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brunobrr / bdc

Check out the vignettes with detailed documentation on each module of the bdc package
https://brunobrr.github.io/bdc
GNU General Public License v3.0
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unable to run bdc_clean_names #259

Closed GilbertAlarcon-Cruz closed 7 months ago

GilbertAlarcon-Cruz commented 7 months ago

Hello. I am trying to run bdc_clean_names following the example in the Taxonomy vignette but using my own data: https://brunobrr.github.io/bdc/articles/taxonomy.html

bdc_clean_names(sci_names=mydata$scientificName, save_outputs = FALSE)

However, when I try to run it, I get an error saying that I am unable to install gnparser:

 `install_gnparser()` was deprecated in rgnparser 0.3.0 and is now defunct.
i Please see help page for deprecation reason and solution.
Run `rlang::last_error()` to see where the error occurred.

Is there a way to work around this? I was able to run gnparser using the Windows command line but I am unsure of how to get it to work with bdc. Thank you.

lucas-jardim commented 7 months ago

Hi Gilbert, thank you for your contribution. The function "install_gnparser" became deprecated in rgnparser package. Now, the users need to install the gnparser by hand. Please, check here how to install gnparser in your system. Let me know if it fixed your problem. We are going to adapt bdc_clean_names to the new rgnparser version.

Att,

GilbertAlarcon-Cruz commented 7 months ago

Hi Gilbert, thank you for your contribution. The function "install_gnparser" became deprecated in rgnparser package. Now, the users need to install the gnparser by hand. Please, check here how to install gnparser in your system. Let me know if it fixed your problem. We are going to adapt bdc_clean_names to the new rgnparser version.

Att,

After installing it, where should I place it so that R can find it? I am using the development version so now it says: GNparser is not installed in your machine. Please follow the instalation guidelines (https://github.com/gnames/gnparser#installation)

I followed the instructions to install it for Windows but don't know how to get R to use it.

GilbertAlarcon-Cruz commented 7 months ago

Hi Gilbert, thank you for your contribution. The function "install_gnparser" became deprecated in rgnparser package. Now, the users need to install the gnparser by hand. Please, check here how to install gnparser in your system. Let me know if it fixed your problem. We are going to adapt bdc_clean_names to the new rgnparser version. Att,

After installing it, where should I place it so that R can find it? I am using the development version so now it says: GNparser is not installed in your machine. Please follow the instalation guidelines (https://github.com/gnames/gnparser#installation)

I followed the instructions to install it for Windows but don't know how to get R to use it.

Never mind. I look at one of the recent commits and put the executable in the correct folder. The function now works for me. Thank you.

lucas-jardim commented 7 months ago

Great Gilbert!!