<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1251"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">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: <div class=""><br class=""></div><div class="">A technical review of the package XXX was performed by YYY, whose work was supported by grant ZZZ. </div><div class=""><br class=""></div><div class="">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. </div><div class=""><br class=""></div><div class="">Please let me know what you think. </div><div class=""><br class=""></div><div class="">best wishes,</div><div class="">Yurii<br class=""><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 10 Oct 2015, at 13:12, Yury Aulchenko <<a href="mailto:yurii.aulchenko@gmail.com" class="">yurii.aulchenko@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Thank you Lars, Xia, for excellent suggestions! One comment below<span class="Apple-converted-space"> </span></span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">On 09 Oct 2015, at 09:25, L.C. Karssen <<a href="mailto:lennart@karssen.org" class="">lennart@karssen.org</a>> wrote:<br class=""><br class="">Hi Xia,<br class=""><br class=""><blockquote type="cite" class="">On 07-10-15 16:12, Xia Shen wrote:<br class="">These are good suggestions by Lennart, Yurii and Lars.<br class=""></blockquote><br class="">Thank you.<br class=""><br class=""><blockquote type="cite" class="">It would be<br class="">nice that someone takes the responsibility to distribute the review<br class="">job to reviewers, or we can at least have a list according to<br class="">Lennart’s point 1) about how many review tasks each author “owes” the<br class="">others.<br class=""></blockquote><br class="">Good point. I will keep that list. Do we want to store it anywhere<br class="">public (like on our SVN server)? Or rather keep it just with me?<br class=""><br class=""><blockquote type="cite" class=""><br class="">I’ve accepted to review RegionABEL and RepeatABEL, and I should<br class="">apologize for any delay in these processes.. So I suggest there<br class="">should also be some sort of deadline for the review task - at least<br class="">myself seem to need that!<br class=""></blockquote><br class="">Ah, yes. That is a good point as well. You seem to know yourself well<br class="">;-). In fact, the same goes for me sometimes.<br class="">What about two weeks, would that be a reasonable period? Or is four<br class="">weeks better?<br class=""></blockquote><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">I think two weeks are better :)</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Yurii<span class="Apple-converted-space"> </span></span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br class="">For now I will take that task upon my shoulders (although I wouldn't<br class="">mind if someone took it over).<br class=""><br class=""><br class="">Best,<br class=""><br class="">Lennart.<br class=""><br class=""><blockquote type="cite" class=""><br class="">Xia<br class=""><br class=""><blockquote type="cite" class="">On 07 Oct 2015, at 12:00,<br class=""><a href="mailto:genabel-devel-request@lists.r-forge.r-project.org" class="">genabel-devel-request@lists.r-forge.r-project.org</a> wrote:<br class=""><br class="">Send genabel-devel mailing list submissions to<span class="Apple-converted-space"> </span><br class=""><a href="mailto:genabel-devel@lists.r-forge.r-project.org" class="">genabel-devel@lists.r-forge.r-project.org</a><br class=""><br class="">To subscribe or unsubscribe via the World Wide Web, visit<span class="Apple-converted-space"> </span><br class="">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel<br class=""></blockquote></blockquote>or, via email, send a message with subject or body 'help' to<br class=""><blockquote type="cite" class=""><blockquote type="cite" class=""><a href="mailto:genabel-devel-request@lists.r-forge.r-project.org" class="">genabel-devel-request@lists.r-forge.r-project.org</a><br class=""><br class="">You can reach the person managing the list at<span class="Apple-converted-space"> </span><br class="">genabel-devel-owner@lists.r-forge.r-project.org<br class=""><br class="">When replying, please edit your Subject line so it is more<br class="">specific than "Re: Contents of genabel-devel digest..."