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### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:SpectralTAD.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --timings SpectralTAD_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/SpectralTAD.Rcheck’
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘SpectralTAD/DESCRIPTION’ ... OK
* this is package ‘SpectralTAD’ version ‘1.14.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SpectralTAD’ 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 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 ... OK
* checking whether the namespace can be unloaded cleanly ... 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
.windowedSpec: no visible binding for global variable ‘Group’
.windowedSpec: no visible binding for global variable ‘group_place’
.windowedSpec: no visible binding for global variable ‘ID’
.windowedSpec: no visible binding for global variable ‘Sil_Score’
SpectralTAD: no visible binding for global variable ‘end’
Undefined global functions or variables:
  Group ID Sil_Score end group_place
Consider adding
  importFrom("stats", "end")
to your NAMESPACE file.
* 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 ‘SpectralTAD-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SpectralTAD
> ### Title: Hierarchical Spectral Clustering of TADs
> ### Aliases: SpectralTAD
> 
> ### ** Examples
> 
> #Read in data
> data("rao_chr20_25_rep")
> #Find TADs
> spec_table <- SpectralTAD(rao_chr20_25_rep, chr= 'chr20')
Converting to n x n matrix
Matrix dimensions: 2517x2517
Estimating resolution
Warning: Unknown or uninitialised column: `Group`.
Warning: Unknown or uninitialised column: `Group`.
Error in `vec_init()`:
! `x` must be a vector, not `NULL`.
Backtrace:
     ▆
  1. ├─SpectralTAD::SpectralTAD(rao_chr20_25_rep, chr = "chr20")
  2. │ ├─... %>% mutate(Level = 1)
  3. │ └─SpectralTAD:::.windowedSpec(...)
  4. │   ├─base::which(end_group$Group == last(end_group$Group))
  5. │   └─dplyr::last(end_group$Group)
  6. │     └─dplyr::nth(x, -1L, order_by = order_by, default = default, na_rm = na_rm)
  7. │       └─dplyr:::check_nth_default(default, x = x)
  8. │         └─vctrs::vec_init(x)
  9. ├─dplyr::mutate(., Level = 1)
 10. └─vctrs:::stop_scalar_type(`<fn>`(NULL), "x", `<fn>`(vec_init()))
 11.   └─vctrs:::stop_vctrs(...)
 12.     └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = vctrs_error_call(call))
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    6. │ ├─... %>% mutate(Level = 1)
    7. │ └─SpectralTAD:::.windowedSpec(...)
    8. │   ├─base::which(end_group$Group == last(end_group$Group))
    9. │   └─dplyr::last(end_group$Group)
   10. │     └─dplyr::nth(x, -1L, order_by = order_by, default = default, na_rm = na_rm)
   11. │       └─dplyr:::check_nth_default(default, x = x)
   12. │         └─vctrs::vec_init(x)
   13. ├─dplyr::mutate(., Level = 1)
   14. └─vctrs:::stop_scalar_type(`<fn>`(NULL), "x", `<fn>`(vec_init()))
   15.   └─vctrs:::stop_vctrs(...)
   16.     └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = vctrs_error_call(call))
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘SpectralTAD.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘SpectralTAD.Rmd’ using rmarkdown
Quitting from lines 166-178 (SpectralTAD.Rmd) 
Error: processing vignette 'SpectralTAD.Rmd' failed with diagnostics:
`x` must be a vector, not `NULL`.
--- failed re-building ‘SpectralTAD.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 3 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/SpectralTAD.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL SpectralTAD
###
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/library’
* installing *source* package ‘SpectralTAD’ ...
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SpectralTAD)

R version 4.2.2 (2022-10-31) -- "Innocent and Trusting"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(SpectralTAD)
> 
> test_check("SpectralTAD")
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 0 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-spectraltad.R:5'): TAD calling works ───────────────────────────
<vctrs_error_scalar_type/vctrs_error/rlang_error/error/condition>
Error in `vec_init()`: `x` must be a vector, not `NULL`.
Backtrace:
     ▆
  1. ├─testthat::expect_equal(...) at test-spectraltad.R:5:2
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. ├─base::nrow(SpectralTAD(rao_chr20_25_rep, "chr20")$Level_1)
  5. ├─SpectralTAD::SpectralTAD(rao_chr20_25_rep, "chr20")
  6. │ ├─... %>% mutate(Level = 1)
  7. │ └─SpectralTAD:::.windowedSpec(...)
  8. │   ├─base::which(end_group$Group == last(end_group$Group))
  9. │   └─dplyr::last(end_group$Group)
 10. │     └─dplyr::nth(x, -1L, order_by = order_by, default = default, na_rm = na_rm)
 11. │       └─dplyr:::check_nth_default(default, x = x)
 12. │         └─vctrs::vec_init(x)
 13. ├─dplyr::mutate(., Level = 1)
 14. └─vctrs:::stop_scalar_type(`<fn>`(NULL), "x", `<fn>`(vec_init()))
 15.   └─vctrs:::stop_vctrs(...)
 16.     └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = vctrs_error_call(call))

[ FAIL 1 | WARN 2 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted