From lennart at karssen.org Tue Oct 6 12:34:39 2015 From: lennart at karssen.org (L.C. Karssen) Date: Tue, 6 Oct 2015 12:34:39 +0200 Subject: [GenABEL-dev] Improving the process of contributing to GenABEL Message-ID: <5613A3BF.1020907@karssen.org> 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: From lrn at du.se Wed Oct 7 10:17:02 2015 From: lrn at du.se (=?iso-8859-1?Q?Lars_R=F6nneg=E5rd?=) Date: Wed, 7 Oct 2015 08:17:02 +0000 Subject: [GenABEL-dev] Improving the process of contributing to GenABEL In-Reply-To: <1444197108686.67934@du.se> References: <5613A3BF.1020907@karssen.org>,<1444197108686.67934@du.se> Message-ID: <1444205844728.29192@du.se> 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 on behalf of L.C. Karssen 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 -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- From shenxia911 at gmail.com Wed Oct 7 16:12:34 2015 From: shenxia911 at gmail.com (Xia Shen) Date: Wed, 7 Oct 2015 16:12:34 +0200 Subject: [GenABEL-dev] genabel-devel Digest, Vol 58, Issue 1 In-Reply-To: References: Message-ID: These are good suggestions by Lennart, Yurii and Lars. 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. 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! Xia > On 07 Oct 2015, at 12:00, 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 > > 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 > > 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" > To: genabel-devel > 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: > > ------------------------------ > > Message: 2 > Date: Wed, 7 Oct 2015 08:17:02 +0000 > From: Lars R?nneg?rd > To: "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 on behalf of L.C. Karssen > 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 > ******************************************** From lennart at karssen.org Fri Oct 9 09:25:09 2015 From: lennart at karssen.org (L.C. Karssen) Date: Fri, 9 Oct 2015 09:25:09 +0200 Subject: [GenABEL-dev] genabel-devel Digest, Vol 58, Issue 1 In-Reply-To: References: Message-ID: <56176BD5.7090809@karssen.org> 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: >> >> Send genabel-devel mailing list submissions to >> 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 >> >> 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" >> To: genabel-devel >> 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: >> >> >> >> ------------------------------ >> >> Message: 2 Date: Wed, 7 Oct 2015 08:17:02 +0000 From: Lars >> R?nneg?rd To: >> "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 >> on behalf of >> L.C. Karssen 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 -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 213 bytes Desc: OpenPGP digital signature URL: From yurii.aulchenko at gmail.com Sat Oct 10 13:12:11 2015 From: yurii.aulchenko at gmail.com (Yury Aulchenko) Date: Sat, 10 Oct 2015 13:12:11 +0200 Subject: [GenABEL-dev] genabel-devel Digest, Vol 58, Issue 1 In-Reply-To: <56176BD5.7090809@karssen.org> References: <56176BD5.7090809@karssen.org> Message-ID: Thank you Lars, Xia, for excellent suggestions! One comment below > On 09 Oct 2015, at 09:25, L.C. Karssen 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: >>> >>> Send genabel-devel mailing list submissions to >>> 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 >>> >>> 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" >>> To: genabel-devel >>> 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: >>> > ------------------------------ >>> >>> Message: 2 Date: Wed, 7 Oct 2015 08:17:02 +0000 From: Lars >>> R?nneg?rd To: >>> "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 >>> on behalf of >>> L.C. Karssen 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 From yurii.aulchenko at gmail.com Wed Oct 14 00:10:23 2015 From: yurii.aulchenko at gmail.com (Yurii Aulchenko) Date: Wed, 14 Oct 2015 00:10:23 +0200 Subject: [GenABEL-dev] genabel-devel Digest, Vol 58, Issue 1 In-Reply-To: References: <56176BD5.7090809@karssen.org> Message-ID: 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 wrote: > > Thank you Lars, Xia, for excellent suggestions! One comment below > >> On 09 Oct 2015, at 09:25, L.C. Karssen 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: >>>> >>>> Send genabel-devel mailing list submissions to >>>> 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 >>>> >>>> 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" >>>> To: genabel-devel >>>> 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: >>>> >> ------------------------------ >>>> >>>> Message: 2 Date: Wed, 7 Oct 2015 08:17:02 +0000 From: Lars >>>> R?nneg?rd To: >>>> "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 >>>> on behalf of >>>> L.C. Karssen 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From l.c.karssen at polyomica.com Wed Oct 14 14:20:54 2015 From: l.c.karssen at polyomica.com (L.C. Karssen) Date: Wed, 14 Oct 2015 14:20:54 +0200 Subject: [GenABEL-dev] Using advertisements (and other ways) to sponsor GenABEL Message-ID: <561E48A6.3040504@polyomica.com> Dear list, As you may have noticed over the past year(s) the contributions to the GenABEL project by Yurii and myself have steadily declined. The main reason for this is simple: lack of funding. We have started our own consulting business and although we have tried to include GenABEL into grant applications wherever we could, we haven't been able to secure any funds for this. On the other side of the balance we do have some fixed costs related to the hosting of the genabel.org website (and some flexible costs related to its maintenance). We therefore propose the following: 1) Given that www.genabel.org does receive a reasonable number of visitors per month we would like to add Google Ads to the pages. This may not generate a lot of revenue but anything many small bits can help (see e.g. [1]). Of course this will lead to a change in layout of the site, but we will try to make this a minimally disruptive as possible so as not to harm the user experience. Of course we understand that this can/should lead to a discussion about who owns/takes care of the incoming funds. We could set up a foundation under Dutch law to take care of that. However, that would require around ?3500 per year in accounting/reporting costs, etc. which is much more than we can invest (and more than we expect to earn from the ads). Therefore we would like to propose the following: Being the main sponsor of the Project PolyOmica will manage the funds (any payment will go to our bank account), and as part of our open policy we will provide a regular (quarterly? annual?) report to the community of the income generated and how it was spent (see e.g [2]). Any money that remains after covering these basic costs can be used to fund further development of the GenABEL Suite packages (maybe via one of the options listed below). We also thought of some alternative ways of generating some income: 2) Add a channel on bountysource.com [3] 3) Make the GenABEL Project a Team on Gratipay (formerly GitTip) [1,2,4,5] 4) Join http://flattr.com Does anyone have experience with any of these micropayment/crowdfunding providers? Please let us know what you think of these ideas. We would really love to make the Project more vibrant and sustainable than it currently is! Lennart & Yurii. [1] http://blogs.perl.org/users/peter_rabbitson/2014/02/i-bought-a-weekly-round-for-my-friends.html [2] http://inside.gratipay.com/appendices/finances [3] https://salt.bountysource.com [4] https://gratipay.com/ [5] https://medium.com/gratipay-blog/gratipay-2-0-2453d3c53077 -- *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* Lennart C. Karssen PolyOmica Groningen The Netherlands l.c.karssen at polyomica.com GPG key ID: 1A15AF2A -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 819 bytes Desc: OpenPGP digital signature URL: From lennart at karssen.org Wed Oct 14 14:23:36 2015 From: lennart at karssen.org (L.C. Karssen) Date: Wed, 14 Oct 2015 14:23:36 +0200 Subject: [GenABEL-dev] genabel-devel Digest, Vol 58, Issue 1 In-Reply-To: References: <56176BD5.7090809@karssen.org> Message-ID: <561E4948.50106@karssen.org> 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 > > wrote: >> >> Thank you Lars, Xia, for excellent suggestions! One comment below >> >>> On 09 Oct 2015, at 09:25, L.C. Karssen >> > 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: >>>>> >>>>> Send genabel-devel mailing list submissions to >>>>> 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 >>>>> >>>>> >>>>> 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" >>>>> > To: genabel-devel >>>>> >>>> > 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: >>>>> >>> ------------------------------ >>>>> >>>>> Message: 2 Date: Wed, 7 Oct 2015 08:17:02 +0000 From: Lars >>>>> R?nneg?rd > To: >>>>> "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 >>>>> >>>>> on behalf of >>>>> L.C. Karssen 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 > -- *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* 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: From lennart at karssen.org Wed Oct 14 14:24:43 2015 From: lennart at karssen.org (L.C. Karssen) Date: Wed, 14 Oct 2015 14:24:43 +0200 Subject: [GenABEL-dev] genabel-devel Digest, Vol 58, Issue 1 In-Reply-To: References: <56176BD5.7090809@karssen.org> Message-ID: <561E498B.40204@karssen.org> Hi all, On 10-10-15 13:12, Yury Aulchenko wrote: >> >> 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 :) OK, let's stick to two weeks then. Xia, your two weeks start now! :-) Lennart. > > 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: >>>> >>>> Send genabel-devel mailing list submissions to >>>> 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 >>>> >>>> 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" >>>> To: genabel-devel >>>> 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: >>>> >> ------------------------------ >>>> >>>> Message: 2 Date: Wed, 7 Oct 2015 08:17:02 +0000 From: Lars >>>> R?nneg?rd To: >>>> "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 >>>> on behalf of >>>> L.C. Karssen 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 -- *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* 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: From m.v.struchalin at mail.ru Thu Oct 15 00:57:50 2015 From: m.v.struchalin at mail.ru (Maksim Struchalin) Date: Thu, 15 Oct 2015 11:57:50 +1300 Subject: [GenABEL-dev] Using advertisements (and other ways) to sponsor GenABEL In-Reply-To: <561E48A6.3040504@polyomica.com> References: <561E48A6.3040504@polyomica.com> Message-ID: <262D9D28-AFD4-4961-A626-D73253B5D681@mail.ru> Hi Lennart & Yurii, The first thing I would do is to introduce a "donation button" in www.genabel.org like on wikipedia. So user can type his/her credit card info and donate some money. I donated some money to wikipedia recently and could do it very quickly through their donation button. Maksim Sent from my phone > On 15 ???. 