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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cbaf.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cbaf_1.33.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/cbaf.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 ‘cbaf/DESCRIPTION’ ... OK
* this is package ‘cbaf’ version ‘1.33.0’
* 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 ‘cbaf’ 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 whether startup messages can be suppressed ... 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) automatedStatistics.Rd:75-81: Only 5 columns allowed in this table (row 1 has 2)
checkRd: (-1) automatedStatistics.Rd:75-81: Only 5 columns allowed in this table (row 2 has 2)
checkRd: (-1) automatedStatistics.Rd:75-81: Only 5 columns allowed in this table (row 3 has 2)
checkRd: (-1) automatedStatistics.Rd:75-81: Only 5 columns allowed in this table (row 4 has 2)
checkRd: (-1) automatedStatistics.Rd:75-81: Only 5 columns allowed in this table (row 5 has 2)
checkRd: (-1) availableData.Rd:30-36: Only 5 columns allowed in this table (row 1 has 2)
checkRd: (-1) availableData.Rd:30-36: Only 5 columns allowed in this table (row 2 has 2)
checkRd: (-1) availableData.Rd:30-36: Only 5 columns allowed in this table (row 3 has 2)
checkRd: (-1) availableData.Rd:30-36: Only 5 columns allowed in this table (row 4 has 2)
checkRd: (-1) availableData.Rd:30-36: Only 5 columns allowed in this table (row 5 has 2)
checkRd: (-1) cleanDatabase.Rd:21-27: Only 5 columns allowed in this table (row 1 has 2)
checkRd: (-1) cleanDatabase.Rd:21-27: Only 5 columns allowed in this table (row 2 has 2)
checkRd: (-1) cleanDatabase.Rd:21-27: Only 5 columns allowed in this table (row 3 has 2)
checkRd: (-1) cleanDatabase.Rd:21-27: Only 5 columns allowed in this table (row 4 has 2)
checkRd: (-1) cleanDatabase.Rd:21-27: Only 5 columns allowed in this table (row 5 has 2)
checkRd: (-1) heatmapOutput.Rd:95-101: Only 5 columns allowed in this table (row 1 has 2)
checkRd: (-1) heatmapOutput.Rd:95-101: Only 5 columns allowed in this table (row 2 has 2)
checkRd: (-1) heatmapOutput.Rd:95-101: Only 5 columns allowed in this table (row 3 has 2)
checkRd: (-1) heatmapOutput.Rd:95-101: Only 5 columns allowed in this table (row 4 has 2)
checkRd: (-1) heatmapOutput.Rd:95-101: Only 5 columns allowed in this table (row 5 has 2)
checkRd: (-1) obtainMultipleStudies.Rd:56-62: Only 5 columns allowed in this table (row 1 has 2)
checkRd: (-1) obtainMultipleStudies.Rd:56-62: Only 5 columns allowed in this table (row 2 has 2)
checkRd: (-1) obtainMultipleStudies.Rd:56-62: Only 5 columns allowed in this table (row 3 has 2)
checkRd: (-1) obtainMultipleStudies.Rd:56-62: Only 5 columns allowed in this table (row 4 has 2)
checkRd: (-1) obtainMultipleStudies.Rd:56-62: Only 5 columns allowed in this table (row 5 has 2)
checkRd: (-1) obtainOneStudy.Rd:54-60: Only 5 columns allowed in this table (row 1 has 2)
checkRd: (-1) obtainOneStudy.Rd:54-60: Only 5 columns allowed in this table (row 2 has 2)
checkRd: (-1) obtainOneStudy.Rd:54-60: Only 5 columns allowed in this table (row 3 has 2)
checkRd: (-1) obtainOneStudy.Rd:54-60: Only 5 columns allowed in this table (row 4 has 2)
checkRd: (-1) obtainOneStudy.Rd:54-60: Only 5 columns allowed in this table (row 5 has 2)
checkRd: (-1) processMultipleStudies.Rd:176-182: Only 5 columns allowed in this table (row 1 has 2)
checkRd: (-1) processMultipleStudies.Rd:176-182: Only 5 columns allowed in this table (row 2 has 2)
checkRd: (-1) processMultipleStudies.Rd:176-182: Only 5 columns allowed in this table (row 3 has 2)
checkRd: (-1) processMultipleStudies.Rd:176-182: Only 5 columns allowed in this table (row 4 has 2)
checkRd: (-1) processMultipleStudies.Rd:176-182: Only 5 columns allowed in this table (row 5 has 2)
checkRd: (-1) processOneStudy.Rd:170-176: Only 5 columns allowed in this table (row 1 has 2)
checkRd: (-1) processOneStudy.Rd:170-176: Only 5 columns allowed in this table (row 2 has 2)
checkRd: (-1) processOneStudy.Rd:170-176: Only 5 columns allowed in this table (row 3 has 2)
checkRd: (-1) processOneStudy.Rd:170-176: Only 5 columns allowed in this table (row 4 has 2)
checkRd: (-1) processOneStudy.Rd:170-176: Only 5 columns allowed in this table (row 5 has 2)
checkRd: (-1) xlsxOutput.Rd:27-33: Only 5 columns allowed in this table (row 1 has 2)
checkRd: (-1) xlsxOutput.Rd:27-33: Only 5 columns allowed in this table (row 2 has 2)
checkRd: (-1) xlsxOutput.Rd:27-33: Only 5 columns allowed in this table (row 3 has 2)
checkRd: (-1) xlsxOutput.Rd:27-33: Only 5 columns allowed in this table (row 4 has 2)
checkRd: (-1) xlsxOutput.Rd:27-33: Only 5 columns allowed in this table (row 5 has 2)
* 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 files in ‘vignettes’ ... OK
* checking examples ... 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/cbaf.Rcheck/00check.log’
for details.