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

L.C. Karssen lennart at karssen.org
Wed Oct 14 14:23:36 CEST 2015 

Hi List,

On 14-10-15 00:10, Yurii Aulchenko wrote:
> 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. 

Sounds like a good idea to me. This increases visibility (while not
directly claiming precious authorships space) and still allows the
reviewer to show some form of accountability to funding organisations.
Of course, if package authors think the reviewer deserves an authorship
I have nothing against that :-).


Best,

Lennart.

> 
> Please let me know what you think. 
> 
> best wishes,
> Yurii
> 
>> On 10 Oct 2015, at 13:12, Yury Aulchenko <yurii.aulchenko at gmail.com
>> <mailto: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
>>> <mailto: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
>>>>> <mailto:genabel-devel-request at lists.r-forge.r-project.org> wrote:
>>>>>
>>>>> Send genabel-devel mailing list submissions to 
>>>>> genabel-devel at lists.r-forge.r-project.org
>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>>>
>>>>> To subscribe or unsubscribe via the World Wide Web, visit 
>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>> or, via email, send a message with subject or body 'help' to
>>>>> genabel-devel-request at lists.r-forge.r-project.org
>>>>> <mailto:genabel-devel-request at lists.r-forge.r-project.org>
>>>>>
>>>>> You can reach the person managing the list at 
>>>>> genabel-devel-owner at lists.r-forge.r-project.org
>>>>>
>>>>> 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 <mailto:lennart at karssen.org>> To: genabel-devel
>>>>> <genabel-devel at lists.r-forge.r-project.org
>>>>> <mailto: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
>>>>> <mailto: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 <http://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
>>>>> <http://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
>>>>> <http://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
>>>>> <http://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 <mailto: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 <mailto:lrn at du.se>> To:
>>>>> "genabel-devel at lists.r-forge.r-project.org
>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org>" 
>>>>> <genabel-devel at lists.r-forge.r-project.org
>>>>> <mailto: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
>>>>> <mailto: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
>>>>> <mailto: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 <mailto: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
>>>>> <mailto: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
>>>> <mailto: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 <mailto: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
> 

-- 
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
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/20151014/330784d5/attachment.sig>

More information about the genabel-devel mailing list