2015 ?., at 1:20, "L.C. Karssen" wrote: > > Dear list, > > As you may have noticed over the past year(s) the contributions to the > GenABEL project by Yurii and myself have steadily declined. The main > reason for this is simple: lack of funding. We have started our own > consulting business and although we have tried to include GenABEL into > grant applications wherever we could, we haven't been able to secure any > funds for this. > > On the other side of the balance we do have some fixed costs related to > the hosting of the genabel.org website (and some flexible costs related > to its maintenance). > > We therefore propose the following: > > 1) Given that www.genabel.org does receive a reasonable number of > visitors per month we would like to add Google Ads to the pages. This > may not generate a lot of revenue but anything many small bits can help > (see e.g. [1]). > Of course this will lead to a change in layout of the site, but we will > try to make this a minimally disruptive as possible so as not to harm > the user experience. > > Of course we understand that this can/should lead to a discussion about > who owns/takes care of the incoming funds. We could set up a foundation > under Dutch law to take care of that. However, that would require around > ?3500 per year in accounting/reporting costs, etc. which is much more > than we can invest (and more than we expect to earn from the ads). > Therefore we would like to propose the following: Being the main sponsor > of the Project PolyOmica will manage the funds (any payment will go to > our bank account), and as part of our open policy we will provide a > regular (quarterly? annual?) report to the community of the income > generated and how it was spent (see e.g [2]). Any money that remains > after covering these basic costs can be used to fund further development > of the GenABEL Suite packages (maybe via one of the options listed below). > > > We also thought of some alternative ways of generating some income: > > 2) Add a channel on bountysource.com [3] > 3) Make the GenABEL Project a Team on Gratipay (formerly GitTip) [1,2,4,5] > 4) Join http://flattr.com > > Does anyone have experience with any of these micropayment/crowdfunding > providers? > > > Please let us know what you think of these ideas. We would really love > to make the Project more vibrant and sustainable than it currently is! > > > Lennart & Yurii. > > > [1] > http://blogs.perl.org/users/peter_rabbitson/2014/02/i-bought-a-weekly-round-for-my-friends.html > [2] http://inside.gratipay.com/appendices/finances > [3] https://salt.bountysource.com > [4] https://gratipay.com/ > [5] https://medium.com/gratipay-blog/gratipay-2-0-2453d3c53077 > > -- > *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* > Lennart C. Karssen > PolyOmica > Groningen > The Netherlands > > l.c.karssen at polyomica.com > GPG key ID: 1A15AF2A > -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- > > _______________________________________________ > 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 From yurii.aulchenko at gmail.com Thu Oct 15 09:44:56 2015 From: yurii.aulchenko at gmail.com (Yurii Aulchenko) Date: Thu, 15 Oct 2015 09:44:56 +0200 Subject: [GenABEL-dev] Using advertisements (and other ways) to sponsor GenABEL In-Reply-To: <262D9D28-AFD4-4961-A626-D73253B5D681@mail.ru> References: <561E48A6.3040504@polyomica.com> <262D9D28-AFD4-4961-A626-D73253B5D681@mail.ru> Message-ID: I agree with Maksim - this is very handy how wikipedia does that. In case people are willing to donate, it should be very simple to do - otherwise people will not do this (my personal experience :)) Yurii > On 15 Oct 2015, at 00:57, Maksim Struchalin wrote: > > Hi Lennart & Yurii, > > The first thing I would do is to introduce a "donation button" in www.genabel.org like on wikipedia. So user can type his/her credit card info and donate some money. I donated some money to wikipedia recently and could do it very quickly through their donation button. > > Maksim > > Sent from my phone > > > >> On 15 ???. 2015 ?., at 1:20, "L.C. Karssen" wrote: >> >> Dear list, >> >> As you may have noticed over the past year(s) the contributions to the >> GenABEL project by Yurii and myself have steadily declined. The main >> reason for this is simple: lack of funding. We have started our own >> consulting business and although we have tried to include GenABEL into >> grant applications wherever we could, we haven't been able to secure any >> funds for this. >> >> On the other side of the balance we do have some fixed costs related to >> the hosting of the genabel.org website (and some flexible costs related >> to its maintenance). >> >> We therefore propose the following: >> >> 1) Given that www.genabel.org does receive a reasonable number of >> visitors per month we would like to add Google Ads to the pages. This >> may not generate a lot of revenue but anything many small bits can help >> (see e.g. [1]). >> Of course this will lead to a change in layout of the site, but we will >> try to make this a minimally disruptive as possible so as not to harm >> the user experience. >> >> Of course we understand that this can/should lead to a discussion about >> who owns/takes care of the incoming funds. We could set up a foundation >> under Dutch law to take care of that. However, that would require around >> ?3500 per year in accounting/reporting costs, etc. which is much more >> than we can invest (and more than we expect to earn from the ads). >> Therefore we would like to propose the following: Being the main sponsor >> of the Project PolyOmica will manage the funds (any payment will go to >> our bank account), and as part of our open policy we will provide a >> regular (quarterly? annual?) report to the community of the income >> generated and how it was spent (see e.g [2]). Any money that remains >> after covering these basic costs can be used to fund further development >> of the GenABEL Suite packages (maybe via one of the options listed below). >> >> >> We also thought of some alternative ways of generating some income: >> >> 2) Add a channel on bountysource.com [3] >> 3) Make the GenABEL Project a Team on Gratipay (formerly GitTip) [1,2,4,5] >> 4) Join http://flattr.com >> >> Does anyone have experience with any of these micropayment/crowdfunding >> providers? >> >> >> Please let us know what you think of these ideas. We would really love >> to make the Project more vibrant and sustainable than it currently is! >> >> >> Lennart & Yurii. >> >> >> [1] >> http://blogs.perl.org/users/peter_rabbitson/2014/02/i-bought-a-weekly-round-for-my-friends.html >> [2] http://inside.gratipay.com/appendices/finances >> [3] https://salt.bountysource.com >> [4] https://gratipay.com/ >> [5] https://medium.com/gratipay-blog/gratipay-2-0-2453d3c53077 >> >> -- >> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* >> Lennart C. Karssen >> PolyOmica >> Groningen >> The Netherlands >> >> l.c.karssen at polyomica.com >> GPG key ID: 1A15AF2A >> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- >> >> _______________________________________________ >> 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 > _______________________________________________ > 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 From lennart at karssen.org Thu Oct 15 10:10:31 2015 From: lennart at karssen.org (L.C. Karssen) Date: Thu, 15 Oct 2015 10:10:31 +0200 Subject: [GenABEL-dev] Using advertisements (and other ways) to sponsor GenABEL In-Reply-To: References: <561E48A6.3040504@polyomica.com> <262D9D28-AFD4-4961-A626-D73253B5D681@mail.ru> Message-ID: <561F5F77.6060207@karssen.org> Hi Maksim, Yurii, Thanks for your input in the discussion. On 15-10-15 09:44, Yurii Aulchenko wrote: > I agree with Maksim - this is very handy how wikipedia does that. In case people are willing to donate, it should be very simple to do - otherwise people will not do this (my personal experience :)) > Sounds like a good option to me too, I hadn't thought of that. My question with this option is how payments are processed. Is there a company that provides this kind of button+service? And what do they charge? For Google and Gratipay I already found those details. The nice thing about Gratipay and BountySource.com is that you can more directly show/inform the audience what the money will be used for. With a donate button and Google Ads that is not so easy. Lennart. > Yurii > >> On 15 Oct 2015, at 00:57, Maksim Struchalin wrote: >> >> Hi Lennart & Yurii, >> >> The first thing I would do is to introduce a "donation button" in www.genabel.org like on wikipedia. So user can type his/her credit card info and donate some money. I donated some money to wikipedia recently and could do it very quickly through their donation button. >> >> Maksim >> >> Sent from my phone >> >> >> >>> On 15 ???. 