[GenABEL-dev] Proposal to remove non-EIGEN code paths from ProbABEL

[L.C. Karssen]

Great, it seems that we have a go-ahead for switching to an EIGEN-only
ProbABEL. I'll start with the removal of the relevant options in
configure.ac.

On 21-04-14 20:18, Maarten Kooyman wrote:
> 
> 
> On 18-04-14 16:35, L.C. Karssen wrote:
>> a) include a copy of the EIGEN source code in the ProbABEL code base (in
>> SVN)
> I strongly oppose to this option: we do not want to maintain this code
> and what should it do in our SVN?

I completely agree.

>> b) include a copy of the EIGEN source code in the official released
>> ProbABEL tar.gz.
> This seems to me as the most foolproof way to distribute ProbABEL as
> code: you control also the versions of dependencies which can be handy
> compared to run into old versions of libraries. This  results sometime
> in faulty binaries or non compiling set ups . Licence wise it looks
> all-right to me (however, I am not a OSS lawyer).

I still want to check that in more detail. I'll post my conclusions in
this thread.

> The EIGEN source files
> as provided on the website are about a megabyte: this should not be a
> problem for distribution. 

Indeed. Size is not an issue for EIGEN. For Boost you already noticed
the problem below.

> If you look at the boost library licence wise
> it seem also fine,

I agree.

> however the download provided as on there site is 60
> megabyte: quite a download! We have to trim down this size one way or an
> other.

Yes, that's my point. That's one more reason why I am not too happy with
'distribution with ProbABEL options'. On the other hand, we may decide
to have a different policy for EIGEN than for Boost.


> 
>> c) don't include the EIGEN source code, but provide very clear
>> instructions on how to obtain EIGEN.
> Reading manuals is often not done. Also this makes it harder for
> inexperience computer user and rises the bar for usage.

True, people don't read. On the other hand, how many 'inexperienced'
users do we have? Probably quite some, but I'm quite sure they don't
know about the ./configure; make; make install steps either. Moreover,
in order to install it themselves (without root privileges), they need
to know about the ./configure --prefix option. Which is also in the
documentation.
So, all in all, I'm not so sure 'inexperienced' users will be able to
successfully compile install ProbABEL without at least some reading.
How about adding (a copy of) the necessary steps to the ProbABEL website
as well? That way users will find them when looking for the source.

> 
>> d) include a script that downloads and extracts the latest EIGEN and
>> mention that script in the installation instructions.
> 
>> e) Automatic download and extraction of the EIGEN source code during the
>> ./configure (or make) process of ProbABEL.
> Sounds nice but right now I have problems to download EIGEN from there
> server.  Maybe we should host the software ourself. 

Hmm, doesn't that (somewhat) contradict what you wrote under a) about
not wanting to host the code ourselves?

> This still causes
> size problems for downloading boost. Option E is as a workflow easier
> then options D. However, this downloading can be buggy since you not
> sure wget/curl is installed on the users system. (This needs also direct
> internet connection to the WWW and this not always the cause on some
> servers)

Yup.

> 
> 
> Why do we not provide a statically  executable? We have Jenkins in place
> to perform the builds.
> 

That's a good suggestion (or actually two). We can certainly do that. I
should also try to get download statistics for source packages (and
later the statically linked binaries) from the web server. That will
help us to get a better idea of which is used.


Thanks for your input! Hoping to see input from others as well on this
matter.


Best,

Lennart.

> 
> Kind regards,
> 
> Maarten
> 
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-- 
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L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
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