packaging stan
I am thinking of packaging stan and rstan, and would appreciate some advice.
stan is a program for doing Bayesian analysis with a variant of
hybrid/Hamiltonian monte carlo. http://mc-stan.org/ homepage; https://github.com/stan-dev/rstan.git
and https://github.com/stan-dev/stan.git for code.
It looks to me as if there are substantial parts of the source that
should not be in the debian source;
http://www.debian.org/doc/manuals/developers-reference/best-pkging-practices.html#bpp-origtargz
indicates this is possible, but not generally advisable. I'd
appreciate feedback on how to handle this both in policy terms--what
if any parts should I omit, and practical terms--best mechanics of
doing this with an upstream git. Most of the other packaging
documentation I've reviewed is silent on this topic (except for
mentioning some git-specific helpers).
In particular, stan includes a lib directory of external libraries.
I assume a debian package should use already packaged versions of
those libraries. I'm assuming stan has not locally modified the
libraries.
Also, rstan includes stan as a subproject; I assume I would package
the source would not. Though perhaps one source could be used to
build stan and rstan.
The system itself is fairly complicated; stan works by translating a
program into C++ and then compiling the program at run-time. Also, it
includes a library as well as a front-end program.
rstan an R package designed to call stan from R. It is set
up so that one downloads the R package and, while installing it in R,
the whole stan system gets built (so the R library source includes all
of stan).
The directory structure of rstan is a bit odd; the "real" R library
source is in
https://github.com/stan-dev/rstan/tree/develop/rstan/rstan, with the
higher directories having meta-stuff (maybe the web page and tools for
building the package including stan).
I'm not a debian developer, but I figured since I was interested in
using the package I might as well try to package it. stan is not
listed for wnpp.
Comments or suggestions welcome.
Thanks.
Ross Boylan
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