I'm forwarding a couple of messages from the support site.
I'd appreciate some discussion.
It seems like jupyter notebooks are becoming increasingly plausible as a
possible vignette format, and I was wondering whether there is any
real-world experience with these, including their pros and cons as
vignettes. For instance...
Developer / build system
- Presumably these notebooks need to be run as part of the package check
-- no sense distributed non-functional notebooks. Are there facilities for
this, along the lines of a traditional vignette that builds and potentially
generates errors during R and / or document processing?
- Are notebooks actually mature enough that, e.g., their format will not
change dramatically?
End-user
- I guess most end users will get static, evaluated versions of the
notebooks, unless they install python & friends. Is that right?
- Can the user easily obtain the equivalent of a Stangle'd vignette, i.e.,
a runnable R script?
- If a typical user only has access to a static version of the notebook,
then what have we gained relative to traditional vignettes?
-------- Forwarded Message --------
Subject: [bioc] A: BiocCheck: REQUIRED: vignette sources in
vignettes/
directory (for custom vignet
Date: Wed, 20 May 2015 16:32:24 -0000
From: Dan Tenenbaum [bioc] <noreply at bioconductor.org>
Reply-To: reply+9665d4a8+code at bioconductor.org
To: mtmorgan at fhcrc.org
Activity on a post you are following on support.bioconductor.org
<https://support.bioconductor.org>
User Dan Tenenbaum <https://support.bioconductor.org/u/4256/> wrote
Answer:
BiocCheck: REQUIRED: vignette sources in vignettes/ directory (for custom
vignettebuilder) <https://support.bioconductor.org/p/67884/#67885>:
BTW, questions about package development and submission should go to the
bioc-devel mailing list <http://bioconductor.org/help/support/#bioc-devel
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.
--------------------------------------------------------------------------------
-------- Forwarded Message --------
Subject: [bioc] BiocCheck: REQUIRED: vignette sources in vignettes/
directory
(for custom vignettebuilder)
Date: Wed, 20 May 2015 16:29:49 -0000
From: flying-sheep [bioc] <noreply at bioconductor.org>
Reply-To: reply+c01911bc+code at bioconductor.org
To: mtmorgan at fhcrc.org
Activity on a post you are following on support.bioconductor.org
<https://support.bioconductor.org>
User flying-sheep <https://support.bioconductor.org/u/7779/> wrote
Question:
BiocCheck: REQUIRED: vignette sources in vignettes/ directory (for custom
vignettebuilder) <https://support.bioconductor.org/p/67884/>:
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?
--------------------------------------------------------------------------------
You may reply via email or visit https://support.bioconductor.org/p/67884/