Question: BiocCheck: REQUIRED: vignette sources in vignettes/ directory (for custom vignettebuilder)
1
4.4 years ago by
flying-sheep10
Germany
flying-sheep10 wrote:

I’m using a .ipynb notebook as source for my Vignette, so I created a Vignette engine inside my package to build it.

That one registers a the necessary extensions, and R CMD build obediently creates a vignette from the .ipynb file.

Yet R CMD BiocCheck still says REQUIRED: vignette sources in vignettes/ directory. should I ignore that when submitting my package, or will the bioconductor people have to fix that check beforehand?

modified 4.4 years ago • written 4.4 years ago by flying-sheep10
Answer: BiocCheck: REQUIRED: vignette sources in vignettes/ directory (for custom vignet
3
4.4 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k wrote:

BTW, questions about package development and submission should go to the bioc-devel mailing list.

We don't yet have a policy about .ipynb vignettes and we'd have to make sure the build system is capable of building them. However, I would ignore the error for now and you can discuss it with your reviewer when you submit the package.

1

I did forward this to the Bioc-devel mailing list, and would appreciate discussion tehre.

Thanks!

About building: Idk how your build process works, but locally, if IPython is installed, R CMD build works (it will call ipython nbconvert, in the future jupyter nbconvert).

I’ll discuss on the mailing list, and will probably fix this bug soon.