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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:katdetectr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings katdetectr_1.11.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/katdetectr.Rcheck’
* using R version 4.5.0 Patched (2025-04-21 r88169)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘katdetectr/DESCRIPTION’ ... OK
* this is package ‘katdetectr’ version ‘1.11.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 23 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 ‘katdetectr’ 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
.addEmptySegments: no visible binding for global variable ‘seqnames’
.annotateKataegisSegments: no visible binding for global variable
  ‘fociID’
.annotateKataegisSegments: no visible binding for global variable
  ‘seqnames’
.annotateKataegisSegments: no visible binding for global variable
  ‘firstVariantID’
.annotateKataegisSegments: no visible binding for global variable
  ‘firstVariantOfSeqname’
.annotateKataegisSegments: no visible binding for global variable
  ‘lastVariantID’
.coerceMAFtoVRanges: no visible binding for global variable ‘start’
.coerceMAFtoVRanges: no visible binding for global variable ‘end’
.convertVariantsToGGplotFormat: no visible binding for global variable
  ‘IMD’
.convertVariantsToGGplotFormat: no visible binding for global variable
  ‘variantType’
.determineInitialProbabilities: no visible binding for global variable
  ‘seqnames’
.determineKataegisSegments: no visible binding for global variable
  ‘meanIMD’
.determineKataegisSegments: no visible binding for global variable
  ‘IMDcutoff’
.determineKataegisSegments: no visible binding for global variable
  ‘seqnames’
.generateBackgroundVariants: no visible binding for global variable
  ‘seqnames’
.generateBackgroundVariants: no visible binding for global variable
  ‘mutType’
.generateBackgroundVariants: no visible binding for global variable
  ‘start’
.generateBackgroundVariants: no visible binding for global variable
  ‘mutLength’
.generateBackgroundVariants: no visible binding for global variable
  ‘REF’
.generateKataegisFoci: no visible binding for global variable
  ‘seqnames’
.generateKataegisFoci: no visible binding for global variable
  ‘startKataegisFoci’
.generateKataegisVariants: no visible binding for global variable
  ‘synthFociID’
.generateKataegisVariants: no visible binding for global variable
  ‘startKataegisFoci’
.generateKataegisVariants: no visible binding for global variable
  ‘endKataegisFoci’
.generateKataegisVariants: no visible binding for global variable
  ‘start’
.generateRainfallPlot: no visible binding for global variable
  ‘variantID’
.generateRainfallPlot: no visible binding for global variable ‘IMD’
.generateRainfallPlot: no visible binding for global variable
  ‘seqnames’
.generateRainfallPlot: no visible binding for global variable
  ‘variantType’
.generateRainfallPlot: no visible binding for global variable
  ‘putativeKataegis’
.generateRainfallPlot: no visible binding for global variable
  ‘firstVariantID’
.generateRainfallPlot: no visible binding for global variable
  ‘lastVariantID’
.generateRainfallPlot: no visible binding for global variable ‘meanIMD’
.mergeKataegisSegments: no visible binding for global variable
  ‘segmentID’
.mergeKataegisSegments: no visible binding for global variable
  ‘seqnames’
.mergeKataegisSegments: no visible binding for global variable ‘fociID’
.mergeKataegisSegments: no visible binding for global variable ‘start’
.mergeKataegisSegments: no visible binding for global variable ‘end’
.mergeKataegisSegments: no visible binding for global variable
  ‘sampleNames’
.mergeKataegisSegments: no visible binding for global variable
  ‘totalVariants’
.mergeKataegisSegments: no visible binding for global variable
  ‘firstVariantID’
.mergeKataegisSegments: no visible binding for global variable
  ‘lastVariantID’
.mergeKataegisSegments: no visible binding for global variable
  ‘meanIMD’
.mergeKataegisSegments: no visible binding for global variable
  ‘IMDcutoff’
.removeValidationColumns: no visible binding for global variable
  ‘seqnames’
.removeValidationColumns: no visible binding for global variable
  ‘start’
.removeValidationColumns: no visible binding for global variable ‘end’
.removeValidationColumns: no visible binding for global variable
  ‘width’
.removeValidationColumns: no visible binding for global variable
  ‘strand’
.removeValidationColumns: no visible binding for global variable ‘ref’
.removeValidationColumns: no visible binding for global variable ‘alt’
.removeValidationColumns: no visible binding for global variable
  ‘totalDepth’
.removeValidationColumns: no visible binding for global variable
  ‘refDepth’
.removeValidationColumns: no visible binding for global variable
  ‘altDepth’
.removeValidationColumns: no visible binding for global variable
  ‘sampleNames’
.selectSequences: no visible binding for global variable ‘seqnames’
determineSegments: no visible binding for global variable ‘sampleNames’
determineSegments: no visible binding for global variable ‘seqnames’
determineSegments: no visible binding for global variable ‘segmentID’
determineSegments: no visible binding for global variable ‘variantID’
determineSegments: no visible binding for global variable ‘start’
determineSegments: no visible binding for global variable ‘IMD’
determineSegments: no visible binding for global variable ‘end’
determineSegments: no visible binding for global variable ‘meanIMD’
determineSegments: no visible binding for global variable
  ‘totalVariants’
determineSegments: no visible binding for global variable
  ‘mutationRate’
rainfallPlot: no visible binding for global variable ‘seqnames’
Undefined global functions or variables:
  IMD IMDcutoff REF alt altDepth end endKataegisFoci firstVariantID
  firstVariantOfSeqname fociID lastVariantID meanIMD mutLength mutType
  mutationRate putativeKataegis ref refDepth sampleNames segmentID
  seqnames start startKataegisFoci strand synthFociID totalDepth
  totalVariants variantID variantType width
Consider adding
  importFrom("stats", "end", "start")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'rainfallPlot.Rd':
  ‘[katdetectr]{KatDetect}’

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 ... 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/katdetectr.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL katdetectr
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘katdetectr’ ...
** this is package ‘katdetectr’ version ‘1.11.1’
** 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 (katdetectr)

R version 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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(katdetectr)
> 
> test_check("katdetectr")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 187 ]
> 
> proc.time()
   user  system elapsed 
 15.011   0.504  15.360