[Bioc-devel] Package submission with library requirement

[Martin Morgan]

On 01/21/2015 10:17 AM, avinash sahu wrote:
> Hi Dan,
>
> Thanks for the reply and quick support. I am sorry for so many issues, I am
> somewhat novice in bioconductor.  I am replying to your comments inline.
>
>
> On Wed, Jan 21, 2015 at 6:55 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
> wrote:
>
>> See my comments below.
>>
>> ----- Original Message -----
>>> From: "avinash sahu" <avinash.sahu at gmail.com>
>>> To: "Karim Mezhoud" <kmezhoud at gmail.com>
>>> Cc: bioc-devel at r-project.org
>>> Sent: Wednesday, January 21, 2015 7:50:38 AM
>>> Subject: Re: [Bioc-devel] Package submission with library requirement
>>>
>>> Thanks for mail Karim.
>>>
>>> I have GOAL staisfies all guidelines.
>>> However, GOAL is not compiling in windows and because of its heavy
>>> computational  requirement its cannot be used with Windows.
>>
>> Can you please be very specific about why the package cannot be used with
>> windows? Wherever possible we want packages to run on all the platforms we
>> support. Have you attempted to compile it under windows and if so, what is
>> the problem you ran into?
>>
>
> Little bit of background first. GOAL is package, that will be a
> accompanying software for the manuscript that we are submitting to nature
> methods, so I would like to be as user friendly as possible. I spend couple
> of days to compile the package in Windows, however it is getting stuck
> because it uses Rcpp libraries along with third party libraries from other
> packages. I tried to get help from Windows regular user but it need someone
> expert in Windows OS to make it work. And I am no longer user of  Windows
> so completely novice in it.

have you thought carefully about the need for third-party libraries? For 
instance, R has extensive random number facilities, and these are available at 
the C level. This is documented in section 6 of RShowDoc("R-exts")

Martin

>
>>
>>> Regarding third party code, bioconductor website mentions (i.e.
>>> ransampl):
>>> "In cases where the external library is complex the author may need
>>> to
>>> supply pre-built binary versions for some platforms." How to provide
>>> such
>>> binaries for linux and Mac to bioconductor.
>>>
>>
>> I'm not sure you need to provide binaries for ransampl. However, can you
>> clarify the type of dependency that your package has on ransampl and GSL?
>> Is the dependency build-time only? If that is the case, then users on Mac
>> and Windows will not need to have ransampl and GSL installed, but they will
>> if they need them at runtime.
>>
>> I clarified in my dependencies that it requires ransampl and GSL.  In
> addition I added details in README about installation instruction of those
> libraries.
>
>>
>>
>>> thanks
>>> avi
>>>
>>> On Wed, Jan 21, 2015 at 2:39 PM, Karim Mezhoud <kmezhoud at gmail.com>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> Before you submit your package, please make sure that it satisfies
>>>> all our
>>>>
>>>> guidelines here.
>>>>
>>>> http://www.bioconductor.org/developers/package­guidelines/
>>>>
>>
>>
>> In the sense that Bioconductor is open source and belongs to everyone,
>> these are 'our' guidelines, but just to be clear, Karim is not affiliated
>> with the core team.
>>
>>
>>>> Be sure that you tested it with the appropriate version of R. To
>>>> work
>>>>
>>>> out which version that is, please have a look at this site here:
>>>>
>>>> http://www.bioconductor.org/developers/how­to/useDevel/
>>>>
>>>> Then use our tracking system for package submission (which can be
>>>>
>>>> found here):
>>>>
>>>> https://tracker.bioconductor.org/
>>>>
>>>> recommended video:
>>>> https://www.youtube.com/watch?v=QfqaK_BHebU
>>>>
>>>> Karim
>>>>
>>>>    Ô__
>>>>   c/ /'_;~~~~kmezhoud
>>>> (*) \(*)   ⴽⴰⵔⵉⵎ  ⵎⴻⵣⵀⵓⴷ
>>>> http://bioinformatics.tn/
>>>>
>>>>
>>>>
>>>> On Wed, Jan 21, 2015 at 2:24 PM, avinash sahu
>>>> <avinash.sahu at gmail.com>
>>>> wrote:
>>>>
>>>>> Hi all,
>>>>>
>>>>> I am trying to submit a package (https://github.com/vinash85/GOAL)
>>>>> in
>>>>> bioconductor. It requires a ransampl (
>>>>> http://sourceforge.net/projects/ransampl/) and gsl libraries
>>>>> already
>>>>> installed in system.
>>>>> The package is failing to install at automated package installer
>>>>> of
>>>>> bioconductor (
>>>>>
>>>>>
>> http://bioconductor.org/spb_reports/GOAL_0.99.0_buildreport_20150121045701.html
>>>>> ).
>>>>> How to take care of additional Libraries?
>>>>>
>>>>> Further, the package is meant for Linux and Mac ( it is NOT
>>>>> currently
>>>>> compiling in windows). Is it possible to submit the package in
>>>>> pre-compiled
>>>>> binaries form for Mac and Linux.
>>>>>
>>
>> I will install ransampl on our build machines (GSL is already installed).
>>
>> Dan
>>
>>
>>>>> This is the first package that I am submitting to BioConductor, so
>>>>> I am
>>>>> not
>>>>> aware of these issues.
>>>>>
>>>>> thanks in advance
>>>>> avi
>>>>>
>>>>>          [[alternative HTML version deleted]]
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>
>>>>
>>>>
>>>
>>>        [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>
> Regards
> Avi
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


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