2015 ?., at 1:20, "L.C. Karssen" wrote: >>> >>> Dear list, >>> >>> As you may have noticed over the past year(s) the contributions to the >>> GenABEL project by Yurii and myself have steadily declined. The main >>> reason for this is simple: lack of funding. We have started our own >>> consulting business and although we have tried to include GenABEL into >>> grant applications wherever we could, we haven't been able to secure any >>> funds for this. >>> >>> On the other side of the balance we do have some fixed costs related to >>> the hosting of the genabel.org website (and some flexible costs related >>> to its maintenance). >>> >>> We therefore propose the following: >>> >>> 1) Given that www.genabel.org does receive a reasonable number of >>> visitors per month we would like to add Google Ads to the pages. This >>> may not generate a lot of revenue but anything many small bits can help >>> (see e.g. [1]). >>> Of course this will lead to a change in layout of the site, but we will >>> try to make this a minimally disruptive as possible so as not to harm >>> the user experience. >>> >>> Of course we understand that this can/should lead to a discussion about >>> who owns/takes care of the incoming funds. We could set up a foundation >>> under Dutch law to take care of that. However, that would require around >>> ?3500 per year in accounting/reporting costs, etc. which is much more >>> than we can invest (and more than we expect to earn from the ads). >>> Therefore we would like to propose the following: Being the main sponsor >>> of the Project PolyOmica will manage the funds (any payment will go to >>> our bank account), and as part of our open policy we will provide a >>> regular (quarterly? annual?) report to the community of the income >>> generated and how it was spent (see e.g [2]). Any money that remains >>> after covering these basic costs can be used to fund further development >>> of the GenABEL Suite packages (maybe via one of the options listed below). >>> >>> >>> We also thought of some alternative ways of generating some income: >>> >>> 2) Add a channel on bountysource.com [3] >>> 3) Make the GenABEL Project a Team on Gratipay (formerly GitTip) [1,2,4,5] >>> 4) Join http://flattr.com >>> >>> Does anyone have experience with any of these micropayment/crowdfunding >>> providers? >>> >>> >>> Please let us know what you think of these ideas. We would really love >>> to make the Project more vibrant and sustainable than it currently is! >>> >>> >>> Lennart & Yurii. >>> >>> >>> [1] >>> http://blogs.perl.org/users/peter_rabbitson/2014/02/i-bought-a-weekly-round-for-my-friends.html >>> [2] http://inside.gratipay.com/appendices/finances >>> [3] https://salt.bountysource.com >>> [4] https://gratipay.com/ >>> [5] https://medium.com/gratipay-blog/gratipay-2-0-2453d3c53077 >>> >>> -- >>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* >>> Lennart C. Karssen >>> PolyOmica >>> Groningen >>> The Netherlands >>> >>> l.c.karssen at polyomica.com >>> GPG key ID: 1A15AF2A >>> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- >>> >>> _______________________________________________ >>> 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 >> _______________________________________________ >> 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 > > _______________________________________________ > 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: From m.v.struchalin at mail.ru Thu Oct 15 11:34:50 2015 From: m.v.struchalin at mail.ru (Maksim Struchalin) Date: Thu, 15 Oct 2015 22:34:50 +1300 Subject: [GenABEL-dev] Using advertisements (and other ways) to sponsor GenABEL In-Reply-To: <561F5F77.6060207@karssen.org> References: <561E48A6.3040504@polyomica.com> <262D9D28-AFD4-4961-A626-D73253B5D681@mail.ru> <561F5F77.6060207@karssen.org> Message-ID: <561F733A.7030406@mail.ru> Hi Lennart, I studied this issue a couple of years ago and my undertanding was at that time that there are many companies which provide such service because there are millions small internet shops in web. They make profit from taking about 5% from each transcation (not much). This might be usfull: https://www.paypal.com/webapps/mpp/get-started/donate-button . Also, you might adviertise this work on one of many websites where freelancers search their jobs and some of them might do it for say $50-$100-$200 (I can do it for $1000 :-) ). p.s. As alterntive, you can make it very simple: Advertises my bank account number on genabel.org as account number for all donations and I will take care of the rest :-). good luck, Maksim On 15/10/2015 21:10, L.C. Karssen wrote: > Hi Maksim, Yurii, > > Thanks for your input in the discussion. > > On 15-10-15 09:44, Yurii Aulchenko wrote: >> I agree with Maksim - this is very handy how wikipedia does that. In case people are willing to donate, it should be very simple to do - otherwise people will not do this (my personal experience :)) >> > Sounds like a good option to me too, I hadn't thought of that. > My question with this option is how payments are processed. Is there a > company that provides this kind of button+service? And what do they charge? > For Google and Gratipay I already found those details. > > The nice thing about Gratipay and BountySource.com is that you can more > directly show/inform the audience what the money will be used for. With > a donate button and Google Ads that is not so easy. > > > Lennart. > >> Yurii >> >>> On 15 Oct 2015, at 00:57, Maksim Struchalin wrote: >>> >>> Hi Lennart & Yurii, >>> >>> The first thing I would do is to introduce a "donation button" in www.genabel.org like on wikipedia. So user can type his/her credit card info and donate some money. I donated some money to wikipedia recently and could do it very quickly through their donation button. >>> >>> Maksim >>> >>> Sent from my phone >>> >>> >>> >>>> On 15 ???. 2015 ?., at 1:20, "L.C. Karssen" wrote: >>>> >>>> Dear list, >>>> >>>> As you may have noticed over the past year(s) the contributions to the >>>> GenABEL project by Yurii and myself have steadily declined. The main >>>> reason for this is simple: lack of funding. We have started our own >>>> consulting business and although we have tried to include GenABEL into >>>> grant applications wherever we could, we haven't been able to secure any >>>> funds for this. >>>> >>>> On the other side of the balance we do have some fixed costs related to >>>> the hosting of the genabel.org website (and some flexible costs related >>>> to its maintenance). >>>> >>>> We therefore propose the following: >>>> >>>> 1) Given that www.genabel.org does receive a reasonable number of >>>> visitors per month we would like to add Google Ads to the pages. This >>>> may not generate a lot of revenue but anything many small bits can help >>>> (see e.g. [1]). >>>> Of course this will lead to a change in layout of the site, but we will >>>> try to make this a minimally disruptive as possible so as not to harm >>>> the user experience. >>>> >>>> Of course we understand that this can/should lead to a discussion about >>>> who owns/takes care of the incoming funds. We could set up a foundation >>>> under Dutch law to take care of that. However, that would require around >>>> EUR3500 per year in accounting/reporting costs, etc. which is much more >>>> than we can invest (and more than we expect to earn from the ads). >>>> Therefore we would like to propose the following: Being the main sponsor >>>> of the Project PolyOmica will manage the funds (any payment will go to >>>> our bank account), and as part of our open policy we will provide a >>>> regular (quarterly? annual?) report to the community of the income >>>> generated and how it was spent (see e.g [2]). Any money that remains >>>> after covering these basic costs can be used to fund further development >>>> of the GenABEL Suite packages (maybe via one of the options listed below). >>>> >>>> >>>> We also thought of some alternative ways of generating some income: >>>> >>>> 2) Add a channel on bountysource.com [3] >>>> 3) Make the GenABEL Project a Team on Gratipay (formerly GitTip) [1,2,4,5] >>>> 4) Join http://flattr.com >>>> >>>> Does anyone have experience with any of these micropayment/crowdfunding >>>> providers? >>>> >>>> >>>> Please let us know what you think of these ideas. We would really love >>>> to make the Project more vibrant and sustainable than it currently is! >>>> >>>> >>>> Lennart & Yurii. >>>> >>>> >>>> [1] >>>> http://blogs.perl.org/users/peter_rabbitson/2014/02/i-bought-a-weekly-round-for-my-friends.html >>>> [2] http://inside.gratipay.com/appendices/finances >>>> [3] https://salt.bountysource.com >>>> [4] https://gratipay.com/ >>>> [5] https://medium.com/gratipay-blog/gratipay-2-0-2453d3c53077 >>>> >>>> -- >>>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* >>>> Lennart C. Karssen >>>> PolyOmica >>>> Groningen >>>> The Netherlands >>>> >>>> l.c.karssen at polyomica.com >>>> GPG key ID: 1A15AF2A >>>> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- >>>> >>>> _______________________________________________ >>>> 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 >>> _______________________________________________ >>> 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 >> _______________________________________________ >> 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 >> > > > _______________________________________________ > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.v.struchalin at mail.ru Thu Oct 15 13:37:29 2015 From: m.v.struchalin at mail.ru (Maksim Struchalin) Date: Fri, 16 Oct 2015 00:37:29 +1300 Subject: [GenABEL-dev] Using advertisements (and other ways) to sponsor GenABEL In-Reply-To: <561F733A.7030406@mail.ru> References: <561E48A6.3040504@polyomica.com> <262D9D28-AFD4-4961-A626-D73253B5D681@mail.ru> <561F5F77.6060207@karssen.org> <561F733A.7030406@mail.ru> Message-ID: <561F8FF9.5000101@mail.ru> Hi Lennart, Looks like the paypal works good for donation. Look at the donation button which I have just created on my CV web site (https://sites.google.com/site/maksimstruchalin/). The button in the bottom. Fee for such transactions is 3.4% + some cents (https://www.paypal.com/nz/cgi-bin/webscr?cmd=_display-fees-outside). I donated $1 to myself and it worked as promised. You will might want to create a buisness account (I used "premier" in this case). Maksim On 15/10/2015 22:34, Maksim Struchalin wrote: > Hi Lennart, > > I studied this issue a couple of years ago and my undertanding was at > that time that there are many companies which provide such service > because there are millions small internet shops in web. They make > profit from taking about 5% from each transcation (not much). This > might be usfull: > https://www.paypal.com/webapps/mpp/get-started/donate-button . Also, > you might adviertise this work on one of many websites where > freelancers search their jobs and some of them might do it for say > $50-$100-$200 (I can do it for $1000 :-) ). > > p.s. As alterntive, you can make it very simple: Advertises my bank > account number on genabel.org as account number for all donations and > I will take care of the rest :-). > > good luck, > Maksim > > > > On 15/10/2015 21:10, L.C. Karssen wrote: >> Hi Maksim, Yurii, >> >> Thanks for your input in the discussion. >> >> On 15-10-15 09:44, Yurii Aulchenko wrote: >>> I agree with Maksim - this is very handy how wikipedia does that. In case people are willing to donate, it should be very simple to do - otherwise people will not do this (my personal experience :)) >>> >> Sounds like a good option to me too, I hadn't thought of that. >> My question with this option is how payments are processed. Is there a >> company that provides this kind of button+service? And what do they charge? >> For Google and Gratipay I already found those details. >> >> The nice thing about Gratipay and BountySource.com is that you can more >> directly show/inform the audience what the money will be used for. With >> a donate button and Google Ads that is not so easy. >> >> >> Lennart. >> >>> Yurii >>> >>>> On 15 Oct 2015, at 00:57, Maksim Struchalin wrote: >>>> >>>> Hi Lennart & Yurii, >>>> >>>> The first thing I would do is to introduce a "donation button" inwww.genabel.org like on wikipedia. So user can type his/her credit card info and donate some money. I donated some money to wikipedia recently and could do it very quickly through their donation button. >>>> >>>> Maksim >>>> >>>> Sent from my phone >>>> >>>> >>>> >>>>> On 15 ???. 2015 ?., at 1:20, "L.C. Karssen" wrote: >>>>> >>>>> Dear list, >>>>> >>>>> As you may have noticed over the past year(s) the contributions to the >>>>> GenABEL project by Yurii and myself have steadily declined. The main >>>>> reason for this is simple: lack of funding. We have started our own >>>>> consulting business and although we have tried to include GenABEL into >>>>> grant applications wherever we could, we haven't been able to secure any >>>>> funds for this. >>>>> >>>>> On the other side of the balance we do have some fixed costs related to >>>>> the hosting of the genabel.org website (and some flexible costs related >>>>> to its maintenance). >>>>> >>>>> We therefore propose the following: >>>>> >>>>> 1) Given thatwww.genabel.org does receive a reasonable number of >>>>> visitors per month we would like to add Google Ads to the pages. This >>>>> may not generate a lot of revenue but anything many small bits can help >>>>> (see e.g. [1]). >>>>> Of course this will lead to a change in layout of the site, but we will >>>>> try to make this a minimally disruptive as possible so as not to harm >>>>> the user experience. >>>>> >>>>> Of course we understand that this can/should lead to a discussion about >>>>> who owns/takes care of the incoming funds. We could set up a foundation >>>>> under Dutch law to take care of that. However, that would require around >>>>> EUR3500 per year in accounting/reporting costs, etc. which is much more >>>>> than we can invest (and more than we expect to earn from the ads). >>>>> Therefore we would like to propose the following: Being the main sponsor >>>>> of the Project PolyOmica will manage the funds (any payment will go to >>>>> our bank account), and as part of our open policy we will provide a >>>>> regular (quarterly? annual?) report to the community of the income >>>>> generated and how it was spent (see e.g [2]). Any money that remains >>>>> after covering these basic costs can be used to fund further development >>>>> of the GenABEL Suite packages (maybe via one of the options listed below). >>>>> >>>>> >>>>> We also thought of some alternative ways of generating some income: >>>>> >>>>> 2) Add a channel on bountysource.com [3] >>>>> 3) Make the GenABEL Project a Team on Gratipay (formerly GitTip) [1,2,4,5] >>>>> 4) Joinhttp://flattr.com >>>>> >>>>> Does anyone have experience with any of these micropayment/crowdfunding >>>>> providers? >>>>> >>>>> >>>>> Please let us know what you think of these ideas. We would really love >>>>> to make the Project more vibrant and sustainable than it currently is! >>>>> >>>>> >>>>> Lennart & Yurii. >>>>> >>>>> >>>>> [1] >>>>> http://blogs.perl.org/users/peter_rabbitson/2014/02/i-bought-a-weekly-round-for-my-friends.html >>>>> [2]http://inside.gratipay.com/appendices/finances >>>>> [3]https://salt.bountysource.com >>>>> [4]https://gratipay.com/ >>>>> [5]https://medium.com/gratipay-blog/gratipay-2-0-2453d3c53077 >>>>> >>>>> -- >>>>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* >>>>> Lennart C. Karssen >>>>> PolyOmica >>>>> Groningen >>>>> The Netherlands >>>>> >>>>> l.c.karssen at polyomica.com >>>>> GPG key ID: 1A15AF2A >>>>> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> _______________________________________________ >>>> 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 >>> _______________________________________________ >>> 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 >>> >> >> >> _______________________________________________ >> 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 > > > > _______________________________________________ > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From lennart at karssen.org Thu Oct 15 14:26:56 2015 From: lennart at karssen.org (L.C. Karssen) Date: Thu, 15 Oct 2015 14:26:56 +0200 Subject: [GenABEL-dev] Using advertisements (and other ways) to sponsor GenABEL In-Reply-To: <561F8FF9.5000101@mail.ru> References: <561E48A6.3040504@polyomica.com> <262D9D28-AFD4-4961-A626-D73253B5D681@mail.ru> <561F5F77.6060207@karssen.org> <561F733A.7030406@mail.ru> <561F8FF9.5000101@mail.ru> Message-ID: <561F9B90.40404@karssen.org> Hi Maksim, Thank you for looking into this! On 15-10-15 13:37, Maksim Struchalin wrote: > Hi Lennart, > > Looks like the paypal works good for donation. Look at the donation > button which I have just created on my CV web site > (https://sites.google.com/site/maksimstruchalin/). The button in the > bottom. > Nice! It seems to work indeed :-). > Fee for such transactions is 3.4% + some cents > (https://www.paypal.com/nz/cgi-bin/webscr?cmd=_display-fees-outside). > > I donated $1 to myself and it worked as promised. > > You will might want to create a buisness account (I used "premier" in > this case). OK, I will look into it. Best, Lennart. > > Maksim > > On 15/10/2015 22:34, Maksim Struchalin wrote: >> Hi Lennart, >> >> I studied this issue a couple of years ago and my undertanding was at >> that time that there are many companies which provide such service >> because there are millions small internet shops in web. They make >> profit from taking about 5% from each transcation (not much). This >> might be usfull: >> https://www.paypal.com/webapps/mpp/get-started/donate-button . Also, >> you might adviertise this work on one of many websites where >> freelancers search their jobs and some of them might do it for say >> $50-$100-$200 (I can do it for $1000 :-) ). >> >> p.s. As alterntive, you can make it very simple: Advertises my bank >> account number on genabel.org as account number for all donations and >> I will take care of the rest :-). >> >> good luck, >> Maksim >> >> >> >> On 15/10/2015 21:10, L.C. Karssen wrote: >>> Hi Maksim, Yurii, >>> >>> Thanks for your input in the discussion. >>> >>> On 15-10-15 09:44, Yurii Aulchenko wrote: >>>> I agree with Maksim - this is very handy how wikipedia does that. In case people are willing to donate, it should be very simple to do - otherwise people will not do this (my personal experience :)) >>>> >>> Sounds like a good option to me too, I hadn't thought of that. >>> My question with this option is how payments are processed. Is there a >>> company that provides this kind of button+service? And what do they charge? >>> For Google and Gratipay I already found those details. >>> >>> The nice thing about Gratipay and BountySource.com is that you can more >>> directly show/inform the audience what the money will be used for. With >>> a donate button and Google Ads that is not so easy. >>> >>> >>> Lennart. >>> >>>> Yurii >>>> >>>>> On 15 Oct 2015, at 00:57, Maksim Struchalin wrote: >>>>> >>>>> Hi Lennart & Yurii, >>>>> >>>>> The first thing I would do is to introduce a "donation button" in www.genabel.org like on wikipedia. So user can type his/her credit card info and donate some money. I donated some money to wikipedia recently and could do it very quickly through their donation button. >>>>> >>>>> Maksim >>>>> >>>>> Sent from my phone >>>>> >>>>> >>>>> >>>>>> On 15 ???. 