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### Running command:
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###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicRanges.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings GenomicRanges_1.52.1.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/GenomicRanges.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GenomicRanges/DESCRIPTION' ... OK
* this is package 'GenomicRanges' version '1.52.1'
* 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 'GenomicRanges' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* 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 ... NOTE
Problems with news in 'NEWS':
  Cannot process chunk/lines:
    SIGNIFICANT USER-VISIBLE CHANGES
  Cannot process chunk/lines:
    DEPRECATED AND DEFUNCT
* checking R 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 ... 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 ... WARNING
checkRd: (5) GRanges-class.Rd:115-165: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:173-176: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:177-182: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:183-187: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:188-191: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:192-195: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:196-199: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:200-204: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:205-208: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:209-218: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:219-223: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:224-228: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:229-238: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:239-245: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:246-251: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:252-257: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:258-263: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:264-267: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:268-276: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:284-299: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:300-307: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:308-322: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:323-332: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:333-342: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:343-349: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:356-361: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:368-371: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:372-376: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:377-380: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:381-394: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:409-415: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:421-427: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:433-445: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:453-466: \item in \describe must have non-empty label
* 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-3.17-bioc/R/library/GenomicRanges/libs/x64/GenomicRanges.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (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 sizes of PDF files under 'inst/doc' ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'GRanges_and_GRangesList_slides.pdf' from 507Kb to 256Kb
     compacted 'Ten_things_slides.pdf' from 277Kb to 150Kb
  consider running tools::compactPDF() on these files
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
genomicvars              38.60   3.72   42.58
GPos-class               34.61   1.72   36.36
absoluteRanges            0.86   0.13   18.75
makeGRangesFromDataFrame  0.73   0.08    7.84
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'run_unitTests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc/meat/GenomicRanges.Rcheck/00check.log'
for details.