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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicTuples.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GenomicTuples_1.40.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/GenomicTuples.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 whether package 'GenomicTuples' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.20-bioc/R/library/GenomicTuples/libs/x64/GenomicTuples.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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
  'F:/biocbuild/bbs-3.20-bioc/meat/GenomicTuples.Rcheck/00check.log'
for details.