R install from GitHub? RStan Wiki on GitHub?

[Bob Carpenter]

For the next release:

1. (Jiqiang:) Would it be too much of a bother to move
RStan's Wiki from Google Code to GitHub?

We can replace the Wiki on Google Code with a link to GitHub
and update the Stan home page to point to GitHub's version.

2. Is it possible to install from GitHub? Here's a relevant
thread on stackoverflow:

http://stackoverflow.com/questions/9656016/how-to-install-development-version-of-r-packages-github-repository

It looks like with

library(devtools)

you get an

install_github()

function. But do we really want to have users install devtools?

- Bob

[Ben Goodrich]

On Thursday, May 30, 2013 6:56:12 PM UTC-4, Bob Carpenter wrote:

2.  Is it possible to install from GitHub?

Once we have tagged releases for rstan on GitHub, it wouldn't be so hard for a user to install. It would just be

1) Download from https://github.com/stan-dev/rstan/archive/vX.Y.Z.tar.gz
2) Follow the appropriate instructions for your platform / GUI to install from a local file

However, Mav does some additional processing to only include the parts of boost that we use when generating the rstan releases on Google Code (that Google wants to crack down on by January). So, they would be downloading a lot more than they need. Alternatively, we could just eliminate the parts of boost that we don't need from the stan-dev/stan repository.

Ben

[Jiqiang Guo]

Please see my answers below. 

--

Jiqiang 

On Thu, May 30, 2013 at 6:56 PM, Bob Carpenter <ca...@alias-i.com> wrote:

For the next release:

1.  (Jiqiang:) Would it be too much of a bother to move
RStan's Wiki from Google Code to GitHub?

This would not take much time. I will do that. 

 

We can replace the Wiki on Google Code with a link to GitHub
and update the Stan home page to point to GitHub's version.

2.  Is it possible to install from GitHub?    Here's a relevant
thread on stackoverflow:

  http://stackoverflow.com/questions/9656016/how-to-install-development-version-of-r-packages-github-repository

It looks like with

  library(devtools)

you get an

  install_github()

function.  But do we really want to have users install devtools?

Not possible.  The way install_github() works is to download the zip file from github and then work from that zip file.  But this zip file does not contain stan/lib and stan/src. 

- Bob




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[Jiqiang Guo]

Yeah.  I forgot that part I did that.  And that is why the whole rstan is just about 4M now. 

[Ben Goodrich]

On Thursday, May 30, 2013 7:21:32 PM UTC-4, Jiqiang Guo wrote:

Not possible.  The way install_github() works is to download the zip file from github and then work from that zip file.  But this zip file does not contain stan/lib and stan/src. 

I forgot about that. We could, in principle, have the install script for rstan download the corresponding branch of stan-dev/stan before proceeding.

Ben

[Ben Goodrich]

Mav, have you considered making Stan a subtree rather than a submodule? Subtrees got added to recent versions of git

https://github.com/apenwarr/git-subtree/blob/master/git-subtree.txt

Ben

[Jiqiang Guo]

I did not know that :(

It would make rstan repo bigger, but then it is possible to use install_github() from package devtools. 

--

Jiqiang 

On Thu, May 30, 2013 at 7:34 PM, Ben Goodrich <goodri...@gmail.com> wrote:

Mav, have you considered making Stan a subtree rather than a submodule? Subtrees got added to recent versions of git

https://github.com/apenwarr/git-subtree/blob/master/git-subtree.txt

[Ben Goodrich]

Disk space is cheap these days, so I'd say it is worth it. Besides, at some point we should prune down boost from the main Stan repository.

Ben

[Jiqiang Guo]

I am experimenting git subtree.  I have not figure out how to easily switch between stan's branches if it is a subdirectory in rstan repo. 

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Jiqiang 

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[Ben Goodrich]

Would we ever need anything other than the master branch of Stan for RStan releases? I suppose if we are just fooling around, it might be nice to use another Stan branch but any of us can just symlink to the local copy of the Stan repo.

