[Bioc-devel] Package submission with library requirement

Marc Carlson mcarlson at fredhutch.org
Fri Jan 30 23:10:53 CET 2015

Hi Avinash,

So the argument for the importance of reproducible research *definitely* 
resonates with us here as it is a major goal of ours.  However while the 
decision to use the same library as your paper helps to make the 
immediate work more reproducible, it simultaneously hampers others from 
benefiting from that because of the engineering problems that it creates 
for end users.

Ultimately, this project has a longstanding commitment to try and 
provide not only a way for your previous work to be validated, but also 
a way for others to build upon and eventually extend that previous 
work.  And both of these goals are crucial if your package is to be 
valuable to the greater scientific community over the long term.

Anyhow I will try and work with you on our issue tracker to see if we 
can find a way to resolve this with you.  Thanks for contributing!


On 01/26/2015 08:14 AM, avinash sahu wrote:
> Hi Dan,
> Now I have included source code of the rsampl.h in the GOAL package.
> Although, rlecuyer is good candidate for random number generator, I
> currently avoid using it because I wanted results of our  submitted
> manuscript to be completely reproducible. I can reproduce the results using
> ransampl library by setting seed that I have stored. Changing to other
> random generator libraries will imply that I have recheck results of the
> manuscript are reproducible and possibly change some of them which is not
> possible at this stage. I will reserve that inclusion for the future. I
> have resubmitted the GOAL package.
> thanks
> avi
> On Fri, Jan 23, 2015 at 9:37 PM, Levi Waldron <levi.waldron at hunter.cuny.edu>
> wrote:
>> On Fri, Jan 23, 2015 at 1:58 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
>> wrote:
>>> However, you should consider using Rlecuyer as it has no external
>> dependencies (see Levi's post to this thread). Then your package should
>> build on windows.
>> I think so too - it's also a standard solution in R, implemented
>> natively in r-core's parallel library and suggested by the snow
>> library.  I used it in my pensim library before transitioning to
>> parallel, and have tested its streams on hyperthreaded CPUs and
>> clusters.
>> --
>> Levi Waldron
>> Assistant Professor of Biostatistics
>> City University of New York School of Public Health, Hunter College
>> 2180 3rd Ave Rm 538
>> New York NY 10035-4003
>> phone: 212-396-7747
>> www.waldronlab.org
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
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