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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SARC.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SARC_1.7.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SARC.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘SARC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SARC’ version ‘1.7.0’
* package encoding: UTF-8
* 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 ‘SARC’ 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
addExonsGenes: no visible global function definition for ‘metadata’
addExonsGenes: no visible global function definition for ‘metadata<-’
anovaOnCNV: no visible global function definition for ‘metadata’
anovaOnCNV: no visible global function definition for ‘metadata<-’
cnvConfidence: no visible global function definition for ‘metadata’
cnvConfidence: no visible global function definition for ‘metadata<-’
pasteExonsGenes: no visible global function definition for ‘metadata’
pasteExonsGenes: no visible global function definition for ‘metadata<-’
phDunnetonCNV: no visible global function definition for ‘metadata’
phDunnetonCNV: no visible global function definition for ‘metadata<-’
plotCovPrep: no visible global function definition for ‘metadata’
plotCovPrep: no visible global function definition for ‘metadata<-’
prepAnova: no visible global function definition for ‘metadata’
prepAnova: no visible global function definition for ‘metadata<-’
regionGrangeMake: no visible global function definition for ‘metadata’
regionGrangeMake: no visible global function definition for
  ‘metadata<-’
regionMean: no visible global function definition for ‘metadata’
regionMean: no visible global function definition for ‘metadata<-’
regionQuantiles: no visible global function definition for ‘metadata’
regionQuantiles: no visible global function definition for ‘metadata<-’
regionSet: no visible global function definition for ‘sortSeqlevels’
regionSet: no visible global function definition for ‘metadata’
regionSet: no visible global function definition for ‘metadata<-’
regionSplit: no visible global function definition for ‘metadata’
regionSplit: no visible global function definition for ‘metadata<-’
setQDplot: no visible global function definition for ‘metadata’
setQDplot: no visible global function definition for ‘metadata<-’
setupCNVplot: no visible global function definition for ‘metadata’
setupCNVplot: no visible global function definition for ‘metadata<-’
Undefined global functions or variables:
  metadata metadata<- sortSeqlevels
* checking Rd files ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘SARC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addExonsGenes
> ### Title: addExonsGenes
> ### Aliases: addExonsGenes
> 
> ### ** Examples
> 
> if (requireNamespace("TxDb.Hsapiens.UCSC.hg38.knownGene", quietly = TRUE)) {
+ require("TxDb.Hsapiens.UCSC.hg38.knownGene")
+ } else {}
Loading required package: TxDb.Hsapiens.UCSC.hg38.knownGene
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> 
> if (requireNamespace("Homo.sapiens", quietly = TRUE)) {
+ require("Homo.sapiens")
+ } else {}


Loading required package: Homo.sapiens
Loading required package: OrganismDbi
Loading required package: GO.db
Loading required package: org.Hs.eg.db
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
> 
> data("test_cnv")
> test_cnv <- test_cnv[c(1),]
> data("test_cov")
> SARC <- regionSet(cnv = test_cnv, cov = test_cov)
> SARC <- plotCovPrep(RE = SARC, cnv = metadata(SARC)[['CNVlist']][[1]],
+                    startlist = metadata(SARC)[[2]],
+                    endlist = metadata(SARC)[[3]])
> SARC <- regionGrangeMake(RE = SARC, covprepped = metadata(SARC)[[4]])
> 
> TxDb(Homo.sapiens) <- TxDb.Hsapiens.UCSC.hg38.knownGene
Error in .updateTxDb(x, value) : 
  Could not load package txdbmaker. Is it installed?

  Note that the TxDb() method for OrganismDb objects requires the txdbmaker
  package. Please install it with:

    BiocManager::install("txdbmaker")
Calls: TxDb<- -> TxDb<- -> .updateTxDb
Execution halted
* 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:
  Error in `.updateTxDb(x, value)`: Could not load package txdbmaker. Is it installed?
  
    Note that the TxDb() method for OrganismDb objects requires the txdbmaker
    package. Please install it with:
  
      BiocManager::install("txdbmaker")
  Backtrace:
      ▆
   1. ├─OrganismDbi::`TxDb<-`(`*tmp*`, value = `<TxDb>`) at test_addExonsGenes.R:42:1
   2. └─OrganismDbi::`TxDb<-`(`*tmp*`, value = `<TxDb>`)
   3.   └─OrganismDbi:::.updateTxDb(x, value)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 26 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘SARC_guide.Rmd’ using rmarkdown

Quitting from SARC_guide.Rmd:157-183 [set up plot]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.updateTxDb()`:
! Could not load package txdbmaker. Is it installed?

  Note that the TxDb() method for OrganismDb objects requires the txdbmaker
  package. Please install it with:

    BiocManager::install("txdbmaker")
---
Backtrace:
    ▆
 1. ├─OrganismDbi::`TxDb<-`(`*tmp*`, value = `<TxDb>`)
 2. └─OrganismDbi::`TxDb<-`(`*tmp*`, value = `<TxDb>`)
 3.   └─OrganismDbi:::.updateTxDb(x, value)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'SARC_guide.Rmd' failed with diagnostics:
Could not load package txdbmaker. Is it installed?

  Note that the TxDb() method for OrganismDb objects requires the txdbmaker
  package. Please install it with:

    BiocManager::install("txdbmaker")
--- failed re-building ‘SARC_guide.Rmd’

SUMMARY: processing the following file failed:
  ‘SARC_guide.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/SARC.Rcheck/00check.log’
for details.