2015 ?., at 1:20, "L.C. Karssen" wrote: >>>>>> >>>>>> Dear list, >>>>>> >>>>>> As you may have noticed over the past year(s) the contributions to the >>>>>> GenABEL project by Yurii and myself have steadily declined. The main >>>>>> reason for this is simple: lack of funding. We have started our own >>>>>> consulting business and although we have tried to include GenABEL into >>>>>> grant applications wherever we could, we haven't been able to secure any >>>>>> funds for this. >>>>>> >>>>>> On the other side of the balance we do have some fixed costs related to >>>>>> the hosting of the genabel.org website (and some flexible costs related >>>>>> to its maintenance). >>>>>> >>>>>> We therefore propose the following: >>>>>> >>>>>> 1) Given that www.genabel.org does receive a reasonable number of >>>>>> visitors per month we would like to add Google Ads to the pages. This >>>>>> may not generate a lot of revenue but anything many small bits can help >>>>>> (see e.g. [1]). >>>>>> Of course this will lead to a change in layout of the site, but we will >>>>>> try to make this a minimally disruptive as possible so as not to harm >>>>>> the user experience. >>>>>> >>>>>> Of course we understand that this can/should lead to a discussion about >>>>>> who owns/takes care of the incoming funds. We could set up a foundation >>>>>> under Dutch law to take care of that. However, that would require around >>>>>> ?3500 per year in accounting/reporting costs, etc. which is much more >>>>>> than we can invest (and more than we expect to earn from the ads). >>>>>> Therefore we would like to propose the following: Being the main sponsor >>>>>> of the Project PolyOmica will manage the funds (any payment will go to >>>>>> our bank account), and as part of our open policy we will provide a >>>>>> regular (quarterly? annual?) report to the community of the income >>>>>> generated and how it was spent (see e.g [2]). Any money that remains >>>>>> after covering these basic costs can be used to fund further development >>>>>> of the GenABEL Suite packages (maybe via one of the options listed below). >>>>>> >>>>>> >>>>>> We also thought of some alternative ways of generating some income: >>>>>> >>>>>> 2) Add a channel on bountysource.com [3] >>>>>> 3) Make the GenABEL Project a Team on Gratipay (formerly GitTip) [1,2,4,5] >>>>>> 4) Join http://flattr.com >>>>>> >>>>>> Does anyone have experience with any of these micropayment/crowdfunding >>>>>> providers? >>>>>> >>>>>> >>>>>> Please let us know what you think of these ideas. We would really love >>>>>> to make the Project more vibrant and sustainable than it currently is! >>>>>> >>>>>> >>>>>> Lennart & Yurii. >>>>>> >>>>>> >>>>>> [1] >>>>>> http://blogs.perl.org/users/peter_rabbitson/2014/02/i-bought-a-weekly-round-for-my-friends.html >>>>>> [2] http://inside.gratipay.com/appendices/finances >>>>>> [3] https://salt.bountysource.com >>>>>> [4] https://gratipay.com/ >>>>>> [5] https://medium.com/gratipay-blog/gratipay-2-0-2453d3c53077 >>>>>> >>>>>> -- >>>>>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* >>>>>> Lennart C. Karssen >>>>>> PolyOmica >>>>>> Groningen >>>>>> The Netherlands >>>>>> >>>>>> l.c.karssen at polyomica.com >>>>>> GPG key ID: 1A15AF2A >>>>>> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>> _______________________________________________ >>>>> 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 >>>> _______________________________________________ >>>> 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 >>>> >>> >>> >>> _______________________________________________ >>> 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 >> >> >> >> _______________________________________________ >> 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 > > > > _______________________________________________ > 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: From yurii.aulchenko at gmail.com Fri Oct 16 10:47:35 2015 From: yurii.aulchenko at gmail.com (Yurii Aulchenko) Date: Fri, 16 Oct 2015 10:47:35 +0200 Subject: [GenABEL-dev] Using advertisements (and other ways) to sponsor GenABEL In-Reply-To: <561F9B90.40404@karssen.org> References: <561E48A6.3040504@polyomica.com> <262D9D28-AFD4-4961-A626-D73253B5D681@mail.ru> <561F5F77.6060207@karssen.org> <561F733A.7030406@mail.ru> <561F8FF9.5000101@mail.ru> <561F9B90.40404@karssen.org> Message-ID: <17DD5048-2D88-46E4-8F8E-83460282CA6B@gmail.com> Maksim, thank you for valuable comments and suggestions! Yurii > On 15 Oct 2015, at 14:26, L.C. Karssen wrote: > > Hi Maksim, > > Thank you for looking into this! > > On 15-10-15 13:37, Maksim Struchalin wrote: >> Hi Lennart, >> >> Looks like the paypal works good for donation. Look at the donation >> button which I have just created on my CV web site >> (https://sites.google.com/site/maksimstruchalin/ ). The button in the >> bottom. >> > > Nice! It seems to work indeed :-). > >> Fee for such transactions is 3.4% + some cents >> (https://www.paypal.com/nz/cgi-bin/webscr?cmd=_display-fees-outside ). >> >> I donated $1 to myself and it worked as promised. >> >> You will might want to create a buisness account (I used "premier" in >> this case). > > OK, I will look into it. > > > Best, > > Lennart. > >> >> Maksim >> >> On 15/10/2015 22:34, Maksim Struchalin wrote: >>> Hi Lennart, >>> >>> I studied this issue a couple of years ago and my undertanding was at >>> that time that there are many companies which provide such service >>> because there are millions small internet shops in web. They make >>> profit from taking about 5% from each transcation (not much). This >>> might be usfull: >>> https://www.paypal.com/webapps/mpp/get-started/donate-button . Also, >>> you might adviertise this work on one of many websites where >>> freelancers search their jobs and some of them might do it for say >>> $50-$100-$200 (I can do it for $1000 :-) ). >>> >>> p.s. As alterntive, you can make it very simple: Advertises my bank >>> account number on genabel.org as account number for all donations and >>> I will take care of the rest :-). >>> >>> good luck, >>> Maksim >>> >>> >>> >>> On 15/10/2015 21:10, L.C. Karssen wrote: >>>> Hi Maksim, Yurii, >>>> >>>> Thanks for your input in the discussion. >>>> >>>> On 15-10-15 09:44, Yurii Aulchenko wrote: >>>>> I agree with Maksim - this is very handy how wikipedia does that. In case people are willing to donate, it should be very simple to do - otherwise people will not do this (my personal experience :)) >>>>> >>>> Sounds like a good option to me too, I hadn't thought of that. >>>> My question with this option is how payments are processed. Is there a >>>> company that provides this kind of button+service? And what do they charge? >>>> For Google and Gratipay I already found those details. >>>> >>>> The nice thing about Gratipay and BountySource.com is that you can more >>>> directly show/inform the audience what the money will be used for. With >>>> a donate button and Google Ads that is not so easy. >>>> >>>> >>>> Lennart. >>>> >>>>> Yurii >>>>> >>>>>> On 15 Oct 2015, at 00:57, Maksim Struchalin wrote: >>>>>> >>>>>> Hi Lennart & Yurii, >>>>>> >>>>>> The first thing I would do is to introduce a "donation button" in www.genabel.org like on wikipedia. So user can type his/her credit card info and donate some money. I donated some money to wikipedia recently and could do it very quickly through their donation button. >>>>>> >>>>>> Maksim >>>>>> >>>>>> Sent from my phone >>>>>> >>>>>> >>>>>> >>>>>>> On 15 ???. 2015 ?., at 1:20, "L.C. Karssen" wrote: >>>>>>> >>>>>>> Dear list, >>>>>>> >>>>>>> As you may have noticed over the past year(s) the contributions to the >>>>>>> GenABEL project by Yurii and myself have steadily declined. The main >>>>>>> reason for this is simple: lack of funding. We have started our own >>>>>>> consulting business and although we have tried to include GenABEL into >>>>>>> grant applications wherever we could, we haven't been able to secure any >>>>>>> funds for this. >>>>>>> >>>>>>> On the other side of the balance we do have some fixed costs related to >>>>>>> the hosting of the genabel.org website (and some flexible costs related >>>>>>> to its maintenance). >>>>>>> >>>>>>> We therefore propose the following: >>>>>>> >>>>>>> 1) Given that www.genabel.org does receive a reasonable number of >>>>>>> visitors per month we would like to add Google Ads to the pages. This >>>>>>> may not generate a lot of revenue but anything many small bits can help >>>>>>> (see e.g. [1]). >>>>>>> Of course this will lead to a change in layout of the site, but we will >>>>>>> try to make this a minimally disruptive as possible so as not to harm >>>>>>> the user experience. >>>>>>> >>>>>>> Of course we understand that this can/should lead to a discussion about >>>>>>> who owns/takes care of the incoming funds. We could set up a foundation >>>>>>> under Dutch law to take care of that. However, that would require around >>>>>>> ?3500 per year in accounting/reporting costs, etc. which is much more >>>>>>> than we can invest (and more than we expect to earn from the ads). >>>>>>> Therefore we would like to propose the following: Being the main sponsor >>>>>>> of the Project PolyOmica will manage the