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’
Running examples in ‘gggenomes-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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
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’
Running examples in ‘gggenomes-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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
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’
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
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’
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
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'
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
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
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’
Running examples in ‘gggenomes-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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
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’
Running examples in ‘gggenomes-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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
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’
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’
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'
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
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
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
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