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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SingleMoleculeFootprinting.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SingleMoleculeFootprinting_2.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SingleMoleculeFootprinting.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘SingleMoleculeFootprinting/DESCRIPTION’ ... OK
* this is package ‘SingleMoleculeFootprinting’ version ‘2.4.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 26 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 ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘qs’
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 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘qs’
  All declared Imports should be used.
* 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
* 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 re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘FootprintCharter.rmd’ using rmarkdown
--- finished re-building ‘FootprintCharter.rmd’

--- re-building ‘methylation_calling_and_QCs.rmd’ using rmarkdown

Quitting from methylation_calling_and_QCs.rmd:84-107 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! SSL connect error [bioconductor.org]:
gnutls_handshake() failed: The TLS connection was non-properly terminated.
  Consider rerunning with 'localHub=TRUE'
---
Backtrace:
    ▆
 1. └─SingleMoleculeFootprintingData::NRF1pair.bam()
 2.   └─ExperimentHub:::.get_ExperimentHub()
 3.     └─ExperimentHub::ExperimentHub()
 4.       └─AnnotationHub::.Hub(...)
 5.         └─base::tryCatch(...)
 6.           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 7.             └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8.               └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'methylation_calling_and_QCs.rmd' failed with diagnostics:
failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! SSL connect error [bioconductor.org]:
gnutls_handshake() failed: The TLS connection was non-properly terminated.
  Consider rerunning with 'localHub=TRUE'
--- failed re-building ‘methylation_calling_and_QCs.rmd’

--- re-building ‘single_molecule_sorting_by_TF.rmd’ using rmarkdown
--- finished re-building ‘single_molecule_sorting_by_TF.rmd’

SUMMARY: processing the following file failed:
  ‘methylation_calling_and_QCs.rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/SingleMoleculeFootprinting.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL SingleMoleculeFootprinting
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘SingleMoleculeFootprinting’ ...
** this is package ‘SingleMoleculeFootprinting’ version ‘2.4.0’
** 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 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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: Seqinfo
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 
 25.238   1.612  27.154