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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:SeqVarTools.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings SeqVarTools_1.45.0.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/SeqVarTools.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 'SeqVarTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SeqVarTools' version '1.45.0'
* 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 'SeqVarTools' can be installed ... OK
* 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 ... 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:
  Iterator-class.Rd: GRanges, GRangesList, DataFrame, SeqVarGDSClass,
    seqSetFilter
  SeqVarData-class.Rd: SeqVarGDSClass, AnnotatedDataFrame,
    seqSetFilter, GRanges, seqVCF2GDS, seqOpen, seqGetData, seqApply,
    seqClose
  SeqVarTools-package.Rd: SeqArray
  allele-methods.Rd: SeqVarGDSClass
  alleleFrequency.Rd: SeqVarGDSClass, seqParallel
  alternateAlleleDetection.Rd: seqSetFilter, SeqVarGDSClass
  applyMethod.Rd: SeqVarGDSClass, seqSetFilter
  chromWithPAR.Rd: SeqVarGDSClass
  countSingletons.Rd: SeqVarGDSClass
  duplicateDiscordance.Rd: seqSetFilter
  getGenotype.Rd: SeqVarGDSClass, seqParallel, Matrix, seqBlockApply,
    seqGetData, seqSetFilter
  getVariableLengthData.Rd: SeqVarGDSClass, seqParallel, seqGetData
  heterozygosity.Rd: SeqVarGDSClass, seqParallel
  hwe.Rd: SeqVarGDSClass, seqParallel, HWExact, GWASExactHW
  imputedDosage.Rd: SeqVarGDSClass
  inbreedCoeff.Rd: SeqVarGDSClass, seqParallel
  isSNV.Rd: SeqVarGDSClass
  isVariant.Rd: SeqVarGDSClass, seqParallel
  meanBySample.Rd: SeqVarGDSClass, seqApply
  mendelErr.Rd: SeqVarGDSClass
  missingGenotypeRate.Rd: SeqVarGDSClass, seqParallel
  pca.Rd: SeqVarGDSClass
  refFrac.Rd: SeqVarGDSClass, seqParallel
  regression.Rd: logistf, seqParallel, seqSetFilter
  setVariantID.Rd: seqVCF2GDS, SeqVarGDSClass
  titv.Rd: SeqVarGDSClass
  variantInfo.Rd: SeqVarGDSClass
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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'test.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: 1 NOTE
See
  'E:/biocbuild/bbs-3.21-bioc/meat/SeqVarTools.Rcheck/00check.log'
for details.