* using log directory 'd:/RCompile/CRANincoming/R-devel/TmCalculator.Rcheck'
* using R Under development (unstable) (2025-08-19 r88650 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'TmCalculator/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TmCalculator' version '1.1.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [10s] NOTE
Maintainer: 'Junhui Li <junhui.li11@umassmed.edu>'

New maintainer:
  Junhui Li <junhui.li11@umassmed.edu>
Old maintainer(s):
  Junhui Li <junhuili@cau.edu.cn>

Possibly misspelled words in DESCRIPTION:
  FASTA (23:45)
  GC (15:36)
  dimethyl (22:27)
  formamide (22:47)
  sulfoxide (22:36)
* 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 'TmCalculator' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [16s] OK
* checking whether the package can be loaded with stated dependencies ... [14s] OK
* checking whether the package can be unloaded cleanly ... [16s] OK
* checking whether the namespace can be loaded with stated dependencies ... [16s] OK
* checking whether the namespace can be unloaded cleanly ... [17s] OK
* checking loading without being on the library search path ... [16s] 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 ... [68s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [47s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [21s] OK
  Running 'testthat.R' [21s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [39s] ERROR
Error(s) in re-building vignettes:
--- re-building 'TmCalculator.Rmd' using rmarkdown

Quitting from TmCalculator.Rmd:125-181 [tm_viz]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<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:
     ▆
  1. └─TmCalculator::plot_tm_heatmap(...)
  2.   ├─ggplot2::ggplot(gr_plot)
  3.   └─ggbio:::ggplot.Vector(gr_plot)
  4.     └─ggbio::GGbio(gg, data = data)
  5.       ├─BiocGenerics::do.call(...)
  6.       ├─base::do.call(...)
  7.       └─methods (local) `<fn>`(...)
  8.         ├─methods::initialize(value, ...)
  9.         └─methods::initialize(value, ...)
 10.           └─methods::validObject(.Object)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'TmCalculator.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 'TmCalculator.Rmd'

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

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [14s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE