[Bioc-devel] Package submission with library requirement

Wed Jan 21 19:48:47 CET 2015

Yes. I tried R internal libraries for random number generator also those
provided by Rcpp but they are were not thread safe so it with
multi-threading. I can try using other libraries, if anyone know random
generator that are thread safe and not slow.

thanks
avi

On Wed, Jan 21, 2015 at 7:38 PM, Martin Morgan <mtmorgan at fredhutch.org>
wrote:

> 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]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>
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