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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Guitar.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Guitar_2.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Guitar.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 ‘Guitar/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Guitar’ version ‘2.22.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'GenomicFeatures', 'rtracklayer', 'AnnotationDbi', 'GenomicRanges',
  'magrittr', 'ggplot2', 'knitr', 'dplyr'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘Guitar’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 15.8Mb
  sub-directories of 1Mb or more:
    extdata  15.7Mb
* 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 ... NOTE
Package in Depends field not imported from: ‘knitr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘GenomicRanges:::get_out_of_bound_index’
  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
.extractComponent: no visible binding for global variable ‘gene_id’
.generate_guitar_coordinates: no visible global function definition for
  ‘makeGuitarCoordsFromTxDb’
.generate_guitar_coordinates: no visible binding for global variable
  ‘noBins’
Undefined global functions or variables:
  gene_id makeGuitarCoordsFromTxDb noBins
* 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 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
GuitarPlot                  29.955  1.123  31.092
GRangesListmapToTranscripts 12.459  0.151  12.625
samplePoints                12.423  0.090  12.517
makeGuitarTxdb              12.318  0.104  12.428
normalize                   11.624  0.084  11.711
* 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/Guitar.Rcheck/00check.log’
for details.