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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SingleMoleculeFootprinting.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings SingleMoleculeFootprinting_2.1.0.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/SingleMoleculeFootprinting.Rcheck'
* using R Under development (unstable) (2025-01-21 r87610 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* 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 '2.1.0'
* 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 'GenomicRanges::subtract' by 'magrittr::subtract' 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'
  Warning: replacing previous import 'magrittr::extract' by 'tidyr::extract' when loading 'SingleMoleculeFootprinting'
See 'E:/biocbuild/bbs-3.21-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
.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 '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'
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'
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'
Plot_FootprintCharter_SM: no visible global function definition for
  'unnest'
Plot_FootprintCharter_SM: no visible binding for global variable
  'x.axis.breaks'
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 TF
  biological.state bulk.SMF coordinate d idx nr.cytosines occupancy
  partition.coverage partition.coverage.cumsum partition.nr read.idx
  unnest x.axis.breaks
* 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 ... ERROR
Running examples in 'SingleMoleculeFootprinting-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PlotFootprints
> ### Title: Plot bulk SMF separately for each partition alognside footprint
> ###   detection results.
> ### Aliases: PlotFootprints
> 
> ### ** Examples
> 
> 
> Methylation = qs::qread(system.file("extdata", "Methylation_4.qs", package="SingleMoleculeFootprinting"))
> MethSM = Methylation[[2]]
> RegionOfInterest = GenomicRanges::GRanges("chr6", IRanges::IRanges(88106000, 88106500))
> RegionOfInterest = IRanges::resize(RegionOfInterest, 80, "center")
> 
> FootprintCharter(
+   MethSM = MethSM,
+   RegionOfInterest = RegionOfInterest,
+   coverage = 30,
+   k = 16,
+   n = 5,
+   TF.length = c(5,75),
+   nucleosome.length = c(120,1000),
+   cytosine.coverage.thr = 5,
+   verbose = TRUE
+   ) -> FC_results
1. Pooling molecules from all samples
2. Computing sliding windows
Discarding 1973/2233 molecules that do not entirely cover the RegionOfInterest
Discarding 41/59 cytosines that are NA in more than 0% of the reads
Discarding 0/260 molecules that have NAs in more than 0% of the remaining cytosines
3. computing distance matrix
4. Partitioning
partitions too slim detected...retrying with k=15
partitions too slim detected...retrying with k=14
partitions too slim detected...retrying with k=13
partitions too slim detected...retrying with k=12
partitions too slim detected...retrying with k=11
partitions too slim detected...retrying with k=10
partitions too slim detected...retrying with k=9
partitions too slim detected...retrying with k=8
5. Footprints detection
6. Footprints annotation (skipping)
7. Footprints aggregation
8. Results wrangling
>   
> PlotFootprints(
+   MethSM = MethSM, 
+   partitioned.molecules = FC_results$partitioned.molecules, 
+   footprints.df = FC_results$footprints.df, 
+   TFBSs = TFBSs
+   )
Error: object 'TFBSs' not found
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
GetSingleMolMethMat 13.19   0.54    13.8
* 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 ERROR, 1 WARNING, 2 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/SingleMoleculeFootprinting.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL SingleMoleculeFootprinting
###
##############################################################################
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'SingleMoleculeFootprinting' ...
** this is package 'SingleMoleculeFootprinting' version '2.1.0'
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
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 'GenomicRanges::subtract' by 'magrittr::subtract' 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'
Warning: replacing previous import 'magrittr::extract' by 'tidyr::extract' when loading 'SingleMoleculeFootprinting'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
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 'GenomicRanges::subtract' by 'magrittr::subtract' 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'
Warning: replacing previous import 'magrittr::extract' by 'tidyr::extract' when loading 'SingleMoleculeFootprinting'
** testing if installed package can be loaded from final location
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 'GenomicRanges::subtract' by 'magrittr::subtract' 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'
Warning: replacing previous import 'magrittr::extract' by 'tidyr::extract' when loading 'SingleMoleculeFootprinting'
** testing if installed package keeps a record of temporary installation path
* DONE (SingleMoleculeFootprinting)

R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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)
There were 14 warnings (use warnings() to see them)
> 
> 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

Attaching package: 'IRanges'

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

    windows

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

Attaching package: 'rtracklayer'

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

    FileForFormat

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 
  47.85    3.71   51.96