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Roleren / ORFik

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RiboQC.plot() error #160

Closed SuhasSrinivasan closed 6 months ago

SuhasSrinivasan commented 6 months ago

While trying the Ribo-seq vignette exactly as is, so that I can then apply to new data. At this step

RiboQC.plot(df.rfp, BPPARAM = BiocParallel::SerialParam(progressbar = TRUE))

The following error and warning is reported

Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
In addition: Warning message:
call dbDisconnect() when finished working with a connection

Unfortunately, traceback() is not available.

Roleren commented 6 months ago

Is it an error or just a message error ? "Error in x$.self$finalize() : attempt to apply non-function" Is a known bug of R since 3.6, they have not fixed it, but converted it to message form. Nothing bad really happens for that as far as I know, if it is not something else of course.

SuhasSrinivasan commented 6 months ago

Thank you again for reviewing!

A few reported issues point to the source of the error as Rcpp.

Could it be from Rcpp for ORFik also?

https://github.com/sneumann/xcms/issues/288

https://github.com/rspatial/terra/issues/30

I am running the latest Rcpp 1.0.12 R 4.3.2 ORFik 1.22.2

Roleren commented 6 months ago

I believe this will be fixed within next release of R hopefully, lets wait and see.

In theory Rcpp 1.0.12 should contain the fix, but obviously there is more going on here.

Will close this issue for now, as this is not related to ORFik, please reopen the issue if you have actual ORFik errors related to this.