parse_taxonomy_table issue

[andrluis]

Hey guys:

I trust you are doing great! Thanks for the awesome package you created.

I'm testing metacodeR through the example of 'voting geography' (https://grunwaldlab.github.io/metacoder_documentation/publication--08--voting.html), and am getting errors when running the function parse_taxonomy_table.

Everything before the below command line was being fine.

Then, I got an error here:

voting_data <- parse_taxonomy_table(input = data, taxon_col = c("class" = -1), other_col_type = "obs_info", class_sep = "\|")

Error:

Error in parse_taxonomy_table(input = data, taxon_col = c(class = -1), : argument "file_path" is missing, with no default

sessionInfo() R version 3.3.2 (2016-10-31) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X El Capitan 10.11.6

locale: [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] metacoder_0.1.2

loaded via a namespace (and not attached): [1] magrittr_1.5 R6_2.2.0 assertthat_0.1 DBI_0.5-1 tools_3.3.2 dplyr_0.5.0
[7] tibble_1.2 Rcpp_0.12.9

Can you please help me to find why this is happening?

Thank you,

Andre

[zachary-foster]

Hi @andrluis, thanks for the report! That example was run using the development version of metacoder, but I forgot to put a notice on the page about that. It should work if you install the development version:

devtools::install_github(repo="grunwaldlab/metacoder@dev")

I will be merging the development version into a CRAN update soon, so it will work with the normal version soon too.

The problem was that the CRAN verison of parse_taxonomy_table only accepts file paths and the new version accepts data.frames as well.

[zachary-foster]

@andrluis said this worked via Google Groups.