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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:TVTB.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings TVTB_1.33.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/TVTB.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (conda-forge gcc 14.2.0-1) 14.2.0
    GNU Fortran (conda-forge gcc 14.2.0-1) 14.2.0
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TVTB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TVTB’ version ‘1.33.0’
* 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 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 loading without being on the library search path ... 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 8.001  0.172   8.375
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/TVTB.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL TVTB
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘TVTB’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (TVTB)

R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(TVTB)
> 
> test_check("TVTB")
Class: Genotypes
  @ref (hom. ref.): "REF" {0/0}
  @het (heter.)   : "HET" {0/1, 1/0}
  @alt (hom. alt.): "ALT" {1/1}class: TVTBparam
@genos: class: Genotypes
    @ref (hom. ref.): "REF" {0|0}
    @het (heter.): "HET" {0|1, 1|0}
    @alt (hom. alt.): "ALT" {1|1}
  @ranges: 0 GRanges on 0 sequence(s)
  @aaf (alt. allele freq.): "AAF"
  @maf (minor allele freq.): "MAF"
  @vep (Ensembl VEP key): "CSQ"
  @svp: <ScanVcfParam object>
  @bp: <SerialParam object>
rs199764262 rs189224179 rs373895181 rs201294244 rs199841831 rs182642366 
       TRUE       FALSE       FALSE       FALSE       FALSE       FALSE 
  rs1426654 rs150379789 rs570906312 rs538198029 rs553496066 rs574775672 
       TRUE        TRUE       FALSE       FALSE        TRUE       FALSE 
rs140666229 rs556950130 rs575303689 rs147513140 rs187525777 rs192454382 
       TRUE       FALSE        TRUE        TRUE       FALSE       FALSE 
rs184818838 rs566886499 rs199924625 rs555872528 rs531820822 rs201353600 
      FALSE       FALSE       FALSE       FALSE       FALSE       FALSE 
rs550201688 rs565338261 rs201239799 rs200461129 rs146726548 
      FALSE       FALSE       FALSE       FALSE        TRUE 
rs199764262 rs189224179 rs373895181 rs201294244 rs199841831 rs182642366 
      FALSE       FALSE       FALSE       FALSE       FALSE       FALSE 
  rs1426654 rs150379789 rs570906312 rs538198029 rs553496066 rs574775672 
      FALSE       FALSE       FALSE       FALSE       FALSE       FALSE 
rs140666229 rs556950130 rs575303689 rs147513140 rs187525777 rs192454382 
      FALSE       FALSE       FALSE       FALSE       FALSE       FALSE 
rs184818838 rs566886499 rs199924625 rs555872528 rs531820822 rs201353600 
      FALSE       FALSE       FALSE       FALSE       FALSE       FALSE 
rs550201688 rs565338261 rs201239799 rs200461129 rs146726548 
      FALSE       FALSE       FALSE       FALSE       FALSE 
rs199764262 rs189224179 rs373895181 rs201294244 rs199841831 rs182642366 
       TRUE       FALSE       FALSE       FALSE       FALSE       FALSE 
  rs1426654 rs150379789 rs570906312 rs538198029 rs553496066 rs574775672 
       TRUE        TRUE       FALSE       FALSE        TRUE       FALSE 
rs140666229 rs556950130 rs575303689 rs147513140 rs187525777 rs192454382 
       TRUE       FALSE        TRUE        TRUE       FALSE       FALSE 
rs184818838 rs566886499 rs199924625 rs555872528 rs531820822 rs201353600 
      FALSE       FALSE       FALSE       FALSE       FALSE       FALSE 
rs550201688 rs565338261 rs201239799 rs200461129 rs146726548 
      FALSE       FALSE       FALSE       FALSE        TRUE 
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 227 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): 'test_VcfFilterRules-class.R:438:1',
  'test_VcfFilterRules-class.R:468:1'

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 227 ]
> 
> proc.time()
   user  system elapsed 
 52.980   1.577  54.619