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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TnT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TnT_1.26.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/TnT.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TnT/DESCRIPTION’ ... OK
* this is package ‘TnT’ version ‘1.26.0’
* 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 ‘TnT’ 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 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘TnT-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: seqinfo
> ### Title: Seqinfo of TnTTrack and TnTBoard
> ### Aliases: seqinfo seqinfo<-,RangeBasedTrack-method
> ###   seqinfo,RangeBasedTrack-method seqlevelsInUse,RangeBasedTrack-method
> ###   seqinfo,TnTBoard-method seqinfo,CompositeTrack-method
> ###   seqinfo<-,CompositeTrack-method seqlevelsInUse,CompositeTrack-method
> 
> ### ** Examples
> 
> btrack1 <- BlockTrack(GRanges("chr1", IRanges(1, 123)))
> btrack2 <- BlockTrack(GRanges("chr2", IRanges(3, 599)))
> ctrack <- merge(btrack1, btrack2)
Warning in .merge_two_Seqinfo_objects(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
Error in .mergeSpec(tracklist) : is.atomic(backgrounds) is not TRUE
Calls: merge ... merge_tracklist -> .merge_tracklist -> .mergeSpec -> stopifnot
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:
    1. ├─testthat::expect_warning(ct <- merge(bt, bt2), "no sequence levels in common") at test-seqinfo.R:17:5
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. ├─base::merge(bt, bt2)
    7. └─TnT::merge(bt, bt2)
    8.   └─TnT:::merge_tracklist(tracklist)
    9.     └─TnT (local) .merge_tracklist(tracklist)
   10.       └─TnT (local) .mergeSpec(tracklist)
   11.         └─base::stopifnot(is.atomic(labels), is.atomic(heights), is.atomic(backgrounds))
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 30 ]
  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: 2 ERRORs
See
  ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/TnT.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TnT
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘TnT’ ...
** using staged installation
** R
** 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 'TnT' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'TnT' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (TnT)

R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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(TnT)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

    anyDuplicated, aperm, append, as.data.frame, basename, cbind,
    colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
    get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
    tapply, union, 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':

    expand.grid, I, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Warning message:
In fun(libname, pkgname) :
  Package 'TnT' is deprecated and will be removed from Bioconductor
  version 3.20
> 
> test_check("TnT")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 30 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-seqinfo.R:17:5'): seqinfo of CompositeTrack ────────────────────
Error in `.mergeSpec(tracklist)`: is.atomic(backgrounds) is not TRUE
Backtrace:
     ▆
  1. ├─testthat::expect_warning(ct <- merge(bt, bt2), "no sequence levels in common") at test-seqinfo.R:17:5
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─base::merge(bt, bt2)
  7. └─TnT::merge(bt, bt2)
  8.   └─TnT:::merge_tracklist(tracklist)
  9.     └─TnT (local) .merge_tracklist(tracklist)
 10.       └─TnT (local) .mergeSpec(tracklist)
 11.         └─base::stopifnot(is.atomic(labels), is.atomic(heights), is.atomic(backgrounds))

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 30 ]
Error: Test failures
Execution halted