error class2tree output

[jrigbr]

Hello, I am facing this error while running class2tree

> sp_worms_id
[1] 138474 138677 104108 494795 138710 125332 130722 144784 129686 231858 369350 124208 127031 133913 273021 123987 124963 132487 140389
[20] 141855

cl <- classification(sp_worms_id, db = 'worms')

head(cl, 3)
$138474

A tibble: 11 × 3

name rank id

1 Animalia Kingdom 2
2 Mollusca Phylum 51
3 Bivalvia Class 105
4 Autobranchia Subclass 1424948
5 Heteroconchia Infraclass 1424949
6 Euheterodonta Subterclass 382296
7 Imparidentia Superorder 869600
8 Cardiida Order 869602
9 Tellinoidea Superfamily 14636
10 Semelidae Family 1781
11 Abra Genus 138474

$138677

A tibble: 11 × 3

name rank id

1 Animalia Kingdom 2
2 Mollusca Phylum 51
3 Polyplacophora Class 55
4 Neoloricata Subclass 57
5 Chitonida Order 382003
6 Acanthochitonina Suborder 90
7 Cryptoplacoidea Superfamily 385402
8 Acanthochitonidae Family 91
9 Acanthochitoninae Subfamily 1353774
10 Acanthochitona Genus 137613
11 Acanthochitona fascicularis Species 138677

$104108

A tibble: 10 × 3

name rank id

1 Animalia Kingdom 2
2 Arthropoda Phylum 1065
3 Crustacea Subphylum 1066
4 Multicrustacea Superclass 845959
5 Copepoda Class 1080
6 Neocopepoda Infraclass 155876
7 Gymnoplea Superorder 155877
8 Calanoida Order 1100
9 Acartiidae Family 104074
10 Acartia Genus 104108

tr <- class2tree(cl)
Get all ranks and their taxIDs
Erreur dans $<-.data.frame(*tmp*, "rank_df", value = character(0)) :
le tableau de remplacement a 0 lignes, le tableau remplacé en a 11

Thank you if you can help me

[trvinh]

Hello @jrigbr ,
class2tree() currently accepts a list of data frames as input, not a list of tibbles.
I have tried to convert your cl list to data frames and it worked.

> sp_worms_id <- c(138474,138677,104108,494795,138710,125332,130722,144784,129686,231858,369350,124208,127031,133913,273021,123987,124963,132487,140389,141855)
> cl <- classification(sp_worms_id, db = 'worms')
> cl <- lapply(cl, as.data.frame)
> tr <- class2tree(cl)
Get all ranks and their taxIDs
Align taxonomy hierarchies...
Taxonomy alignment done!
Calculate distance matrix
Add node labels
> tr$phylo

Phylogenetic tree with 20 tips and 11 internal nodes.

Tip labels:
  Abra, Acanthochitona fascicularis, Acartia, Acetabularia acetabulum, Aeolidiella alderi, Alcyonium coralloides, ...
Node labels:
  NA, Plantae, Animalia, Demospongiae, Teleostei, Echinodermata, ...

Unrooted; includes branch lengths.

I hope it will help you!
Best,
Vinh