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### Running command:
###
###   /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_1.7.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SARC.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘SARC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SARC’ version ‘1.7.1’
* 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 whether startup messages can be suppressed ... 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:
      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)
  ── Failure ('test_plotCNV.R:19:1'): (code run outside of `test_that()`) ────────
  class(p)[[1]] not equal to "gg".
  1/1 mismatches
  x[1]: "ggplot2::ggplot"
  y[1]: "gg"
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 25 ]
  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.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL SARC
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘SARC’ ...
** this is package ‘SARC’ version ‘1.7.1’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'SARC' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'SARC' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (SARC)

R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

> #test SARC unit tests
> #unit test check
> library(testthat)
> library(SARC)
Loading required package: RaggedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
Warning message:
In fun(libname, pkgname) :
  Package 'SARC' is deprecated and will be removed from Bioconductor
  version 3.23
> test_check(package = "SARC")
[1] "All CNVs are fine for further evaluation"
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 25 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_addExonsGenes.R:42:1'): (code run outside of `test_that()`) ────
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)
── Failure ('test_plotCNV.R:19:1'): (code run outside of `test_that()`) ────────
class(p)[[1]] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 25 ]
Error: Test failures
Execution halted