* using log directory 'd:/Rcompile/CRANpkg/local/4.4/PopPsiSeqR.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'PopPsiSeqR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PopPsiSeqR' version '1.0.0'
* 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 whether package 'PopPsiSeqR' 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 ... [4s] OK
* checking whether the package can be loaded with stated dependencies ... [3s] OK
* checking whether the package can be unloaded cleanly ... [3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s] OK
* checking whether the namespace can be unloaded cleanly ... [4s] OK
* checking loading without being on the library search path ... [3s] OK
* checking use of S3 registration ... 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 ... [9s] OK
* checking Rd files ... [1s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [4s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [32s] ERROR
  Running 'testthat.R' [32s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(PopPsiSeqR)
  > 
  > test_check("PopPsiSeqR")
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 9 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-plot.R:26:5'): returns a plot ────────────────────────────────
  Expected `mock.plot <- windowedFrequencyShift.plotter(mock_data)` to run without any errors.
  i Actually got a <simpleError> with text:
    invalid class "GGbio" object: invalid object for slot "ggplot" in class "GGbio": got class "ggplot2::ggplot", should be or extend class "gg_OR_NULL"
  ── Error ('test-plot.R:27:5'): returns a plot ──────────────────────────────────
  Error in `eval(code, test_env)`: object 'mock.plot' not found
  Backtrace:
      ▆
   1. ├─testthat::expect_true(ggplot2::is.ggplot(mock.plot@ggplot)) at test-plot.R:27:5
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─ggplot2::is.ggplot(mock.plot@ggplot)
   5.   └─ggplot2::is_ggplot(x)
   6.     └─S7::S7_inherits(x, class_ggplot)
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 9 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [31s] ERROR
Error(s) in re-building vignettes:
--- re-building 'PopPsiSeq_and_Helpers.Rmd' using rmarkdown

Quitting from PopPsiSeq_and_Helpers.Rmd:120-124 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `validObject()`:
! invalid class "GGbio" object: invalid object for slot "ggplot" in class "GGbio": got class "ggplot2::ggplot", should be or extend class "gg_OR_NULL"
---
Backtrace:
     x
  1. +-ggplot2::autoplot(...)
  2. \-ggbio::autoplot(...)
  3.   \-ggbio (local) .local(object, ...)
  4.     +-BiocGenerics::do.call(ggplot, c(list(data = object), list(aes.res)))
  5.     +-base::do.call(ggplot, c(list(data = object), list(aes.res)))
  6.     +-ggplot2 (local) `<fn>`(data = `<GRanges>`, `<ggplt2::>`)
  7.     \-ggbio:::ggplot.Vector(data = `<GRanges>`, `<ggplt2::>`)
  8.       \-ggbio::GGbio(gg, data = data)
  9.         +-BiocGenerics::do.call(...)
 10.         +-base::do.call(...)
 11.         \-methods (local) `<fn>`(...)
 12.           +-methods::initialize(value, ...)
 13.           \-methods::initialize(value, ...)
 14.             \-methods::validObject(.Object)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'PopPsiSeq_and_Helpers.Rmd' failed with diagnostics:
invalid class "GGbio" object: invalid object for slot "ggplot" in class "GGbio": got class "ggplot2::ggplot", should be or extend class "gg_OR_NULL"
--- failed re-building 'PopPsiSeq_and_Helpers.Rmd'

SUMMARY: processing the following file failed:
  'PopPsiSeq_and_Helpers.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [17s] OK
* checking HTML version of manual ... [1s] OK
* DONE
Status: 2 ERRORs