Ben

[Jiqiang Guo]

I thought mainly we are trying to let users be able to use develop branch easily if they want.  For master, if Google does not work in the future, we can stick the binary package to github and use install_url in package devtools, which is suboptimal but as good as using a subtree.  So I would prefer to keep the rstsn repo in its current way.

Jiqiang

[Ben Goodrich]

If that works it would be fine, but I thought GitHub was actually the first to prevent downloads of arbitrary files and Google Code was copying GitHub's policy?

[Jiqiang Guo]

For each file on github, you can access it through the "raw" method.  But github only does https, which is not supported by R's install.packages function. And that is why devtools uses package RCurl.  Currently Google code somehow allows http.  And we are not using Google code download for rstan, so I do not know if it will be shut down or not in the future.

Jiqiang

[Ben Goodrich]

OK, we can certainly continue downloading from Google Code for 7 months and figure out what is the best thing to do in the meantime.

[Ben Goodrich]

Previously, if ~/.R/Makevars had a CXX line, the installation of rstan would use that compiler. Now that we are ignoring the CFLAGS in ~/.R/Makevars it seems that CXX is ignored too; i.e. it uses g++ even if CXX=clang++. Is that avoidable without having to go into rstan locally and change things?

Ben

[Jiqiang Guo]

Only if you unset R_MAKEVARS_USERS (then ~/.R/Makevars is used) or let it point to a file you set CXX

Jiqiang

[Bob Carpenter]

On 5/31/13 10:02 AM, Jiqiang Guo wrote:
> I thought mainly we are trying to let users be able to use develop branch easily if they want.

That's even better than what I was suggesting.

I just want to migrate everything we currently host on
Google off of Google. As is, I think using Google Code
and GitHub is confusing to users (for instance, there are
still older versions of Stan on Google Code).

> For master, if Google
> does not work in the future, we can stick the binary package to github and use install_url in package devtools, which is
> suboptimal but as good as using a subtree. So I would prefer to keep the rstsn repo in its current way.

That's what I was afraid of from looking at the doc.
So we'll have to find some other anonymous host when we
need to if we can't just use GitHub.

- Bob

> Jiqiang
>
> Would we ever need anything other than the master branch of Stan for RStan releases? I suppose if we are just fooling
> around, it might be nice to use another Stan branch but any of us can just symlink to the local copy of the Stan repo.
>
> Ben
>
> On Thursday, May 30, 2013 10:52:10 PM UTC-4, Jiqiang Guo wrote:
>
> I am experimenting git subtree. I have not figure out how to easily switch between stan's branches if it is a
> subdirectory in rstan repo.
>
> --
> Jiqiang
>
> On Thu, May 30, 2013 at 9:13 PM, Ben Goodrich <goodri...@gmail.com> wrote:
>
> Disk space is cheap these days, so I'd say it is worth it. Besides, at some point we should prune down boost
> from the main Stan repository.
>
> Ben
>
>
>
> On Thursday, May 30, 2013 9:03:07 PM UTC-4, Jiqiang Guo wrote:
>
> I did not know that :(
>
> It would make rstan repo bigger, but then it is possible to use install_github() from package devtools.
>
> --
> Jiqiang
>
> On Thu, May 30, 2013 at 7:34 PM, Ben Goodrich <goodri...@gmail.com> wrote:
>
> Mav, have you considered making Stan a subtree rather than a submodule? Subtrees got added to recent
> versions of git
>

> https://github.com/apenwarr/__gi__t-subtree/blob/master/git-__subt__ree.txt
> <https://github.com/apenwarr/git-subtree/blob/master/git-subtree.txt>

>
>
>
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[Jiqiang Guo]

I added a R_Makevars in the same folder with the makefile used for build/install rstan.  In the makefile, R_MAKEVARS_USER points to the new file instead of the original empty string.  So you can change R_Makevars file, for example, for using CXX = clang++, if you use the makefile to install rstan.  

--

Jiqiang