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Description
Describe the bug
The row names for "HMP_2012.relative_abundance" return what seems to be extra text in the rownames. When setting rownames = "NCBI".
To Reproduce
library(curatedMetagenomicData)
res <- curatedMetagenomicData("HMP_2012.relative_abundance", dryrun = FALSE, counts = TRUE, rownames = "NCBI")
#>
#> $`2021-03-31.HMP_2012.relative_abundance`
#> dropping rows without rowTree matches:
#> k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella_profusa
#> k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella_stercoris
#> k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma|s__[Collinsella]_massiliensis
#> k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillales_unclassified|g__Gemella|s__Gemella_bergeri
#> k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella_elegans
#> k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Ruminococcus|s__Ruminococcus_champanellensis
#> k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia|s__Bulleidia_extructa
#> k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella_parvirubra
#> k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus|s__Cloacibacillus_evryensis
resource_row_names <- rownames(res[[1]]) |> head()
resource_row_names
#> [1] "species:46503" "species:821" "species:246787" "species:823"
#> [5] "species:1262753" "species:28116"Expected behavior
library(testthat)
expect_silent(base::as.integer(resource_row_names))Reactions are currently unavailable