[GenABEL-dev] Proposing the CollapsABEL R package for inclusion

[L.C. Karssen]

Dear Kaiyin,

A quick update on the package review: I'm having some troubles with my R
development environment. I hope to resolve them today so that I can
continue with my review of your package.


Lennart.

On 14-04-15 11:24, L.C. Karssen wrote:
> Dear Kaiyin,
> 
> 
> On 13-04-15 10:05, K. Zhong wrote:
>> Dear all,
>>
>> I have read through the technical review guidelines 
> 
> Thank you for that. Also thanks for bringing CollapsABEL back to our
> attention, unfortunately it fell of my radar.
> 
>> and I think
>> CollapsABEL satisfies all requirements except that `R CMD check` and `R
>> CMD check -as-cran` both produces one warning and two notes. The warning
>> is about my .git folder, which is for version control, and won¹t be
>> present once a binary package is built, so this is a non-issue. 
> 
> I agree.
> 
>> The notes
>> are about some ³global variable² that are not global at all, and this is a
>> known bug of `R CMD check` (see http://tinyurl.com/o9p6vxf for an
>> example). 
> 
> Aha. This is more reason for concern. From my own experience the CRAN
> staff is quite strickt. Thanks for looking into "prior art". Since the
> SE post you refer to is three years old and the GranovaGG package it
> relates to is now in CRAN, I agree that we should see if it gets
> accepted. However, be prepared to act in case of comments from CRAN.
> 
>>
>> So could anyone please review this package? The submission of our paper is
>> waiting on this. Thanks!
> 
> I will review the package today. I will also try to contact other
> potential reviewers directly.
> 
> 
> Best regards,
> 
> Lennart.
> 
>>
>>
>> Best regards,
>> Kaiyin ZHONG
>> ------------------
>> FMB, Erasmus MC
>> kaiyin.co.vu <http://kaiyin.co.vu>
>> k.zhong at erasmusmc.nl
>> kindlychung at gmail.com
>>
>>
>>
>>
>>
>>
>>
>>
>> On 23/02/15 14:42, "K. Zhong" <k.zhong at erasmusmc.nl> wrote:
>>
>>> Dear Lennart,
>>>
>>> At the moment I think it would be nice to keep the function as it is for
>>> current users of it and show them a message about the new package. Thank
>>> you for bringing this up.
>>>
>>> Best regards,
>>> Kaiyin ZHONG
>>> ------------------
>>> FMB, Erasmus MC
>>> kaiyin.co.vu <http://kaiyin.co.vu>
>>> k.zhong at erasmusmc.nl
>>> kindlychung at gmail.com
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 22/02/15 22:16, "L.C. Karssen" <lennart at karssen.org> wrote:
>>>
>>>> Dear Kaiyin,
>>>>
>>>> Thank you for your willingness to contribute to the GenABEL project.
>>>>
>>>> On 19-02-15 14:27, K. Zhong wrote:
>>>>> Dear all,
>>>>>
>>>>> I have recently finished an R package for compound heterozygosity
>>>>> analysis for microarray/NGS data. This package (named CollapsABEL)
>>>>> implements an extended version of the CDH test
>>>>>
>>>>> <http://journals.plos.org/plosone/article?id=10.1371/journal.pone.002814
>>>>> 5
>>>>>> (see
>>>>> DOI: 10.1371/journal.pone.0028145) in a flexible, efficient and user
>>>>> friendly way  and has already proved useful for our analysis with
>>>>> certain dermatology traits.
>>>>
>>>> That sounds interesting indeed! To me it sounds like a useful addition
>>>> to the GenABEL suite.
>>>>
>>>>> CDH test has been implemented before as a
>>>>> function in the GenABEL package, but due to the simplicity of the
>>>>> method
>>>>> itself and restriction from the data format it uses, it is practically
>>>>> not very useful. CollapsABEL overcomes these limitations and provides a
>>>>> nice streamlined solution in your hands, for which reason I think it
>>>>> would be a nice addition to the GenABEL family.
>>>>
>>>> Do you have a suggestion on what to do with the current CDH test in the
>>>> GenABEL package? Is it worth to spend time maintaining it, or should we
>>>> replace it with a message pointing people to CollapsABEL (of course
>>>> assuming CollapsABEL gets accepted into the GenaBEL suite)?
>>>>
>>>>>
>>>>> The project is hosted on
>>>>> bitbucket: https://bitbucket.org/kindlychung/collapsabel/overview
>>>>> The R manual and an extensive tutorial can be found here:
>>>>> https://bitbucket.org/kindlychung/collapsabel/downloads
>>>>
>>>> Thank you for providing these links.
>>>>
>>>>>
>>>>> If you are willing to review this package, please let me know.
>>>>
>>>> I hope someone will step forward to do this. If you don't get a reaction
>>>> in the coming few weeks, please feel free to send a reminder to the list.
>>>>
>>>>
>>>> Best regards,
>>>>
>>>> Lennart Karssen.
>>>>
>>>>>
>>>>>
>>>>> Best regards,
>>>>>
>>>>> Kaiyin ZHONG
>>>>> ------------------
>>>>> FMB, Erasmus MC
>>>>> kaiyin.co.vu <http://kaiyin.co.vu>
>>>>> k.zhong at erasmusmc.nl <mailto:k.zhong at erasmusmc.nl>
>>>>> kindlychung at gmail.com <mailto:kindlychung at gmail.com>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> genabel-devel mailing list
>>>>> genabel-devel at lists.r-forge.r-project.org
>>>>>
>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-dev
>>>>> e
>>>>> l
>>>>>
>>>>
>>>> -- 
>>>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
>>>> L.C. Karssen
>>>> Utrecht
>>>> The Netherlands
>>>>
>>>> lennart at karssen.org
>>>> http://blog.karssen.org
>>>> GPG key ID: A88F554A
>>>> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>>>>
>>>
>>
> 
> 
> 
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-- 
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

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