<br class=""><br class=""><br class="">Today's Topics:<br class=""><br class="">1. Improving the process of contributing to GenABEL (L.C. Karssen)<span class="Apple-converted-space"> </span><br class="">2. Re: Improving the process of contributing to GenABEL (Lars<br class="">R?nneg?rd)<br class=""><br class=""><br class="">----------------------------------------------------------------------<br class=""></blockquote></blockquote>Message: 1<br class=""><blockquote type="cite" class=""><blockquote type="cite" class="">Date: Tue, 6 Oct 2015 12:34:39 +0200 From: "L.C. Karssen"<br class=""><<a href="mailto:lennart@karssen.org" class="">lennart@karssen.org</a>> To: genabel-devel<br class=""><<a href="mailto:genabel-devel@lists.r-forge.r-project.org" class="">genabel-devel@lists.r-forge.r-project.org</a>> Subject: [GenABEL-dev]<br class="">Improving the process of contributing to GenABEL Message-ID:<br class=""><<a href="mailto:5613A3BF.1020907@karssen.org" class="">5613A3BF.1020907@karssen.org</a>> Content-Type: text/plain;<br class="">charset="utf-8"<br class=""><br class="">Dear list,<br class=""><br class="">In the past few months we have seen several packages being proposed<br class="">on this list, which is a great thing! However, we also observed<br class="">that finding people willing to do package reviews was difficult.<br class="">Obviously, we would like to improve this.<br class=""><br class="">Yurii and I have discussed this recently and we came up with the<span class="Apple-converted-space"> </span><br class="">following ideas:<br class=""><br class="">1) Require from every author of a package that is accepted into<br class="">the GenABEL suite to review at least two packages. [NOTE in case we<br class="">want two reviewers for each package we should require four packages<br class="">to be reviewed]<br class=""><br class="">2) In order to create a visible record of package review activities<br class="">the reviews for the accepted packages could be posted online and<br class="">given a DOI (e.g. via <a href="http://zenodo.org" class="">zenodo.org</a>). This means that reviews can also<br class="">add "Technical review for the GenABEL project" to their CVs.<br class=""><br class="">3) Instate a contributor/maintainer agreement similar to the one<br class="">from Bioconductor [1]. In this agreement we can not only<br class="">incorporate point 1), but also the fact that we expect authors to<br class="">maintain their package and provide user support on the forum.<br class=""><br class="">To start the discussion, what do you think about the following<br class="">text: -------------------------------------------------------<span class="Apple-converted-space"> </span><br class="">Package Author and Maintainer Responsibilities<br class=""><br class="">Acceptance of packages into the GenABEL suit brings with it<br class="">ongoing responsibility for package maintenance. These<br class="">responsibilities include: - Subscription to the GenABEL-devel<br class="">mailing list. - Registration on the forum<br class="">(<a href="http://forum.genabel.org" class="">http://forum.genabel.org</a>) - Response to bug reports and questions<br class="">from users regarding your package, as posted on the GenABEL forum<br class="">or directly to developers. - Package maintenance through software<br class="">release cycles, including prompt updates to software and<br class="">documentation necessitated by e.g. underlying changes in R,<br class="">compiler, libraries etc. - If you do not take the opportunity to<br class="">maintain a web page for your package on <a href="http://www.genabel.org" class="">www.genabel.org</a> (see<br class="">below), you should provide a URL of the released package and most<br class="">up-to-date source code (e.g. link to the CRAN page would be enough<br class="">for this purpose); this URL will be put on the <a href="http://genabel.org" class="">genabel.org</a> site. -<br class="">The licence that covers you package should be one of the standard<br class="">open source licences accepted by CRAN [3] (even if you package is<br class="">not an R package).<br class=""><br class="">You also will be given the opportunity (and we encourage everyone<br class="">to use it) to: - Maintain the package page on the <a href="http://genabel.org" class="">genabel.org</a> site<br class="">(see e.g. [2]) - Use GenABEL R-forge for bug tracking (you will<br class="">need to register on R-forge in order to use this functionality) -<br class="">Keep version control of the source code using GenABEL R-forge SVN<br class=""><br class="">-------------------------------------------------------<br class=""><br class=""><br class="">Looking forward to your opinions,<br class=""><br class="">Lennart & Yurii.