BiocCheck: REQUIRED: vignette sources in vignettes/ directory (for custom vignettebuilder)
1
1
Entering edit mode
flying-sheep ▴ 10
@flying-sheep-7779
Last seen 6.3 years ago
Germany

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?

package bioconductor bioc-devel developers • 959 views
ADD COMMENT
3
Entering edit mode
Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 7 months ago
United States

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 COMMENT
1
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 507 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6