funds (any payment will go to >>>>>>> our bank account), and as part of our open policy we will provide a >>>>>>> regular (quarterly? annual?) report to the community of the income >>>>>>> generated and how it was spent (see e.g [2]). Any money that remains >>>>>>> after covering these basic costs can be used to fund further development >>>>>>> of the GenABEL Suite packages (maybe via one of the options listed below). >>>>>>> >>>>>>> >>>>>>> We also thought of some alternative ways of generating some income: >>>>>>> >>>>>>> 2) Add a channel on bountysource.com [3] >>>>>>> 3) Make the GenABEL Project a Team on Gratipay (formerly GitTip) [1,2,4,5] >>>>>>> 4) Join http://flattr.com >>>>>>> >>>>>>> Does anyone have experience with any of these micropayment/crowdfunding >>>>>>> providers? >>>>>>> >>>>>>> >>>>>>> Please let us know what you think of these ideas. We would really love >>>>>>> to make the Project more vibrant and sustainable than it currently is! >>>>>>> >>>>>>> >>>>>>> Lennart & Yurii. >>>>>>> >>>>>>> >>>>>>> [1] >>>>>>> http://blogs.perl.org/users/peter_rabbitson/2014/02/i-bought-a-weekly-round-for-my-friends.html >>>>>>> [2] http://inside.gratipay.com/appendices/finances >>>>>>> [3] https://salt.bountysource.com >>>>>>> [4] https://gratipay.com/ >>>>>>> [5] https://medium.com/gratipay-blog/gratipay-2-0-2453d3c53077 >>>>>>> >>>>>>> -- >>>>>>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* >>>>>>> Lennart C. Karssen >>>>>>> PolyOmica >>>>>>> Groningen >>>>>>> The Netherlands >>>>>>> >>>>>>> l.c.karssen at polyomica.com >>>>>>> GPG key ID: 1A15AF2A >>>>>>> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- >>>>>>> >>>>>>> _______________________________________________ >>>>>>> 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 >>>>>> _______________________________________________ >>>>>> 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 >>>>> _______________________________________________ >>>>> 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 >>>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >>> >>> _______________________________________________ >>> 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 >> >> >> >> _______________________________________________ >> 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.v.struchalin at mail.ru Fri Oct 16 12:04:52 2015 From: m.v.struchalin at mail.ru (Maksim Struchalin) Date: Fri, 16 Oct 2015 23:04:52 +1300 Subject: [GenABEL-dev] Using advertisements (and other ways) to sponsor GenABEL In-Reply-To: <17DD5048-2D88-46E4-8F8E-83460282CA6B@gmail.com> References: <561E48A6.3040504@polyomica.com> <262D9D28-AFD4-4961-A626-D73253B5D681@mail.ru> <561F5F77.6060207@karssen.org> <561F733A.7030406@mail.ru> <561F8FF9.5000101@mail.ru> <561F9B90.40404@karssen.org> <17DD5048-2D88-46E4-8F8E-83460282CA6B@gmail.com> Message-ID: <5620CBC4.7040903@mail.ru> My pleasure. Maksim On 16/10/2015 21:47, Yurii Aulchenko wrote: > Maksim, thank you for valuable comments and suggestions! Yurii > >> On 15 Oct 2015, at 14:26, L.C. Karssen > > wrote: >> >> Hi Maksim, >> >> Thank you for looking into this! >> >> On 15-10-15 13:37, Maksim Struchalin wrote: >>> Hi Lennart, >>> >>> Looks like the paypal works good for donation. Look at the donation >>> button which I have just created on my CV web site >>> (https://sites.google.com/site/maksimstruchalin/). The button in the >>> bottom. >>> >> >> Nice! It seems to work indeed :-). >> >>> Fee for such transactions is 3.4% + some cents >>> (https://www.paypal.com/nz/cgi-bin/webscr?cmd=_display-fees-outside). >>> >>> I donated $1 to myself and it worked as promised. >>> >>> You will might want to create a buisness account (I used "premier" in >>> this case). >> >> OK, I will look into it. >> >> >> Best, >> >> Lennart. >> >>> >>> Maksim >>> >>> On 15/10/2015 22:34, Maksim Struchalin wrote: >>>> Hi Lennart, >>>> >>>> I studied this issue a couple of years ago and my undertanding was at >>>> that time that there are many companies which provide such service >>>> because there are millions small internet shops in web. They make >>>> profit from taking about 5% from each transcation (not much). This >>>> might be usfull: >>>> https://www.paypal.com/webapps/mpp/get-started/donate-button . Also, >>>> you might adviertise this work on one of many websites where >>>> freelancers search their jobs and some of them might do it for say >>>> $50-$100-$200 (I can do it for $1000 :-) ). >>>> >>>> p.s. As alterntive, you can make it very simple: Advertises my bank >>>> account number on genabel.org as account >>>> number for all donations and >>>> I will take care of the rest :-). >>>> >>>> good luck, >>>> Maksim >>>> >>>> >>>> >>>> On 15/10/2015 21:10, L.C. Karssen wrote: >>>>> Hi Maksim, Yurii, >>>>> >>>>> Thanks for your input in the discussion. >>>>> >>>>> On 15-10-15 09:44, Yurii Aulchenko wrote: >>>>>> I agree with Maksim - this is very handy how wikipedia does that. >>>>>> In case people are willing to donate, it should be very simple to >>>>>> do - otherwise people will not do this (my personal experience :)) >>>>>> >>>>> Sounds like a good option to me too, I hadn't thought of that. >>>>> My question with this option is how payments are processed. Is there a >>>>> company that provides this kind of button+service? And what do >>>>> they charge? >>>>> For Google and Gratipay I already found those details. >>>>> >>>>> The nice thing about Gratipay and BountySource.com >>>>> is that you can more >>>>> directly show/inform the audience what the money will be used for. >>>>> With >>>>> a donate button and Google Ads that is not so easy. >>>>> >>>>> >>>>> Lennart. >>>>> >>>>>> Yurii >>>>>> >>>>>>> On 15 Oct 2015, at 00:57, Maksim Struchalin >>>>>>> > wrote: >>>>>>> >>>>>>> Hi Lennart & Yurii, >>>>>>> >>>>>>> The first thing I would do is to introduce a "donation button" >>>>>>> in www.genabel.org like on wikipedia. >>>>>>> So user can type his/her credit card info and donate some money. >>>>>>> I donated some money to wikipedia recently and could do it very >>>>>>> quickly through their donation button. >>>>>>> >>>>>>> Maksim >>>>>>> >>>>>>> Sent from my phone >>>>>>> >>>>>>> >>>>>>> >>>>>>>> On 15 ???. 2015 ?., at 1:20, "L.C. Karssen" >>>>>>>> > >>>>>>>> wrote: >>>>>>>> >>>>>>>> Dear list, >>>>>>>> >>>>>>>> As you may have noticed over the past year(s) the contributions >>>>>>>> to the >>>>>>>> GenABEL project by Yurii and myself have steadily declined. The >>>>>>>> main >>>>>>>> reason for this is simple: lack of funding. We have started our own >>>>>>>> consulting business and although we have tried to include >>>>>>>> GenABEL into >>>>>>>> grant applications wherever we could, we haven't been able to >>>>>>>> secure any >>>>>>>> funds for this. >>>>>>>> >>>>>>>> On the other side of the balance we do have some fixed costs >>>>>>>> related to >>>>>>>> the hosting of the genabel.org website >>>>>>>> (and some flexible costs related >>>>>>>> to its maintenance). >>>>>>>> >>>>>>>> We therefore propose the following: >>>>>>>> >>>>>>>> 1) Given that www.genabel.org does >>>>>>>> receive a reasonable number of >>>>>>>> visitors per month we would like to add Google Ads to the >>>>>>>> pages. This >>>>>>>> may not generate a lot of revenue but anything many small bits >>>>>>>> can help >>>>>>>> (see e.g. [1]). >>>>>>>> Of course this will lead to a change in layout of the site, but >>>>>>>> we will >>>>>>>> try to make this a minimally disruptive as possible so as not >>>>>>>> to harm >>>>>>>> the user experience. >>>>>>>> >>>>>>>> Of course we understand that this can/should lead to a >>>>>>>> discussion about >>>>>>>> who owns/takes care of the incoming funds. We could set up a >>>>>>>> foundation >>>>>>>> under Dutch law to take care of that. However, that would >>>>>>>> require around >>>>>>>> EUR3500 per year in accounting/reporting costs, etc. which is >>>>>>>> much more >>>>>>>> than we can invest (and more than we expect to earn from the ads). >>>>>>>> Therefore we would like to propose the following: Being the >>>>>>>> main sponsor >>>>>>>> of the Project PolyOmica will manage the funds (any payment >>>>>>>> will go to >>>>>>>> our bank account), and as part of our open policy we will provide a >>>>>>>> regular (quarterly? annual?) report to the community of the income >>>>>>>> generated and how it was spent (see e.g [2]). Any money that >>>>>>>> remains >>>>>>>> after covering these basic costs can be used to fund further >>>>>>>> development >>>>>>>> of the GenABEL Suite packages (maybe via one of the options >>>>>>>> listed below). >>>>>>>> >>>>>>>> >>>>>>>> We also thought of some alternative ways of generating some income: >>>>>>>> >>>>>>>> 2) Add a channel on bountysource.com [3] >>>>>>>> 3) Make the GenABEL Project a Team on Gratipay (formerly >>>>>>>> GitTip) [1,2,4,5] >>>>>>>> 4) Join http://flattr.com >>>>>>>> >>>>>>>> Does anyone have experience with any of these >>>>>>>> micropayment/crowdfunding >>>>>>>> providers? >>>>>>>> >>>>>>>> >>>>>>>> Please let us know what you think of these ideas. We would >>>>>>>> really love >>>>>>>> to make the Project more vibrant and sustainable than it >>>>>>>> currently is! >>>>>>>> >>>>>>>> >>>>>>>> Lennart & Yurii. >>>>>>>> >>>>>>>> >>>>>>>> [1] >>>>>>>> http://blogs.perl.org/users/peter_rabbitson/2014/02/i-bought-a-weekly-round-for-my-friends.html >>>>>>>> [2] http://inside.gratipay.com/appendices/finances >>>>>>>> [3] https://salt.bountysource.com >>>>>>>> [4] https://gratipay.com/ >>>>>>>> [5] https://medium.com/gratipay-blog/gratipay-2-0-2453d3c53077 >>>>>>>> >>>>>>>> -- >>>>>>>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* >>>>>>>> Lennart C. Karssen >>>>>>>> PolyOmica >>>>>>>> Groningen >>>>>>>> The