[GenABEL-dev] genabel-devel Digest, Vol 58, Issue 1

L.C. Karssen lennart at karssen.org
Fri Oct 9 09:25:09 CEST 2015 

Hi Xia,

On 07-10-15 16:12, Xia Shen wrote:
> These are good suggestions by Lennart, Yurii and Lars.

Thank you.

> It would be
> nice that someone takes the responsibility to distribute the review
> job to reviewers, or we can at least have a list according to
> Lennart’s point 1) about how many review tasks each author “owes” the
> others.

Good point. I will keep that list. Do we want to store it anywhere
public (like on our SVN server)? Or rather keep it just with me?

> 
> I’ve accepted to review RegionABEL and RepeatABEL, and I should
> apologize for any delay in these processes.. So I suggest there
> should also be some sort of deadline for the review task - at least
> myself seem to need that!

Ah, yes. That is a good point as well. You seem to know yourself well
;-). In fact, the same goes for me sometimes.
What about two weeks, would that be a reasonable period? Or is four
weeks better?

For now I will take that task upon my shoulders (although I wouldn't
mind if someone took it over).


Best,

Lennart.

> 
> Xia
> 
>> On 07 Oct 2015, at 12:00,
>> genabel-devel-request at lists.r-forge.r-project.org wrote:
>> 
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>> 
>> Today's Topics:
>> 
>> 1. Improving the process of contributing to GenABEL (L.C. Karssen) 
>> 2. Re: Improving the process of contributing to GenABEL (Lars
>> R?nneg?rd)
>> 
>> 
>> ----------------------------------------------------------------------
>>
>>
>> 
Message: 1
>> Date: Tue, 6 Oct 2015 12:34:39 +0200 From: "L.C. Karssen"
>> <lennart at karssen.org> To: genabel-devel
>> <genabel-devel at lists.r-forge.r-project.org> Subject: [GenABEL-dev]
>> Improving the process of contributing to GenABEL Message-ID:
>> <5613A3BF.1020907 at karssen.org> Content-Type: text/plain;
>> charset="utf-8"
>> 
>> Dear list,
>> 
>> In the past few months we have seen several packages being proposed
>> on this list, which is a great thing! However, we also observed
>> that finding people willing to do package reviews was difficult.
>> Obviously, we would like to improve this.
>> 
>> Yurii and I have discussed this recently and we came up with the 
>> following ideas:
>> 
>> 1) Require from every author of a package that is accepted into
>> the GenABEL suite to review at least two packages. [NOTE in case we
>> want two reviewers for each package we should require four packages
>> to be reviewed]
>> 
>> 2) In order to create a visible record of package review activities
>> the reviews for the accepted packages could be posted online and
>> given a DOI (e.g. via zenodo.org). This means that reviews can also
>> add "Technical review for the GenABEL project" to their CVs.
>> 
>> 3) Instate a contributor/maintainer agreement similar to the one
>> from Bioconductor [1]. In this agreement we can not only
>> incorporate point 1), but also the fact that we expect authors to
>> maintain their package and provide user support on the forum.
>> 
>> To start the discussion, what do you think about the following
>> text: ------------------------------------------------------- 
>> Package Author and Maintainer Responsibilities
>> 
>> Acceptance of packages into the GenABEL suit brings with it
>> ongoing responsibility for package maintenance. These
>> responsibilities include: - Subscription to the GenABEL-devel
>> mailing list. - Registration on the forum
>> (http://forum.genabel.org) - Response to bug reports and questions
>> from users regarding your package, as posted on the GenABEL forum
>> or directly to developers. - Package maintenance through software
>> release cycles, including prompt updates to software and
>> documentation necessitated by e.g. underlying changes in R,
>> compiler, libraries etc. - If you do not take the opportunity to
>> maintain a web page for your package on www.genabel.org (see
>> below), you should provide a URL of the released package and most
>> up-to-date source code (e.g. link to the CRAN page would be enough
>> for this purpose); this URL will be put on the genabel.org site. -
>> The licence that covers you package should be one of the standard
>> open source licences accepted by CRAN [3] (even if you package is
>> not an R package).
>> 
>> You also will be given the opportunity (and we encourage everyone
>> to use it) to: - Maintain the package page on the genabel.org site
>> (see e.g. [2]) - Use GenABEL R-forge for bug tracking (you will
>> need to register on R-forge in order to use this functionality) -
>> Keep version control of the source code using GenABEL R-forge SVN
>> 
>> -------------------------------------------------------
>> 
>> 
>> Looking forward to your opinions,
>> 
>> Lennart & Yurii.
>> 
>> 
>> [1]
>> http://bioconductor.org/developers/package-guidelines/#responsibilities
>>
>> 
[2] http://www.genabel.org/packages/PredictABEL
>> [3] https://svn.r-project.org/R/trunk/share/licenses/license.db
>> 
>> -- *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* L.C. Karssen 
>> Utrecht The Netherlands
>> 
>> lennart at karssen.org http://blog.karssen.org GPG key ID: A88F554A 
>> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>> 
