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### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:podkat.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings podkat_1.39.0.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/podkat.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'podkat/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'podkat' version '1.39.0'
* 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 'podkat' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
* checking installed package size ... INFO
  installed size is 12.8Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs  11.3Mb
* 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 ... 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AssocTestResultRanges-class.Rd: GRanges-class
  GenotypeMatrix-class.Rd: dgCMatrix-class
  VariantInfo-class.Rd: GRanges-class
  assocTest-methods.Rd: GRanges-class, GRangesList-class
  computeKernel.Rd: Matrix-class
  filterResult-methods.Rd: GRanges-class, GRangesList-class
  genotypeMatrix-methods.Rd: dgCMatrix-class, GRanges-class
  hgA.Rd: GRanges-class
  partitionRegions-methods.Rd: GRanges-class, GRangesList-class
  plot-methods.Rd: GRanges-class
  readGenotypeMatrix-methods.Rd: TabixFile-class, GRanges-class
  readRegionsFromBedFile.Rd: GRanges-class, Seqinfo-class
  readSampleNamesFromVcfHeader.Rd: TabixFile-class, scanBcfHeader
  readVariantInfo-methods.Rd: TabixFile-class, GRanges-class
  sort-methods.Rd: GRanges-class
  split-methods.Rd: GRanges-class, GRangesList-class
  unmasked-datasets.Rd: GRangesList-class, GRanges-class
  unmaskedRegions.Rd: GRangesList-class, GRanges-class
  weights-methods.Rd: GRanges-class, GRangesList-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ... INFO
GNU make is a SystemRequirements.
* 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 for x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/podkat/libs/x64/podkat.dll':
  Found '_assert', possibly from 'assert' (C)
  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 sizes of PDF files under 'inst/doc' ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'podkat.pdf' from 928Kb to 811Kb
  consider running tools::compactPDF() on these files,
  or build the source package with --compact-vignettes
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
unmaskedRegions      193.65   4.76  201.93
assocTest-methods     12.03   0.75   12.78
plot-methods          10.57   0.59   11.17
GenotypeMatrix-class   4.16   0.24    6.27
* 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
  'E:/biocbuild/bbs-3.21-bioc/meat/podkat.Rcheck/00check.log'
for details.