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rsilvabioinfo / ProbMetab

Provides probability ranking to candidate compounds assigned to masses, with the prior assumption of connected sample and additional previous and spectral information modeled by the user.
http://labpib.fmrp.usp.br/methods/probmetab
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build.database.kegg("ath") Fail #3

Open lecorguille opened 7 years ago

lecorguille commented 7 years ago

Hi,

We get this error message when we want to specify an organism like in your use case.

> ath=build.database.kegg("ath")
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
  cannot open URL 'http://rest.kegg.jp/link/ath/compound': HTTP status was '400 Bad Request'

Is it an issue from Kegg or have they change something?

rsilvabioinfo commented 7 years ago

Yes, it seems that kegg changed the link function: http://www.kegg.jp/kegg/rest/keggapi.html

I just added a small change to use other functions and solve the problem.

This code does not handle exceptions very well, you may want to rewrite or use other application for that, such as: http://bioconductor.org/packages/release/bioc/html/KEGGREST.html

Also, I just want to point that the function 'gibbs.samp.R' on github is different from the website http://labpib.fmrp.usp.br/methods/probmetab/, so if you are using the full functionalities I recommend a short benchmark.

Sorry about that, I'm not using the package in my current project and it is hard to maintain and improve it.

Thanks, Ricardo

2017-04-11 8:28 GMT-07:00 Gildas Le Corguillé notifications@github.com:

Hi,

We get this error message when we want to specify an organism like in your use case.

ath=build.database.kegg("ath")Error in file(file, "rt") : cannot open the connectionIn addition: Warning message:In file(file, "rt") : cannot open URL 'http://rest.kegg.jp/link/ath/compound': HTTP status was '400 Bad Request'

Is it an issue from Kegg or have they change something?

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