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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TVTB.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TVTB_1.35.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/TVTB.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TVTB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TVTB’ version ‘1.35.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘TVTB’ 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 ... NOTE
checkRd: (7) NEWS.Rd:361-363: Tag \code is invalid in a \code block
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Genotypes-class.Rd: VCF-class
  TVTBParam-class.Rd: ScanVcfParam-class, VCF-class, ExpandedVCF-class,
    BiocParallelParam-class
  VcfBasicRules-class.Rd: FilterRules-class, List-class,
    eval,FilterRules,ANY-method, VCF-class
  VcfFilterRules-class.Rd: FilterRules-class, Vector-class, List-class,
    eval,FilterRules,ANY-method, VCF-class
  addCountGenos-methods.Rd: geno,VCF-method
  addFrequencies-methods.Rd: VCF-class
  addOverallFrequencies-methods.Rd: VCF-class
  addPhenoLevelFrequencies-methods.Rd: VCF-class
  countGenos-methods.Rd: VCF-class
  dropInfo-methods.Rd: VCF-class
  pairsInfo-methods.Rd: ggpairs, VCF-class
  plotInfo-methods.Rd: EnsDb-class, DataTrack-class, plotTracks,
    VCF-class
  readVcf-methods.Rd: readVcf, ScanVcfParam-class, DataFrame,
    readVcf,TabixFile,ScanVcfParam-method, VCF-class
  tSVE.Rd: runEnsDbApp
  variantsInSamples-methods.Rd: VCF-class
  vepInPhenoLevel-methods.Rd: VCF-class, GRanges-class, DataFrame-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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
plotInfo-methods 8.211  0.231    8.54
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  rs550201688 rs565338261 rs201239799 rs200461129 rs146726548 
        FALSE       FALSE       FALSE       FALSE        TRUE 
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 226 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • empty test (2): 'test_VcfFilterRules-class.R:438:1',
    'test_VcfFilterRules-class.R:468:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_pairsInfo-methods.R:28:5'): all signatures work to completion ──
  pairsInfo(vcf, "MAF", "super_pop") inherits from 'ggmatrix'/'GGally::ggmatrix'/'S7_object' not 'gg'/'ggplot'.
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 226 ]
  Error: Test failures
  Execution halted
* 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 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/TVTB.Rcheck/00check.log’
for details.