Re: [PATCH 2/7] gnu: Add r-rbgl.

[Roel Janssen]

Ricardo Wurmus writes:

> Roel Janssen <address@hidden> writes:
>
>> Ricardo Wurmus writes:
>>
>>> Roel Janssen <address@hidden> writes:
>>>
>>>> * gnu/packages/bioinformatics.scm (r-rbgl): New variable.
>>>> ---
>>>>  gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++++++
>>>>  1 file changed, 24 insertions(+)
>>>>
>>>> diff --git a/gnu/packages/bioinformatics.scm 
>>>> b/gnu/packages/bioinformatics.scm
>>>> index ffb9692..3d607cc 100644
>>>> --- a/gnu/packages/bioinformatics.scm
>>>> +++ b/gnu/packages/bioinformatics.scm
>>>> @@ -5309,6 +5309,30 @@ packages.")
>>>>  CRAN, and (some) github packages.")
>>>>      (license license:artistic2.0)))
>>>>  
>>>> +(define-public r-rbgl
>>>> +  (package
>>>> +    (name "r-rbgl")
>>>> +    (version "1.49.3")
>>>> +    (source (origin
>>>> +              (method url-fetch)
>>>> +              (uri (string-append
>>>> +                    
>>>> "https://bioconductor.org/packages/3.4/bioc/src/contrib/";
>>>> +                    "RBGL_" version ".tar.gz"))
>>>
>>> Shouldn’t this be “(bioconductor-uri "RBGL" version)”?
>>
>> You are right, it should be “(bioconductor-uri "RBGL" version)”.
>
> Okay.  I’ll make the change before pushing.

If you want I can do the modifications as well and push.  Saves you some
valuable time :)

>>>> +              (sha256
>>>> +               (base32
>>>> +                "0rpiqpalbxk82jkwv3l0fimq9y2hrdi0f7ca4v21318541vfsncs"))))
>>>> +    (properties
>>>> +     `((upstream-name . "RBGL")))
>>>> +    (build-system r-build-system)
>>>> +    (propagated-inputs
>>>> +     `(("r-graph" ,r-graph)))
>>>> +    (home-page "http://bioconductor.org/packages/RBGL";)
>>>> +    (synopsis "Interface to the graph algorithms from Boost")
>>>> +    (description
>>>> +     "This package provides a fairly extensive and comprehensive 
>>>> interface to
>>>> +the graph algorithms contained in the Boost library.")
>>>> +    (license license:artistic2.0)))
>>>> +
>>>
>>> This package looks very familiar.  Chances are that I packaged this
>>> already and forgot about it… :)
>>
>> Do you whether you stripped the Boost source code in this package and
>> used the Boost library from Guix?  I wanted to do so, but couldn't
>> figure out how it gets build!  Plus, they use Boost 1.61.0 on this RBGL
>> release, and we are stuck at 1.60.0.
>
> I didn’t try to swap out the sources.  In my opinion this should be
> treated as a fork.  It’s a subset of Boost with R-specific adaptations.
> Other R packages may depend on this particular “flavour” and might not
> work well otherwise.
>
> If someone made the effort to change this, it would need to be checked
> each time we updated our Boost package.  I don’t think we have the
> infrastructure to keep track of these things, so I’d rather err on the
> side of keeping things as upstream has them.

Right.  I didn't compare the original boost sources with the one
provided with the RBGL package, so I didn't know there were differences
in code.

I agree to keep the "forked" Boost code instead of using the upstream
Boost code for additional reasons:

1. It makes the package recipe much simpler.
2. It keeps the package as the maintainer of RBGL meant to distribute
it.  The compile-time overhead is manageable (building the package on my
machine takes less than ten minutes).

I will take care of upstreaming this package and the other six I proposed.

Kind regards,
Roel Janssen