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

Fri May 22 16:52:50 CEST 2015

Dear Kaiyin,

Please find attached my review of the CollapsABEL package. All in all I
must say the package is well-written and I would be happy to include it
in the GenABEL suite once the issues mentioned in the review have been
dealt with.

With my apologies for the delay in the review process.
Best regards,

Lennart Karssen.

On 16-04-15 15:09, L.C. Karssen 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.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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>>
> 
> 
> 
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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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