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Is your feature request related to a problem? Please describe.
I'm running into an issue where I can run a shiny app (https://github.com/Sage-Bionetworks/polypharmacology-db) locally and on a Shiny Server with no issues, but when I deploy it to shinyapps.io, rcdk is no longer able to parse valid smiles. I think it's probably related to a dependency, but I'm having trouble narrowing down the source of the failure. If I export the packaged app from shinyapps.io and run it locally, it works fine. This makes me think that it's something that's happening in Java/CDK but some diagnostic messages would be useful to narrow down the cause.
Describe the solution you'd like
It could be helpful if there was a 'verbose' mode that printed CDK messages and/or warnings.
Additional context
Feel free to close if this is not realistic, or impossible, which it might be. :)
The error I get on shinyapps.io is:
2022-02-23T20:39:34.521424+00:00 shinyapps[5401584]: SEND {"errors":{},"values":{},"inputMessages":[{"id":"smiles","message":{"value":"O=C1O/C(=C/Br)CCC1c1cccc2ccccc12"}}]}
2022-02-23T20:39:34.667965+00:00 shinyapps[5401584]: SEND {"progress":{"type":"binding","message":{"id":"structureimage"}}}
2022-02-23T20:39:34.695932+00:00 shinyapps[5401584]: SEND {"recalculating":{"name":"sims","status":"recalculating"}}
2022-02-23T20:39:34.727783+00:00 shinyapps[5401584]: O=C1O/C(=C/Br)CCC1c1cccc2ccccc12Warning in rcdk::parse.smiles(as.character(input)) :
2022-02-23T20:39:34.727785+00:00 shinyapps[5401584]: 1 out of 1 SMILES were not successfully parsed, resulting in NULLs.
Locally, I don't see this - the smiles above parses just fine:
The text was updated successfully, but these errors were encountered:
allaway
changed the title
If possible, provide more info on parse.smiles failures
If possible, provide more verbose messaging on parse.smiles failures
Feb 23, 2022
Is your feature request related to a problem? Please describe.
I'm running into an issue where I can run a shiny app (https://github.com/Sage-Bionetworks/polypharmacology-db) locally and on a Shiny Server with no issues, but when I deploy it to shinyapps.io,
rcdk
is no longer able to parse valid smiles. I think it's probably related to a dependency, but I'm having trouble narrowing down the source of the failure. If I export the packaged app from shinyapps.io and run it locally, it works fine. This makes me think that it's something that's happening in Java/CDK but some diagnostic messages would be useful to narrow down the cause.Describe the solution you'd like
It could be helpful if there was a 'verbose' mode that printed CDK messages and/or warnings.
Additional context
Feel free to close if this is not realistic, or impossible, which it might be. :)
The error I get on shinyapps.io is:
Locally, I don't see this - the smiles above parses just fine:
The text was updated successfully, but these errors were encountered: