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

Yury Aulchenko yurii.aulchenko at gmail.com
Sat Oct 10 13:12:11 CEST 2015 

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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>>> 
>>> 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 
>>> Size: 213 bytes Desc: OpenPGP digital signature URL:
>>> <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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