
> test_check("SingleMoleculeFootprinting")
Loading required package: BSgenome
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: BiocIO
Loading required package: rtracklayer
all necessary alignment files found
Detected experiment type: DE
all necessary alignment files found
see ?SingleMoleculeFootprintingData and browseVignettes('SingleMoleculeFootprintingData') for documentation
loading from cache
counting alignments...done
counting alignments...done
all necessary alignment files found
5334 reads found mapping to the - strand, collapsing to +
5334 reads found mapping to the - strand, collapsing to +
Detected experiment type: DE
Collecting summarized methylation for bins
Subsetting those reads that cover all bins
Summarizing reads into patterns
Splitting reads by pattern
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 6 ]
> 
> proc.time()
   user  system elapsed 
 50.492   3.901  55.096