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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomicTuples.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomicTuples_1.40.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GenomicTuples.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 ‘GenomicTuples/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomicTuples’ version ‘1.40.0’
* 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 ‘GenomicTuples’ 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 ... 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
Unexported objects imported by ':::' calls:
  ‘GenomicRanges:::extraColumnSlotNames’
  ‘GenomicRanges:::extraColumnSlots’
  ‘GenomicRanges:::extraColumnSlotsAsDF’ ‘S4Vectors:::VH_recycle’
  ‘S4Vectors:::orderBy’
  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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) intra-tuple-methods.Rd:39-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) intra-tuple-methods.Rd:44-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nearest-methods.Rd:84-90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nearest-methods.Rd:91-97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nearest-methods.Rd:98-104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nearest-methods.Rd:105-133: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nearest-methods.Rd:120-123: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nearest-methods.Rd:124-127: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nearest-methods.Rd:128-131: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nearest-methods.Rd:134-136: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nearest-methods.Rd:137-141: Lost braces in \itemize; meant \describe ?
* 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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/GenomicTuples.Rcheck/00check.log’
for details.