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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FRASER.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FRASER_2.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/FRASER.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FRASER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FRASER’ version ‘2.2.0’
* 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 ‘FRASER’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... NOTE
Unexported objects imported by ':::' calls:
  'S4Vectors:::selectSome' 'ggbio:::.buildFacetsFromArgs'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
annotateRangesWithTxDb: no visible binding for global variable
  ‘include’
calculatePadjValuesOnSubset : <anonymous>: no visible binding for
  global variable ‘gene_rowIdx’
plotVolcano.FRASER: no visible binding for global variable
  ‘aberrantLabel’
plotVolcano,FraserDataSet: no visible binding for global variable
  ‘aberrantLabel’
results,FraserDataSet: no visible binding for global variable ‘padjust’
results,FraserDataSet: no visible binding for global variable
  ‘pValueGene’
results,FraserDataSet: no visible binding for global variable
  ‘padjustGene’
Undefined global functions or variables:
  aberrantLabel gene_rowIdx include pValueGene padjust padjustGene
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
plotFunctions              120.557  1.974 122.499
potentialImpactAnnotations  50.365  1.135  51.355
FRASER                      37.334  0.644  38.297
injectOutliers              28.093  0.667  25.335
results                     21.612  0.385  21.578
annotateRanges              20.568  0.423  21.407
optimHyperParams            19.199  0.165  19.390
mergeExternalData           19.020  0.218  19.041
calculatePSIValues          16.474  0.194  16.451
counts                      16.108  0.145  16.050
filtering                   15.666  0.159  15.616
fds-methods                 15.603  0.199  15.735
createTestFraserDataSet     14.609  0.156  14.537
getter_setter_functions     14.530  0.158  14.470
subset                      14.241  0.150  14.268
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/FRASER.Rcheck/00check.log’
for details.