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

Yurii Aulchenko yurii.aulchenko at gmail.com
Wed Oct 14 00:10:23 CEST 2015 

I have yet another suggestion: in principle, when a technical review is open, and the people who submit the package are publishing a paper, we could probably ask that a statement is added in the acknowledgements, something like: 

A technical review of the package XXX was performed by YYY, whose work was supported by grant ZZZ. 

What do you think? This is not claiming a co-authorship, but, still, I think the person who did the review could then use this for reporting. 

Please let me know what you think. 

best wishes,
Yurii

> On 10 Oct 2015, at 13:12, Yury Aulchenko <yurii.aulchenko at gmail.com> wrote:
> 
> Thank you Lars, Xia, for excellent suggestions! One comment below 
> 
>> On 09 Oct 2015, at 09:25, L.C. Karssen <lennart at karssen.org> wrote:
>> 
>> 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?
> 
> I think two weeks are better :)
> 
> Yurii 
> 
>> 
>> 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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>>>> genabel-devel at lists.r-forge.r-project.org
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>>>> 
>>>> When replying, please edit your Subject line so it is more
>>>> specific than "Re: Contents of genabel-devel digest..."
>>>> 
>>>> 
>>>> 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 
>>>> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>>>> 
>>>> -------------- next part -------------- A non-text attachment was
>>>> scrubbed... Name: signature.asc Type: application/pgp-signature 
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>>>> <http://lists.r-forge.r-project.org/pipermail/genabel-devel/attachments/20151006/9dff5f1e/attachment-0001.sig>
>> ------------------------------
>>>> 
>>>> 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
>>>> ********************************************
>>> 
>>> _______________________________________________ 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
>> -- 
>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
>> 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

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