<br class=""><br class=""><br class="">[1]<br class=""><a href="http://bioconductor.org/developers/package-guidelines/#responsibilities" class="">http://bioconductor.org/developers/package-guidelines/#responsibilities</a><br class=""></blockquote></blockquote>[2] <a href="http://www.genabel.org/packages/PredictABEL" class="">http://www.genabel.org/packages/PredictABEL</a><br class=""><blockquote type="cite" class=""><blockquote type="cite" class="">[3] <a href="https://svn.r-project.org/R/trunk/share/licenses/license.db" class="">https://svn.r-project.org/R/trunk/share/licenses/license.db</a><br class=""><br class="">-- *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* L.C. Karssen<span class="Apple-converted-space"> </span><br class="">Utrecht The Netherlands<br class=""><br class=""><a href="mailto:lennart@karssen.org" class="">lennart@karssen.org</a> <a href="http://blog.karssen.org" class="">http://blog.karssen.org</a> GPG key ID: A88F554A<span class="Apple-converted-space"> </span><br class="">-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-<br class=""><br class="">-------------- next part -------------- A non-text attachment was<br class="">scrubbed... Name: signature.asc Type: application/pgp-signature<span class="Apple-converted-space"> </span><br class="">Size: 213 bytes Desc: OpenPGP digital signature URL:<br class=""><<a href="http://lists.r-forge.r-project.org/pipermail/genabel-devel/attachments/20151006/9dff5f1e/attachment-0001.sig" class="">http://lists.r-forge.r-project.org/pipermail/genabel-devel/attachments/20151006/9dff5f1e/attachment-0001.sig</a>><br class=""></blockquote></blockquote>------------------------------<br class=""><blockquote type="cite" class=""><blockquote type="cite" class=""><br class="">Message: 2 Date: Wed, 7 Oct 2015 08:17:02 +0000 From: Lars<br class="">R?nneg?rd <<a href="mailto:lrn@du.se" class="">lrn@du.se</a>> To:<br class="">"<a href="mailto:genabel-devel@lists.r-forge.r-project.org" class="">genabel-devel@lists.r-forge.r-project.org</a>"<span class="Apple-converted-space"> </span><br class=""><<a href="mailto:genabel-devel@lists.r-forge.r-project.org" class="">genabel-devel@lists.r-forge.r-project.org</a>> Subject: Re:<br class="">[GenABEL-dev] Improving the process of contributing to GenABEL<span class="Apple-converted-space"> </span><br class="">Message-ID: <<a href="mailto:1444205844728.29192@du.se" class="">1444205844728.29192@du.se</a>> Content-Type: text/plain;<br class="">charset="iso-8859-1"<br class=""><br class="">This seems to me to be an excellent way of setting up a system<br class="">where packages can be contributed, reviewed and maintained. The<br class="">difficulty seems to be to find reviewers for proposed packages to<br class="">be included within the GenABEL suite (which I have experienced<br class="">myself), and ideas 1)-2) below should get a review system rolling.<br class=""><br class="">Perhaps there also should be someone responsible for distributing<br class="">the review jobs? Not that I believe that there is any reason to<br class="">have the reviewers anonymous, but just to make the process a bit<br class="">more fluent. This is a responsibility I guess someone would like to<br class="">have on their CV too (if we come up with a good name for this<br class="">position, and if the responsibility is time limited).<br class=""><br class="">Any other ideas?<br class=""><br class="">Best regards, Lars R?nneg?rd<br class=""><br class=""><br class="">________________________________________ From:<br class=""><a href="mailto:genabel-devel-bounces@lists.r-forge.r-project.org" class="">genabel-devel-bounces@lists.r-forge.r-project.org</a><br class=""><genabel-devel-bounces@lists.r-forge.r-project.org> on behalf of<br class="">L.C. Karssen <lennart@karssen.org> Sent: Tuesday, October 6, 2015<br class="">12:34 To: genabel-devel Subject: [GenABEL-dev] Improving the<br class="">process of contributing to GenABEL<br class=""><br class="">Dear list,<br class=""><br class="">In the past few months we have seen several packages being proposed<br class="">on this list, which is a great thing! However, we also observed<br class="">that finding people willing to do package reviews was difficult.<br class="">Obviously, we would like to improve this.<br class=""><br class="">Yurii and I have discussed this recently and we came up with the<span class="Apple-converted-space"> </span><br class="">following ideas:<br class=""><br class="">1) Require from every author of a package that is accepted into<br class="">the GenABEL suite to review at least two packages. [NOTE in case we<br class="">want two reviewers for each package we should require four packages<br class="">to be reviewed]<br class=""><br class="">2) In order to create a visible record of package review activities<br class="">the reviews for the accepted packages could be posted online and<br class="">given a DOI (e.g. via zenodo.org). This means that reviews can also<br class="">add "Technical review for the GenABEL project" to their CVs.<br class=""><br class="">3) Instate a contributor/maintainer agreement similar to the one<br class="">from Bioconductor [1]. In this agreement we can not only<br class="">incorporate point 1), but also the fact that we expect authors to<br class="">maintain their package and provide user support on the forum.