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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SubCellBarCode.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SubCellBarCode_1.27.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/SubCellBarCode.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* 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 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SubCellBarCode/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SubCellBarCode’ version ‘1.27.0’
* 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 ‘SubCellBarCode’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘SubCellBarCode’
See ‘/Users/biocbuild/bbs-3.23-bioc/meat/SubCellBarCode.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
calculateCoveredProtein: no visible binding for global variable
  ‘Compartments’
calculateCoveredProtein: no visible binding for global variable
  ‘ProteinCoverage’
candidateRelocatedProteins: no visible binding for global variable
  ‘Pearson.Corr’
markerQualityControl: no visible binding for global variable
  ‘Correlation’
markerQualityControl: no visible binding for global variable ‘Pearson’
markerQualityControl: no visible binding for global variable ‘Spearman’
plotBarcode: no visible binding for global variable ‘Level’
plotBarcode: no visible binding for global variable ‘Probability’
plotBarcode: no visible binding for global variable ‘Locs’
plotMultipleProtein: no visible binding for global variable
  ‘Neighborhood’
plotMultipleProtein: no visible binding for global variable ‘Count’
plotMultipleProtein: no visible binding for global variable
  ‘Compartment’
Undefined global functions or variables:
  Compartment Compartments Correlation Count Level Locs Neighborhood
  Pearson Pearson.Corr Probability ProteinCoverage Spearman
* 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 LazyData ... 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
applyThresholdCompartment 5.228  0.128   5.644
* 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/SubCellBarCode.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SubCellBarCode
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘SubCellBarCode’ ...
** this is package ‘SubCellBarCode’ version ‘1.27.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘SubCellBarCode’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘SubCellBarCode’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘SubCellBarCode’
** testing if installed package keeps a record of temporary installation path
* DONE (SubCellBarCode)