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### Running command:
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###   set _R_CHECK_FORCE_SUGGESTS_=0&& E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:crisprDesign.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings crisprDesign_1.9.0.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/crisprDesign.Rcheck'
* using R Under development (unstable) (2025-01-21 r87610 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 'crisprDesign/DESCRIPTION' ... OK
* this is package 'crisprDesign' version '1.9.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Packages suggested but not available for checking: 'crisprBwa', 'Rbwa'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'crisprDesign' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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:
  GuideSet-class.Rd: CrisprNuclease-class, BSgenome-class,
    DNAStringSet-class, Seqinfo-class
  PairedGuideSet-class.Rd: DNAStringSet-class
  TxDb2GRangesList.Rd: TxDb-class, GRangesList-class
  addCrispraiScores.Rd: GRanges-class
  addEditedAlleles.Rd: BaseEditor-class
  addExonTable.Rd: TxDb-class, GRangesList-class
  addGeneAnnotation.Rd: TxDb-class, GRangesList-class
  addNtcs.Rd: Seqinfo-class
  addPamScores.Rd: CrisprNuclease-class
  addPfamDomains.Rd: DataFrame-class
  addRepeats.Rd: GRanges-class
  addSNPAnnotation.Rd: VCF-class
  addSpacerAlignments.Rd: TxDb-class, GRangesList-class, GRanges-class,
    BSgenome-class, CrisprNuclease-class
  addTssAnnotation.Rd: GRanges-class
  addTxTable.Rd: TxDb-class, GRangesList-class
  completeSpacers.Rd: CrisprNuclease-class, BSgenome-class
  designCompleteAnnotation.Rd: BSgenome-class, GRanges-class,
    VCF-class, CrisprNuclease-class, TxDb-class, GRangesList-class,
    DataFrame-class
  findSpacerPairs.Rd: GRanges-class, DNAStringSet-class,
    DNAString-class, CrisprNuclease-class, BSgenome-class
  findSpacers.Rd: GRanges-class, DNAStringSet-class, DNAString-class,
    CrisprNuclease-class, BSgenome-class
  getConsensusIsoform.Rd: TxDb-class, GRangesList-class
  getMrnaSequences.Rd: TxDb-class, GRangesList-class, BSgenome-class,
    DNAStringSet-class
  getPreMrnaSequences.Rd: TxDb-class, GRangesList-class,
    BSgenome-class, DNAStringSet-class
  getTssObjectFromTxObject.Rd: TxDb-class, GRangesList-class
  getTxDb.Rd: TxDb-class, makeTxDbFromGFF, makeTxDbFromEnsembl
  getTxInfoDataFrame.Rd: TxDb-class, GRangesList-class, BSgenome-class,
    GRanges-class
  grListExample.Rd: TxDb-class, GRangesList-class
  grRepeatsExample.Rd: GRanges-class
  preparePfamTable.Rd: TxDb-class, GRangesList-class, DataFrame-class
  queryTss.Rd: GRanges-class
  queryTxObject.Rd: TxDb-class, GRangesList-class, GRanges-class
  removeRepeats.Rd: GRanges-class
  tssObjectExample.Rd: GRanges-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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
addEditedAlleles 14.14   0.34   14.48
addSNPAnnotation 14.00   0.13   14.14
* 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
  'E:/biocbuild/bbs-3.21-bioc/meat/crisprDesign.Rcheck/00check.log'
for details.