biomarkertmle fails on data transposition about biotmle HOT 3 CLOSED

Resolved by #43.

from biotmle.

Thanks for your bug report. It will likely take me a bit of time to investigate this as I have not had the opportunity to maintain the biotmle R package well.

The error appears to stem from the fact that some piece of the code for cleaning/re-shaping the input data in the biomarkertmle wrapper function attempts to use t() to transpose the data, which apparently fails when the data is not of class matrix --- in this case, it appears to be of class data.frame (hence the mention of as.data.frame in the traceback shown).

With regard to the vignette source code (on Bioconductor and elsewhere): The code chunk you've excerpted is set to eval = FALSE in order to avoid actually running the biomarkertmle function, which will cause the build time of the vignette to exceed the time allotted by the Bioconductor (and, I believe, CRAN as well) build/check systems. This should not be a concern, as the relevant code is still subject to unit tests that (seem to) verify its integrity.

from biotmle.

It appears that the bug reported here originates from a change in the expected behavior of SummarizedExperiment::assay() (likely at some point during the transition to Bioconductor 3.7 recently) where the class of the object returned by assay() is DataFrame rather than the expected Matrix. This causes a failure in both t() and other downstream function calls meant to prepare the data for invoking the TML estimation procedure. This has been fixed in 2e78b7f in #43, which will likely be merged very soon.

from biotmle.