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### Running command:
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###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DuplexDiscovereR.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings DuplexDiscovereR_1.3.1.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/DuplexDiscovereR.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'DuplexDiscovereR/DESCRIPTION' ... OK
* this is package 'DuplexDiscovereR' version '1.3.1'
* 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 'DuplexDiscovereR' 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
.filterAlignmentLength: no visible binding for global variable
  'aln_lenA'
.filterAlignmentLength: no visible binding for global variable
  'aln_lenB'
.filterAlignmentLength: no visible binding for global variable
  'len_not_ok'
collapseSimilarChimeras: no visible binding for global variable
  'n_seqnames'
preproc_chim_junction_out_pe: no visible binding for global variable
  'lA'
preproc_chim_junction_out_pe: no visible binding for global variable
  'lB'
runDuplexDiscoPreproc: no visible binding for global variable
  'aln_lenA'
runDuplexDiscoPreproc: no visible binding for global variable
  'aln_lenB'
runDuplexDiscoverer: no visible binding for global variable
  'n_seqnames'
trimAroundJunction: no visible binding for global variable 'jA'
trimAroundJunction: no visible binding for global variable 'jB'
trimAroundJunction: no visible binding for global variable 't1'
trimAroundJunction: no visible binding for global variable 't2'
trimAroundJunction: no visible binding for global variable 't3'
trimAroundJunction: no visible binding for global variable 't4'
trimAroundJunction: no visible binding for global variable 'value'
trimAroundJunction: no visible binding for global variable 'aln_lenA'
trimAroundJunction: no visible binding for global variable 'aln_lenB'
Undefined global functions or variables:
  aln_lenA aln_lenB jA jB lA lB len_not_ok n_seqnames t1 t2 t3 t4 value
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'computeGISelfOverlaps.Rd':
  '[InteractionSet:overlaps]{InteractionSet::findOverlaps()}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'collapseSimilarChimeras.Rd'
  'min_nodes'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... NOTE
Argument items with no description in Rd file 'trimAroundJunction.Rd':
  'extract_len'
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
runDuplexDiscoverer         10.47   0.08   10.55
DuplexDiscovererResults      8.81   0.20    9.02
dd_get_chimeric_reads_stats  7.86   0.05    7.91
dd_get_chimeric_reads        7.80   0.05    7.86
dd_get_reads_classes         7.60   0.05    7.69
dd_get_duplex_groups         7.50   0.06    7.56
dd_get_run_stats             7.46   0.04    7.50
compareMultipleInteractions  7.37   0.03    7.41
* 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, 3 NOTEs
See
  'F:/biocbuild/bbs-3.22-bioc/meat/DuplexDiscovereR.Rcheck/00check.log'
for details.