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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:TVTB.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings TVTB_1.25.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/TVTB.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘TVTB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TVTB’ version ‘1.25.0’
* 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 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 R 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 ... WARNING
Killed

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... WARNING
Error in library(TVTB, lib.loc = "/home/biocbuild/bbs-3.17-bioc/R/library") : 
  there is no package called ‘TVTB’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* 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 ... WARNING
checkRd: (5) VcfBasicRules-class.Rd:133-136: \item in \describe must have non-empty label
checkRd: (5) VcfBasicRules-class.Rd:137-140: \item in \describe must have non-empty label
checkRd: (5) VcfBasicRules-class.Rd:141-146: \item in \describe must have non-empty label
checkRd: (5) VcfBasicRules-class.Rd:147-151: \item in \describe must have non-empty label
checkRd: (5) VcfBasicRules-class.Rd:161-164: \item in \describe must have non-empty label
checkRd: (5) VcfBasicRules-class.Rd:165-168: \item in \describe must have non-empty label
checkRd: (5) VcfBasicRules-class.Rd:179-192: \item in \describe must have non-empty label
checkRd: (5) VcfBasicRules-class.Rd:193-201: \item in \describe must have non-empty label
checkRd: (5) VcfFilterRules-class.Rd:85-92: \item in \describe must have non-empty label
checkRd: (5) VcfFilterRules-class.Rd:93-96: \item in \describe must have non-empty label
checkRd: (5) VcfFilterRules-class.Rd:97-103: \item in \describe must have non-empty label
checkRd: (5) VcfFilterRules-class.Rd:104-108: \item in \describe must have non-empty label
checkRd: (5) VcfFilterRules-class.Rd:120-123: \item in \describe must have non-empty label
checkRd: (5) VcfFilterRules-class.Rd:124-127: \item in \describe must have non-empty label
checkRd: (5) VcfFilterRules-class.Rd:134-140: \item in \describe must have non-empty label
checkRd: (5) VcfFilterRules-class.Rd:141-149: \item in \describe must have non-empty label
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 ... SKIPPED
* 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:
  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>
  Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘Introduction.Rmd’ using ‘UTF-8’... OK
  ‘VcfFilterRules.Rmd’ using ‘UTF-8’... OK
  ‘tSVE.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 WARNINGs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/TVTB.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL TVTB
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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>
Killed