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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:SubCellBarCode.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings SubCellBarCode_1.27.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/SubCellBarCode.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘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 ‘/home/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 loading without being on the library search path ... 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    14.924  0.533  15.460
computeThresholdCompartment  12.091  0.085  12.179
applyThresholdNeighborhood   11.277  0.108  11.386
computeThresholdNeighborhood 10.175  0.041  10.216
svmExternalData               9.860  0.077   9.936
svmClassification             8.042  0.060   8.103
candidateRelocatedProteins    6.761  0.000   6.762
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/SubCellBarCode.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL SubCellBarCode
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-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)