<br class=""><br class="">To start the discussion, what do you think about the following<br class="">text: -------------------------------------------------------<span class="Apple-converted-space"> </span><br class="">Package Author and Maintainer Responsibilities<br class=""><br class="">Acceptance of packages into the GenABEL suit brings with it<br class="">ongoing responsibility for package maintenance. These<br class="">responsibilities include: - Subscription to the GenABEL-devel<br class="">mailing list. - Registration on the forum<br class="">(http://forum.genabel.org) - Response to bug reports and questions<br class="">from users regarding your package, as posted on the GenABEL forum<br class="">or directly to developers. - Package maintenance through software<br class="">release cycles, including prompt updates to software and<br class="">documentation necessitated by e.g. underlying changes in R,<br class="">compiler, libraries etc. - If you do not take the opportunity to<br class="">maintain a web page for your package on www.genabel.org (see<br class="">below), you should provide a URL of the released package and most<br class="">up-to-date source code (e.g. link to the CRAN page would be enough<br class="">for this purpose); this URL will be put on the genabel.org site. -<br class="">The licence that covers you package should be one of the standard<br class="">open source licences accepted by CRAN [3] (even if you package is<br class="">not an R package).<br class=""><br class="">You also will be given the opportunity (and we encourage everyone<br class="">to use it) to: - Maintain the package page on the genabel.org site<br class="">(see e.g. [2]) - Use GenABEL R-forge for bug tracking (you will<br class="">need to register on R-forge in order to use this functionality) -<br class="">Keep version control of the source code using GenABEL R-forge SVN<br class=""><br class="">-------------------------------------------------------<br class=""><br class=""><br class="">Looking forward to your opinions,<br class=""><br class="">Lennart & Yurii.<br class=""><br class=""><br class="">[1]<br class="">http://bioconductor.org/developers/package-guidelines/#responsibilities<br class=""></blockquote></blockquote>[2] <a href="http://www.genabel.org/packages/PredictABEL" class="">http://www.genabel.org/packages/PredictABEL</a><br class=""><blockquote type="cite" class=""><blockquote type="cite" class="">[3] <a href="https://svn.r-project.org/R/trunk/share/licenses/license.db" class="">https://svn.r-project.org/R/trunk/share/licenses/license.db</a><br class=""><br class="">-- *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* L.C. Karssen<span class="Apple-converted-space"> </span><br class="">Utrecht The Netherlands<br class=""><br class=""><a href="mailto:lennart@karssen.org" class="">lennart@karssen.org</a> <a href="http://blog.karssen.org" class="">http://blog.karssen.org</a> GPG key ID: A88F554A<span class="Apple-converted-space"> </span><br class="">-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-<br class=""><br class=""><br class="">------------------------------<br class=""><br class="">_______________________________________________ genabel-devel<br class="">mailing list <a href="mailto:genabel-devel@lists.r-forge.r-project.org" class="">genabel-devel@lists.r-forge.r-project.org</a><span class="Apple-converted-space"> </span><br class=""><a href="https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel" class="">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel</a><br class=""></blockquote></blockquote>End of genabel-devel Digest, Vol 58, Issue 1<br class=""><blockquote type="cite" class=""><blockquote type="cite" class="">********************************************<br class=""></blockquote><br class="">_______________________________________________ genabel-devel mailing<br class="">list <a href="mailto:genabel-devel@lists.r-forge.r-project.org" class="">genabel-devel@lists.r-forge.r-project.org</a><span class="Apple-converted-space"> </span><br class=""><a href="https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel" class="">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel</a><br class=""></blockquote>--<span class="Apple-converted-space"> </span><br class="">*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*<br class="">L.C. Karssen<br class="">Utrecht<br class="">The Netherlands<br class=""><br class=""><a href="mailto:lennart@karssen.org" class="">lennart@karssen.org</a><br class="">http://blog.karssen.org<br class="">GPG key ID: A88F554A<br class="">-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-<br class=""><br class="">_______________________________________________<br class="">genabel-devel mailing list<br class="">genabel-devel@lists.r-forge.r-project.org<br class="">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel</blockquote></div></blockquote></div><br class=""></div></div></body></html>