Last updated on 2025-09-13 13:50:30 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| gggenomes | 5 | 6 | 2 |
Current CRAN status: ERROR: 5, NOTE: 6, OK: 2
Version: 1.0.1
Check: DESCRIPTION meta-information
Result: 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’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-windows-x86_64
Version: 1.0.1
Check: examples
Result: ERROR
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
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.0.1
Check: re-building of vignette outputs
Result: 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
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.0.1
Check: examples
Result: 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
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-oldrel-windows-x86_64
Version: 1.0.1
Check: re-building of vignette outputs
Result: 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
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.0.1
Check: DESCRIPTION meta-information
Result: 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’
Flavor: r-release-macos-x86_64
Version: 1.0.1
Check: re-building of vignette outputs
Result: 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
Flavor: r-oldrel-windows-x86_64