Netherlands >>>>>>>> >>>>>>>> l.c.karssen at polyomica.com >>>>>>>> GPG key ID: 1A15AF2A >>>>>>>> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> 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 >>>>>>> _______________________________________________ >>>>>>> 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 >>>>>> _______________________________________________ >>>>>> 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 >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >>> >>> _______________________________________________ >>> 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 > > > > _______________________________________________ > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From lennart at karssen.org Mon Oct 19 22:20:52 2015 From: lennart at karssen.org (L.C. Karssen) Date: Mon, 19 Oct 2015 22:20:52 +0200 Subject: [GenABEL-dev] Proposal to move to Github In-Reply-To: References: <20140428094937.65E8B186FC6@r-forge.r-project.org> <535E2774.6030606@karssen.org> <535E422F.4080402@gmail.com> <535E69D7.1050005@karssen.org> <535E6BDB.3000206@karssen.org> <535EA05E.40201@gmail.com> <535EB58D.6010900@karssen.org> <5362836C.4000105@aices.rwth-aachen.de> Message-ID: <562550A4.5010906@karssen.org> Dear list, With this e-mail I'm digging up a conversation from the past (April/May 2014). Back then we discussed (see below) the idea of moving (some of) the GenABEL suite tools to a Git repository like GitHub. Since then I have gained more experience with Git and I love it. So I'm all for giving it a try. This brings up the following questions on which I'd like to hear your opinion: 1) Which package(s) do we migrate first? 2) Where do we migrate to? Regarding 1): I think OmicABEL and OmicABELnoMM are the easiest to start with. They have a linear history (no branches etc.) so conversion is straightforward. I'd love to migrate ProbABEL, but I've spent several hours in vain trying to keep the branches and history correct. More time needed there (if someone has experience in SVN -> Git migration, please let me know). Regarding 2): Either GitHub or BitBucket is an option for me. I have some experience with both. Github is more popular/the de facto standard, but the nice thing about Bitbucket is that it allows private repositories (for up to 5 collaborators) also in their free plan. Not sure if this is of any use for GenABEL. Once we reach agreement on 1 and 2 I volunteer to do the migration. Best, Lennart. On 02-05-14 10:27, Yurii Aulchenko wrote: > On Fri, May 2, 2014 at 12:25 AM, Diego Fabregat > > > wrote: > > I like the idea of moving to git. I have no experience with github, > but I'm using git on an almost daily basis (we have our own git > server in our group for code and papers). I would have no problem in > uploading OmicABEL to a git repo. > > Does dropping R-forge have a (bad) impact on the visibility of the > project or on the user experience (e.g., installation of R packages)? > > > In my opinion - not really (visibility: I do not think we get many users > because they've found us at r-forge; also we can keep the account and > make links from there; as for installation, the argument partly holds > only for R-packages). What we need to think is of course how we > keep/move all parts such as a) code b) trackers c) project docs such as > code guidelines > > To me it seems that the idea to migrate few packages first is the most > reasonable; few are likely to stay at r-forge for long > > Yurii > > > > On 04/28/2014 10:09 PM, L.C. Karssen wrote: >> Dear Maarten, dear all, >> >> Moving to github... Hmm... That is quite a decision, so I've renamed the >> subject to better reflect the discussion. I've also dropped the older >> e-mails from the bottom of the thread. >> >> First off, are there any people that have experience with git and/or >> github? I've got some git experience (still learning), but no real >> experience with github. >> >> I agree with Maarten that SVN is showing its age. As he indicates things >> like branching are much easier in git. Moreover, since I'm travelling >> regularly being able to work without internet connection is a pro. >> >> On the other hand, moving to git (whether github or elsewhere) means >> leaving R-forge, which is our well-known infrastructure. Furthermore, >> such a move operation will cost quite some time, I guess. Moving all >> bugs, features, etc... If we decide to move we should plan well and not >> rush. And then the current developers will need to learn git if they >> don't already know how to use it. >> >> One thing I think we should definitely do is migrate slowly, package by >> package. Given that Maarten is positive about such a move and that I am >> in a bit of limbo but not fully against, it seems logical that ProbABEL >> is the first package to try such a migration. >> >> >> Looking forward to your comments! >> >> >> Lennart. >> >> >> On 28-04-14 20:39, Maarten Kooyman wrote: >>> Dear all, >>> >>> I think it is easier to use for code review github: >>> >>> Please check to get a impression >>> :https://github.com/jquery/jquery/pull/1241/files >>> >>> I think we should reconsider an other the software version system: the >>> current system is not up to date to current usability. Bug tracking and >>> branching is quite hard in terms of usability. Please have a look at >>> github.com to get a impression what is possible. >>> >>> Kind regards, >>> >>> Maarten >>> >>> >> -- >> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* >> 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 > > > _______________________________________________ > 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 > > > > > -- > ----------------------------------------------------- > Yurii S. Aulchenko > > [ LinkedIn ] [ Twitter > ] [ Blog > ] > > > _______________________________________________ > 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: From k.zhong at erasmusmc.nl Mon Oct 19 22:28:50 2015 From: k.zhong at erasmusmc.nl (K. Zhong) Date: Mon, 19 Oct 2015 20:28:50 +0000 Subject: [GenABEL-dev] Proposal to move to Github In-Reply-To: <562550A4.5010906@karssen.org> References: <20140428094937.65E8B186FC6@r-forge.r-project.org> <535E2774.6030606@karssen.org> <535E422F.4080402@gmail.com> <535E69D7.1050005@karssen.org> <535E6BDB.3000206@karssen.org> <535EA05E.40201@gmail.com> <535EB58D.6010900@karssen.org> <5362836C.4000105@aices.rwth-aachen.de> <562550A4.5010906@karssen.org> Message-ID: Hi, Lennart. Regarding to (2), it?s possible to start in Bitbucket and then create a mirror in Github painlessly (or vice-versa). But for published packages a private repo seems unnecessary? My 2 cents. Best regards, Kaiyin ZHONG ------------------ FMB, Erasmus MC http://kaiyin.co.vu k.zhong at erasmusmc.nl kindlychung at gmail.com On 19/10/2015 22:20, "genabel-devel-bounces at lists.r-forge.r-project.org on behalf of L.C. Karssen" wrote: >Dear list, > >With this e-mail I'm digging up a conversation from the past (April/May >2014). Back then we discussed (see below) the idea of moving (some of) >the GenABEL suite tools to a Git repository like GitHub. > >Since then I have gained more experience with Git and I love it. So I'm >all for giving it a try. This brings up the following questions on which >I'd like to hear your opinion: > >1) Which package(s) do we migrate first? > >2) Where do we migrate to? > > >Regarding 1): I think OmicABEL and OmicABELnoMM are the easiest to start >with. They have a linear history (no branches etc.) so conversion is >straightforward. I'd love to migrate ProbABEL, but I've spent several >hours in vain trying to keep the branches and history correct. More time >needed there (if someone has experience in SVN -> Git migration, please >let me know). > >Regarding 2): Either GitHub or BitBucket is an option for me. I have >some experience with both. Github is more popular/the de facto standard, >but the nice thing about Bitbucket is that it allows private >repositories (for up to 5 collaborators) also in their free plan. Not >sure if this is of any use for GenABEL. > > >Once we reach agreement on 1 and 2 I volunteer to do the migration. > > >Best, > >Lennart. > > >On 02-05-14 10:27, Yurii Aulchenko wrote: >> On Fri, May 2, 2014 at 12:25 AM, Diego Fabregat >> > >> wrote: >> >> I like the idea of moving to git. I have no experience with github, >> but I'm using git on an almost daily basis (we have our own git >> server in our group for code and papers). I would have no problem in >> uploading OmicABEL to a git repo. >> >> Does dropping R-forge have a (bad) impact on the visibility of the >> project or on the user experience (e.g., installation of R >>packages)? >> >> >> In my opinion - not really (visibility: I do not think we get many users >> because they've found us at r-forge; also we can keep the account and >> make links from there; as for installation, the argument partly holds >> only for R-packages). What we need to think is of course how we >> keep/move all parts such as a) code b) trackers c) project docs such as >> code guidelines >> >> To me it seems that the idea to migrate few packages first is the most >> reasonable; few are likely to stay at r-forge for long >> >> Yurii >> >> >> >> On 04/28/2014 10:09 PM, L.C. Karssen wrote: >>> Dear Maarten, dear all, >>> >>> Moving to github... Hmm... That is quite a decision, so I've >>>renamed the >>> subject to better reflect the discussion. I've also dropped the >>>older >>> e-mails from the bottom of the thread. >>> >>> First off, are there any people that have experience with git >>>and/or >>> github? I've got some git experience (still learning), but no real >>> experience with github. >>> >>> I agree with Maarten that SVN is showing