• using R Under development (unstable) (2025-09-11 r88813)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 21.1.1     flang version 21.1.1
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘gggenomes/DESCRIPTION’ ... OK
• this is package ‘gggenomes’ version ‘1.0.1’
• 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 executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘gggenomes’ can be installed ... [20s/28s] OK See the install log for details.
• checking installed package size ... OK
• checking package directory ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... NOTE   Missing dependency on R >= 4.1.0 because package code uses the pipe   |> or function shorthand \(...) syntax added in R 4.1.0.   File(s) using such syntax:     ‘aaa.R’ ‘flip.R’ ‘geom_link.Rd’ ‘geom_seq.Rd’ ‘geom_seq_break.Rd’     ‘shift.Rd’ ‘track_info.Rd’
• 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 loading without being on the library search path ... 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 ... [30s/41s] OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... INFO Undeclared package ‘ape’ in Rd xrefs
• 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 sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... 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 ... OK   Running ‘testthat.R’
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [15s/21s] ERROR Error(s) in re-building vignettes: --- re-building ‘emales.Rmd’ using rmarkdown [WARNING] Deprecated: --no-highlight. Use --syntax-highlighting=none instead. --- 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 Data sets in package 'gggenomes': emale_ava All-versus-all whole genome alignments of 6                         EMALE genomes emale_cogs Clusters of orthologs of 6 EMALE proteomes emale_gc Relative GC-content along 6 EMALE genomes emale_genes Gene annotations if 6 EMALE genomes (endogenous                         virophages) emale_ngaros Integrated Ngaro retrotransposons of 6 EMALE                         genomes emale_prot_ava All-versus-all alignments 6 EMALE proteomes emale_seqs Sequence index of 6 EMALE genomes (endogenous                         virophages) emale_tirs Terminal inverted repeats of 6 EMALE genomes 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 ... [12s/19s] OK
• checking HTML version of manual ... [6s/11s] OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 2 ERRORs, 1 NOTE