brendanf / funguildr Goto Github PK

Hi,
I am having trouble downloading the database/running the code. I am wondering if the FUNGuild database is down at the moment and if there is an ETA for when it will be back online.
Thanks.

Hi,

Thank you for creating this package, I think it will be very useful! I am trying use it now but I am having an issue where the resulting table is filled with e.g.:
Taxonomy taxon guid mbNumber taxonomicLevel trophicMode guild confidenceRanking growthForm trait notes citationSource
1 Acanthobasidium delicatum
2 Acephala NA

I tried manually downloading the database to see if that helped but no luck, this is the code I ran:
guilds <- funguild_assign(taxonomy, db = fung)

Still ran into the same issue. As a sanity check I did make sure that my species are in the database and after checking a few they definitely are.

The only error message I have had is the following during package install:
Warning messages:
1: In file.copy(savedcopy, lib, recursive = TRUE) :
problem copying C:\Users\Brandon\AppData\Local\R\win-library\4.3\00LOCK\vctrs\libs\x64\vctrs.dll to C:\Users\Brandon\AppData\Local\R\win-library\4.3\vctrs\libs\x64\vctrs.dll: Permission denied
2: In file.copy(savedcopy, lib, recursive = TRUE) :
problem copying C:\Users\Brandon\AppData\Local\R\win-library\4.3\00LOCK\fansi\libs\x64\fansi.dll to C:\Users\Brandon\AppData\Local\R\win-library\4.3\fansi\libs\x64\fansi.dll: Permission denied
3: In file.copy(savedcopy, lib, recursive = TRUE) :
problem copying C:\Users\Brandon\AppData\Local\R\win-library\4.3\00LOCK\purrr\libs\x64\purrr.dll to C:\Users\Brandon\AppData\Local\R\win-library\4.3\purrr\libs\x64\purrr.dll: Permission denied
4: In file.copy(savedcopy, lib, recursive = TRUE) :
problem copying C:\Users\Brandon\AppData\Local\R\win-library\4.3\00LOCK\dplyr\libs\x64\dplyr.dll to C:\Users\Brandon\AppData\Local\R\win-library\4.3\dplyr\libs\x64\dplyr.dll: Permission denied
5: In file.copy(savedcopy, lib, recursive = TRUE) :
problem copying C:\Users\Brandon\AppData\Local\R\win-library\4.3\00LOCK\jsonlite\libs\x64\jsonlite.dll to C:\Users\Brandon\AppData\Local\R\win-library\4.3\jsonlite\libs\x64\jsonlite.dll: Permission denied
6: In file.copy(savedcopy, lib, recursive = TRUE) :
problem copying C:\Users\Brandon\AppData\Local\R\win-library\4.3\00LOCK\curl\libs\x64\curl.dll to C:\Users\Brandon\AppData\Local\R\win-library\4.3\curl\libs\x64\curl.dll: Permission denied

Thank you for any help!

I'm running the funguild database to my dataset in R using this code:

fung <- get_funguild_db()
data_guilds <- lapply(ITS.taxonomy1, funguild_assign, db = fung)
funguild<- funguild_assign(ITS.taxonomy1, db = funguild_testdb)

However, my output has nothing but NAs for functional guilds, etc. Any idea what's going on here? I'm almost positive it's how I've set up my data frame, but I'm not sure where I went wrong. See screenshot below.

I'm really new to using R for microbiome data analysis, so sorry in advance if i am not using the language properly.

Last week I succesfully installed FUNGuildR by using this:

install.packages("remotes")
remotes::install_github("brendanf/FUNGuildR")
library(FUNGuildR)

and when using the function funguild_assign () I succesfully obtained a new table with trophicModes, guild, growthForm, ....

Today, i'm trying to analyze new data but i am not capable to obtain anything.

The error that I get when running the funguild_assign function is this:

otu_fun<- funguild_assign(otu_mat, db = get_funguild_db(), tax_col = "Taxonomy")
Error: lexical error: invalid char in json text.

                                   </body>
                 (right here) ------^

Does anybody knows what the problem is?
Thank you.

Hello,
I am trying to use FUNguildR,
but I get the following error, with both the function
get_funguild_db() and funguild_assign
for example:

get_funguild_db()
Error: lexical error: invalid char in json text.

(right here) ------^

help appreciated!!
Thanks for your work!!!

Gabri