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>> 
------------------------------
>> 
>> Message: 2 Date: Wed, 7 Oct 2015 08:17:02 +0000 From: Lars
>> R?nneg?rd <lrn at du.se> To:
>> "genabel-devel at lists.r-forge.r-project.org" 
>> <genabel-devel at lists.r-forge.r-project.org> Subject: Re:
>> [GenABEL-dev] Improving the process of contributing to GenABEL 
>> Message-ID: <1444205844728.29192 at du.se> Content-Type: text/plain;
>> charset="iso-8859-1"
>> 
>> This seems to me to be an excellent way of setting up a system
>> where packages can be contributed, reviewed and maintained. The
>> difficulty seems to be to find reviewers for proposed packages to
>> be included within the GenABEL suite (which I have experienced
>> myself), and ideas 1)-2) below should get a review system rolling.
>> 
>> Perhaps there also should be someone responsible for distributing
>> the review jobs? Not that I believe that there is any reason to
>> have the reviewers anonymous, but just to make the process a bit
>> more fluent. This is a responsibility I guess someone would like to
>> have on their CV too (if we come up with a good name for this
>> position, and if the responsibility is time limited).
>> 
>> Any other ideas?
>> 
>> Best regards, Lars R?nneg?rd
>> 
>> 
>> ________________________________________ From:
>> genabel-devel-bounces at lists.r-forge.r-project.org
>> <genabel-devel-bounces at lists.r-forge.r-project.org> on behalf of
>> L.C. Karssen <lennart at karssen.org> Sent: Tuesday, October 6, 2015
>> 12:34 To: genabel-devel Subject: [GenABEL-dev] Improving the
>> process of contributing to GenABEL
>> 
>> Dear list,
>> 
>> In the past few months we have seen several packages being proposed
>> on this list, which is a great thing! However, we also observed
>> that finding people willing to do package reviews was difficult.
>> Obviously, we would like to improve this.
>> 
>> Yurii and I have discussed this recently and we came up with the 
>> following ideas:
>> 
>> 1) Require from every author of a package that is accepted into
>> the GenABEL suite to review at least two packages. [NOTE in case we
>> want two reviewers for each package we should require four packages
>> to be reviewed]
>> 
>> 2) In order to create a visible record of package review activities
>> the reviews for the accepted packages could be posted online and
>> given a DOI (e.g. via zenodo.org). This means that reviews can also
>> add "Technical review for the GenABEL project" to their CVs.
>> 
>> 3) Instate a contributor/maintainer agreement similar to the one
>> from Bioconductor [1]. In this agreement we can not only
>> incorporate point 1), but also the fact that we expect authors to
>> maintain their package and provide user support on the forum.
>> 
>> To start the discussion, what do you think about the following
>> text: ------------------------------------------------------- 
>> Package Author and Maintainer Responsibilities
>> 
>> Acceptance of packages into the GenABEL suit brings with it
>> ongoing responsibility for package maintenance. These
>> responsibilities include: - Subscription to the GenABEL-devel
>> mailing list. - Registration on the forum
>> (http://forum.genabel.org) - Response to bug reports and questions
>> from users regarding your package, as posted on the GenABEL forum
>> or directly to developers. - Package maintenance through software
>> release cycles, including prompt updates to software and
>> documentation necessitated by e.g. underlying changes in R,
>> compiler, libraries etc. - If you do not take the opportunity to
>> maintain a web page for your package on www.genabel.org (see
>> below), you should provide a URL of the released package and most
>> up-to-date source code (e.g. link to the CRAN page would be enough
>> for this purpose); this URL will be put on the genabel.org site. -
>> The licence that covers you package should be one of the standard
>> open source licences accepted by CRAN [3] (even if you package is
>> not an R package).
>> 
>> You also will be given the opportunity (and we encourage everyone
>> to use it) to: - Maintain the package page on the genabel.org site
>> (see e.g. [2]) - Use GenABEL R-forge for bug tracking (you will
>> need to register on R-forge in order to use this functionality) -
>> Keep version control of the source code using GenABEL R-forge SVN
>> 
>> -------------------------------------------------------
>> 
>> 
>> Looking forward to your opinions,
>> 
>> Lennart & Yurii.
>> 
>> 
>> [1]
>> http://bioconductor.org/developers/package-guidelines/#responsibilities
>>
>> 
[2] http://www.genabel.org/packages/PredictABEL
>> [3] https://svn.r-project.org/R/trunk/share/licenses/license.db
>> 
>> -- *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* 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-devel
>>
>>
>> 
End of genabel-devel Digest, Vol 58, Issue 1
>> ********************************************
> 
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> list genabel-devel at lists.r-forge.r-project.org 
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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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