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

[Ricardo Wurmus]

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.

>>> +              (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.

~~ Ricardo