• 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 'gggenomes/DESCRIPTION' ... OK
• this is package 'gggenomes' version '1.0.1'
• package encoding: UTF-8
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• checking whether package 'gggenomes' can be installed ... OK See the install log for details.
• 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
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• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [3s] OK
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• checking whether the package can be unloaded cleanly ... [2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [2s] OK
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• checking loading without being on the library search path ... [3s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
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• checking foreign function calls ... OK
• checking R code for possible problems ... [15s] OK
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• checking for unstated dependencies in examples ... OK
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• checking sizes of PDF files under 'inst/doc' ... OK
• checking installed files from 'inst/doc' ... OK
• checking files in 'vignettes' ... OK
• checking examples ... [3s] ERROR Running examples in 'gggenomes-Ex.R' failed The error most likely occurred in: > ### Name: add_feats > ### Title: Add different types of tracks > ### Aliases: add_feats add_links add_subfeats add_sublinks add_clusters > ### add_tracks > > ### ** Examples > > # Add some repeat annotations > gggenomes(seqs = emale_seqs) %>% + add_feats(repeats = emale_tirs) + + geom_seq() + geom_feat() Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0. ℹ Please use the `linewidth` argument instead. ℹ The deprecated feature was likely used in the gggenomes package.   Please report the issue at <https://github.com/thackl/gggenomes/issues>. Error in UseMethod("add_feats") :   no applicable method for 'add_feats' applied to an object of class "NULL" Calls: %>% -> add_feats Execution halted
• checking for unstated dependencies in 'tests' ... OK
• checking tests ... [4s] OK   Running 'testthat.R' [4s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [13s] ERROR Error(s) in re-building vignettes: --- re-building 'emales.Rmd' using rmarkdown --- finished re-building 'emales.Rmd' --- re-building 'flip.Rmd' using rmarkdown Quitting from flip.Rmd:16-44 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `UseMethod()`: ! no applicable method for 'add_links' applied to an object of class "NULL" --- Backtrace:     ▆  1. ├─p %>% add_links(emale_ava)  2. └─gggenomes::add_links(., emale_ava) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'flip.Rmd' failed with diagnostics: no applicable method for 'add_links' applied to an object of class "NULL" --- failed re-building 'flip.Rmd' --- re-building 'gggenomes.Rmd' using rmarkdown Quitting from gggenomes.Rmd:78-99 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `UseMethod()`: ! no applicable method for 'track_info' applied to an object of class "NULL" --- Backtrace:     x  1. +-p %>% track_info  2. \-gggenomes::track_info(.) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'gggenomes.Rmd' failed with diagnostics: no applicable method for 'track_info' applied to an object of class "NULL" --- failed re-building 'gggenomes.Rmd' SUMMARY: processing the following files failed:   'flip.Rmd' 'gggenomes.Rmd' Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [22s] OK
• checking HTML version of manual ... [17s] OK
• DONE

Status: 2 ERRORs