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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SparseSignatures.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SparseSignatures_2.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SparseSignatures.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SparseSignatures/DESCRIPTION’ ... OK
* this is package ‘SparseSignatures’ version ‘2.16.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SparseSignatures’ 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
import.trinucleotides.counts: no visible global function definition for
  ‘.’
patients.plot: no visible binding for global variable ‘Context’
patients.plot: no visible binding for global variable ‘alt’
patients.plot: no visible binding for global variable ‘patient’
patients.plot: no visible binding for global variable ‘value’
signatures.plot: no visible binding for global variable ‘Context’
signatures.plot: no visible binding for global variable ‘alt’
signatures.plot: no visible binding for global variable ‘value’
Undefined global functions or variables:
  . Context alt patient value
* 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 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 ...

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SparseSignatures
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘SparseSignatures’ ...
** using staged installation
** R
** data
** 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 (SparseSignatures)