Search
Question: BiocCheck: REQUIRED: vignette sources in vignettes/ directory (for custom vignettebuilder)
1
gravatar for flying-sheep
2.5 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?

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by flying-sheep10
3
gravatar for Dan Tenenbaum
2.5 years ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k 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.

ADD COMMENTlink written 2.5 years ago by Dan Tenenbaum ♦♦ 8.2k
1

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

ADD REPLYlink written 2.5 years ago by Martin Morgan ♦♦ 20k

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.

ADD REPLYlink written 2.5 years ago by flying-sheep10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 285 users visited in the last hour