[Bioc-devel] Package submission with library requirement
On 01/21/2015 11:16 AM, avinash sahu wrote:
Both the libraries are not thread safe. Although boost random genrator in limited situation can be thread safe. I have tried them earlier they were failing with multi-threading. One way out might be, if I include the source code of ransampl with package source code. There license allows this, I can also mail ask the developer of Ransampl about the permission. Will this be acceptable to bioconductor folks?
yes, provided the license of the library allows for it, it is a good solution.
There is guidance in RShowDoc("R-exts") on acknowledging this in the
DESCRIPTION (and possibly LICENSE) file.
Martin
thanks
avi
On Wed, Jan 21, 2015 at 7:57 PM, Steve Lianoglou <lianoglou.steve at gene.com
<mailto:lianoglou.steve at gene.com>> wrote:
Does the boost RNGs qualify?
He's a vignette showing how to use them through R/Rcpp
http://gallery.rcpp.org/articles/timing-normal-rngs/
Boost headers are provided via the BH library:
https://github.com/eddelbuettel/bh
-steve
On Wed, Jan 21, 2015 at 10:48 AM, avinash sahu <avinash.sahu at gmail.com
<mailto:avinash.sahu at gmail.com>> wrote:
> 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
<mailto: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
<mailto:dtenenba at fredhutch.org>>
>>> wrote:
>>>
>>> See my comments below.
>>>>
>>>> ----- Original Message -----
>>>>
>>>>> From: "avinash sahu" <avinash.sahu at gmail.com
<mailto:avinash.sahu at gmail.com>>
>>>>> To: "Karim Mezhoud" <kmezhoud at gmail.com <mailto:kmezhoud at gmail.com>>
>>>>> Cc: bioc-devel at r-project.org <mailto: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
<mailto: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/package?guidelines/
>>>>>>
>>>>>>
>>>>
>>>> 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/how?to/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
>>>>>>
>>>>>> ?__
>>>>>> c/ /'_;~~~~kmezhoud
>>>>>> (*) \(*) ????? ??????
>>>>>> http://bioinformatics.tn/
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Wed, Jan 21, 2015 at 2:24 PM, avinash sahu
>>>>>> <avinash.sahu at gmail.com <mailto: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 <mailto: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 <mailto: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 <mailto:Bioc-devel at r-project.org> mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
>>
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Steve Lianoglou
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Genentech
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