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

[K. Zhong]

Dear Lennart, 

Concerning the R CMD check notes I reported last time, they are solved by
some hack found on stack overflow. The latest package passes all checks:

https://bitbucket.org/kindlychung/collapsabel/downloads/CollapsABEL_0.9.2.t
ar.gz

Best regards,
Kaiyin ZHONG
------------------
FMB, Erasmus MC
kaiyin.co.vu <http://kaiyin.co.vu>
k.zhong at erasmusmc.nl
kindlychung at gmail.com








On 16/04/15 15:09, "L.C. Karssen" <lennart at karssen.org> wrote:

>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.002
>>>>>>814
>>>>>> 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
>>>>> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>>>>>
>>>>
>>>
>> 
>> 
>> 
>> _______________________________________________
>> 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-deve
>>l
>> 
>
>-- 
>*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
>L.C. Karssen
>Utrecht
>The Netherlands
>
>lennart at karssen.org
>http://blog.karssen.org
>GPG key ID: A88F554A
>-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>