Error in ChemmineR function propOB() and ChemmineOB prop_OB()
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@user-24352
Last seen 7 months ago

I got the following error using ChemmineR function propOB() to obtain molecular decrsiptors from an sdf file. This is the code as in the manual example and for some reason it keeps throwing this error.

> library(ChemmineR)
> data(sdfsample)
# Call propOB()
> propOB(sdfsample)
Error in getClass(Class, where = topenv(parent.frame())) :
“_p_std__string” is not a defined class


This function is very similar to the one from package ChemmineOB, and get the same error using the example

> library(ChemmineOB)
> molRefs = forEachMol("SMILES","C1CCCCC1\ttest-compound-name",identity)
> prop_OB(molRefs)
Error in getClass(Class, where = topenv(parent.frame())) :
“_p_std__string” is not a defined class


R version 4.0.3 (2020-10-10)

Anyone encountered and solved this problem? Thanks

ChemmineR ChemmineOB • 516 views
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Hey, I am getting the same error too. Although I had written the code much earlier and it was working then but today I am getting the same error.

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Thanks for reporting this bug. It should be fixed soon. It has to do with an oversight on our end after the recent upgrade of ChemmineR/ChemmineOB to Open Babel version >=3.x.x.

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Hello Dr.Girke, I wanted to know if the issue is resolved? I am still getting the same error.

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It is working now but the update is only partially life on Bioc due to some problems we are experiencing with dependencies on the build systems. This should be resolved soon as well. If you are on Windows or Mac then you might be able to install the updated version ChemmineOB_1.28.1 from the Bioc release version 3.12 immediately. Under Linux you can get the update (ChemmineOB_1.29.3) from the Bioc development version 3.13. Not an ideal way of installing things across the 3 OSs but it could provide you with the update you are looking for right away. Once everything is fully resolved as it should, then I will report it back here.