Last updated on 2025-12-07 07:50:45 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| gggenomes | 1 | 1 | 11 |
Current CRAN status: ERROR: 1, NOTE: 1, OK: 11
Version: 1.1.2
Check: package dependencies
Result: WARN
Cannot process vignettes
Packages suggested but not available for checking:
'ggtree', 'Hmisc', 'knitr', 'rmarkdown'
VignetteBuilder package required for checking but not installed: ‘knitr’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.2
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: gggenomes
> ### Title: Plot genomes, features and synteny maps
> ### Aliases: gggenomes
>
> ### ** Examples
>
> # Compare the genomic organization of three viral elements
> # EMALEs: endogenous mavirus-like elements (example data shipped with gggenomes)
> gggenomes(emale_genes, emale_seqs, emale_tirs, emale_ava) +
+ geom_seq() + geom_bin_label() + # chromosomes and labels
+ geom_feat(linewidth= 8) + # terminal inverted repeats
+ geom_gene(aes(fill = strand), position = "strand") + # genes
+ geom_link(offset = 0.15) # synteny-blocks
>
> # with some more information
> gggenomes(emale_genes, emale_seqs, emale_tirs, emale_ava) %>%
+ add_feats(emale_ngaros, emale_gc) %>%
+ add_clusters(emale_cogs) %>%
+ sync() +
+ geom_link(offset = 0.15, color = "white") + # synteny-blocks
+ geom_seq() + geom_bin_label() + # chromosomes and labels
+ # thistle4, salmon4, burlywood4
+ geom_feat(linewidth= 6, position = "identity") + # terminal inverted repeats
+ geom_feat(
+ data = feats(emale_ngaros), color = "turquoise4", alpha = .3,
+ position = "strand", linewidth = 16
+ ) +
+ geom_feat_note(aes(label = type),
+ data = feats(emale_ngaros),
+ position = "strand", nudge_y = .3
+ ) +
+ geom_gene(aes(fill = cluster_id), position = "strand") + # genes
+ geom_wiggle(aes(z = score, linetype = "GC-content"), feats(emale_gc),
+ fill = "lavenderblush4", position = position_nudge(y = -.2), height = .2
+ ) +
+ scale_fill_brewer("Conserved genes", palette = "Dark2", na.value = "cornsilk3")
Joining with `by = join_by(feat_id)`
Flipping: Cflag_017B,BVI_069,BVI_008A
Error in loadNamespace(x) : there is no package called ‘Hmisc’
Calls: geom_wiggle ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
focus 6.442 0.196 7.913
add_tracks 5.724 0.268 6.388
geom_gene 5.136 0.223 5.883
geom_link 4.799 0.183 5.392
align 4.721 0.070 5.077
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.2
Check: package vignettes
Result: NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Flavor: r-devel-linux-x86_64-debian-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’ ‘geom_link.Rd’ ‘geom_seq.Rd’ ‘geom_seq_break.Rd’
‘shift.Rd’ ‘track_info.Rd’
Flavor: r-release-macos-arm64