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janhoo / worms

data mining and scraping taxonomic information from www.marinespecies.org
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wormsbynames r_parsed error is back #4

Open PierreENOlivier opened 5 years ago

PierreENOlivier commented 5 years ago

Hi @janhoo, the issue reported in April for the wormsbyname function is back. I had to switch to a different package. Yesterday, I have been advised to use "worms" package again and still having this "Error in r_parsed[[i]][[1]] : subscript out of bounds" issue even with a different data set.

Could you look into this? Or someone else?

screenshot 2019-02-22 09 56 16

janhoo commented 5 years ago

Sry to hear this. I am writing you so you know I received your mail. I might have a look into this. I fear that this problem is recurrent since I badly designed the kernel of this particular function. Since I shifted my occupation I do consider abandoning the package sooner or later, bc it actually needs a major rewrite. I will notify you about my decision within several days.

My first uninformed guess is that it might have something to do with two flavors of the same species occurring (pomatoshistus). Have you tried removing the 2nd occurrence? Might be unrelated though. WORMS keeps changing their protocols without notification so its a pain figuring what kind of flexibility the code must have.

So, long story short. If you know someone who wants to take over the project pls let me know. I will gladly assist in unraveling the code.

Best, Jan

Am 22. Februar 2019 um 08:56:41, PierreOcean (notifications@github.com) schrieb:

Hi @janhoo https://github.com/janhoo, the issue reported in April for the wormsbyname function is back. I had to switch to a different package. Yesterday, I have been advised to use "worms" package again and still having this "Error in r_parsed[[i]][[1]] : subscript out of bounds" issue even with a different data set.

Could you look into this? Or someone else?

[image: screenshot 2019-02-22 09 56 16] https://user-images.githubusercontent.com/10992175/53227845-21adc800-3688-11e9-8e99-a6aad918544a.png

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/janhoo/worms/issues/4, or mute the thread https://github.com/notifications/unsubscribe-auth/AFH-6W4g0x23aLO98MibXJAKVQ4TN5cDks5vP6K5gaJpZM4bJDnB .

PierreENOlivier commented 5 years ago

Hi @janhoo, I do not think the two "Pomatoschistus" are the problem here. First they were included as P. spp. and P. sp. (combination of two datasets). I still had the same problem. I tried a different package (taxize) which did not recognize the "spp." and "sp." terms, if I am recalling it right.

I just tried again... and the function works today! With and without the duplicates Pomatoschistus. Did you work on a fix? Really weird that it keeps on coming back.

Anyway, I do not know who could replace you but maybe Scott Chamberlain from the 'taxize' package? Or he might know who could take over the worms package.

pieterprovoost commented 5 years ago

@janhoo @PierreOcean There is a WoRMS package by @sckott already, see https://github.com/ropensci/worrms

PierreENOlivier commented 5 years ago

@pieterprovoost Aware of this package. I have been in touch with @sckott and his woRRms package is at the core of taxize. Not sure it is implied to work as a standalone. Both taxize and worms give different output formats so I usually use both but for different purposes.