its age. As he indicates >>>things >>> like branching are much easier in git. Moreover, since I'm >>>travelling >>> regularly being able to work without internet connection is a pro. >>> >>> On the other hand, moving to git (whether github or elsewhere) >>>means >>> leaving R-forge, which is our well-known infrastructure. >>>Furthermore, >>> such a move operation will cost quite some time, I guess. Moving >>>all >>> bugs, features, etc... If we decide to move we should plan well >>>and not >>> rush. And then the current developers will need to learn git if >>>they >>> don't already know how to use it. >>> >>> One thing I think we should definitely do is migrate slowly, >>>package by >>> package. Given that Maarten is positive about such a move and that >>>I am >>> in a bit of limbo but not fully against, it seems logical that >>>ProbABEL >>> is the first package to try such a migration. >>> >>> >>> Looking forward to your comments! >>> >>> >>> Lennart. >>> >>> >>> On 28-04-14 20:39, Maarten Kooyman wrote: >>>> Dear all, >>>> >>>> I think it is easier to use for code review github: >>>> >>>> Please check to get a impression >>>> :https://github.com/jquery/jquery/pull/1241/files >>>> >>>> I think we should reconsider an other the software version >>>>system: the >>>> current system is not up to date to current usability. Bug >>>>tracking and >>>> branching is quite hard in terms of usability. Please have a look >>>>at >>>> github.com to get a impression what is >>>>possible. >>>> >>>> Kind regards, >>>> >>>> Maarten >>>> >>>> >>> -- >>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* >>> 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-dev >>>el >> >> >> _______________________________________________ >> 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-deve >>l >> >> >> >> >> -- >> ----------------------------------------------------- >> Yurii S. Aulchenko >> >> [ LinkedIn ] [ Twitter >> ] [ Blog >> ] >> >> >> _______________________________________________ >> 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-deve >>l >> > >-- >*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* >L.C. Karssen >Utrecht >The Netherlands > >lennart at karssen.org >http://blog.karssen.org >GPG key ID: A88F554A >-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- > From lennart at karssen.org Mon Oct 19 22:43:39 2015 From: lennart at karssen.org (L.C. Karssen) Date: Mon, 19 Oct 2015 22:43:39 +0200 Subject: [GenABEL-dev] Proposal to move to Github In-Reply-To: References: <20140428094937.65E8B186FC6@r-forge.r-project.org> <535E2774.6030606@karssen.org> <535E422F.4080402@gmail.com> <535E69D7.1050005@karssen.org> <535E6BDB.3000206@karssen.org> <535EA05E.40201@gmail.com> <535EB58D.6010900@karssen.org> <5362836C.4000105@aices.rwth-aachen.de> <562550A4.5010906@karssen.org> Message-ID: <562555FB.7080106@karssen.org> hi Kaiyin, On 19-10-15 22:28, K. Zhong wrote: > Hi, Lennart. > > Regarding to (2), it?s possible to start in Bitbucket and then create a > mirror in Github painlessly (or vice-versa). Interesting! I didn't think of that. Thanks for bringing it up. I do think that for 'communication' purposes it wouldbe best to have one 'main/official location' for the packages (either Github or Bitbucket), to keep possible confusion to a minimum. Now (almost) all development is done on R-forge's SVN. Nice and clean. Given Git's improvements to the development process and the fact that Github/Bitucket give a push towards social coding I have no objections to have both R-forge and a Git repo, but IMHO spreading packages across three platforms doesn't sound very good. > But for published packages a > private repo seems unnecessary? True. I thought maybe a private repo could be used by packages that are still under consideration. Or where the authors are not ready yet to develop 'in broad daylight' yet. Not really in the GenABEL spirit, but we could be open to that. Lennart. > My 2 cents. > > > > Best regards, > Kaiyin ZHONG > ------------------ > FMB, Erasmus MC > http://kaiyin.co.vu > k.zhong at erasmusmc.nl > kindlychung at gmail.com > > > > > > > > > On 19/10/2015 22:20, "genabel-devel-bounces at lists.r-forge.r-project.org on > behalf of L.C. Karssen" on behalf of lennart at karssen.org> wrote: > >> Dear list, >> >> With this e-mail I'm digging up a conversation from the past (April/May >> 2014). Back then we discussed (see below) the idea of moving (some of) >> the GenABEL suite tools to a Git repository like GitHub. >> >> Since then I have gained more experience with Git and I love it. So I'm >> all for giving it a try. This brings up the following questions on which >> I'd like to hear your opinion: >> >> 1) Which package(s) do we migrate first? >> >> 2) Where do we migrate to? >> >> >> Regarding 1): I think OmicABEL and OmicABELnoMM are the easiest to start >> with. They have a linear history (no branches etc.) so conversion is >> straightforward. I'd love to migrate ProbABEL, but I've spent several >> hours in vain trying to keep the branches and history correct. More time >> needed there (if someone has experience in SVN -> Git migration, please >> let me know). >> >> Regarding 2): Either GitHub or BitBucket is an option for me. I have >> some experience with both. Github is more popular/the de facto standard, >> but the nice thing about Bitbucket is that it allows private >> repositories (for up to 5 collaborators) also in their free plan. Not >> sure if this is of any use for GenABEL. >> >> >> Once we reach agreement on 1 and 2 I volunteer to do the migration. >> >> >> Best, >> >> Lennart. >> >> >> On 02-05-14 10:27, Yurii Aulchenko wrote: >>> On Fri, May 2, 2014 at 12:25 AM, Diego Fabregat >>> > >>> wrote: >>> >>> I like the idea of moving to git. I have no experience with github, >>> but I'm using git on an almost daily basis (we have our own git >>> server in our group for code and papers). I would have no problem in >>> uploading OmicABEL to a git repo. >>> >>> Does dropping R-forge have a (bad) impact on the visibility of the >>> project or on the user experience (e.g., installation of R >>> packages)? >>> >>> >>> In my opinion - not really (visibility: I do not think we get many users >>> because they've found us at r-forge; also we can keep the account and >>> make links from there; as for installation, the argument partly holds >>> only for R-packages). What we need to think is of course how we >>> keep/move all parts such as a) code b) trackers c) project docs such as >>> code guidelines >>> >>> To me it seems that the idea to migrate few packages first is the most >>> reasonable; few are likely to stay at r-forge for long >>> >>> Yurii >>> >>> >>> >>> On 04/28/2014 10:09 PM, L.C. Karssen wrote: >>>> Dear Maarten, dear all, >>>> >>>> Moving to github... Hmm... That is quite a decision, so I've >>>> renamed the >>>> subject to better reflect the discussion. I've also dropped the >>>> older >>>> e-mails from the bottom of the thread. >>>> >>>> First off, are there any people that have experience with git >>>> and/or >>>> github? I've got some git experience (still learning), but no real >>>> experience with github. >>>> >>>> I agree with Maarten that SVN is showing its age. As he indicates >>>> things >>>> like branching are much easier in git. Moreover, since I'm >>>> travelling >>>> regularly being able to work without internet connection is a pro. >>>> >>>> On the other hand, moving to git (whether github or elsewhere) >>>> means >>>> leaving R-forge, which is our well-known infrastructure. >>>> Furthermore, >>>> such a move operation will cost quite some time, I guess. Moving >>>> all >>>> bugs, features, etc... If we decide to move we should plan well >>>> and not >>>> rush. And then the current developers will need to learn git if >>>> they >>>> don't already know how to use it. >>>> >>>> One thing I think we should definitely do is migrate slowly, >>>> package by >>>> package. Given that Maarten is positive about such a move and that >>>> I am >>>> in a bit of limbo but not fully against, it seems logical that >>>> ProbABEL >>>> is the first package to try such a migration. >>>> >>>> >>>> Looking forward to your comments! >>>> >>>> >>>> Lennart. >>>> >>>> >>>> On 28-04-14 20:39, Maarten Kooyman wrote: >>>>> Dear all, >>>>> >>>>> I think it is easier to use for code review github: >>>>> >>>>> Please check to get a impression >>>>> :https://github.com/jquery/jquery/pull/1241/files >>>>> >>>>> I think we should reconsider an other the software version >>>>> system: the >>>>> current system is not up to date to current usability. Bug >>>>> tracking and >>>>> branching is quite hard in terms of usability. Please have a look >>>>> at >>>>> github.com to get a impression what is >>>>> possible. >>>>> >>>>> Kind regards, >>>>> >>>>> Maarten >>>>> >>>>> >>>> -- >>>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* >>>> 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-dev >>>> el >>> >>> >>> _______________________________________________ >>> 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-deve >>> l >>> >>> >>> >>> >>> -- >>> ----------------------------------------------------- >>> Yurii S. Aulchenko >>> >>> [ LinkedIn ] [ Twitter >>> ] [ Blog >>> ] >>> >>> >>> _______________________________________________ >>> 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-deve >>> l >>> >> >> -- >> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* >> 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 > -- *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* 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: From lennart at karssen.org Mon Oct 19 23:09:41 2015 From: lennart at karssen.org (L.C. Karssen) Date: Mon, 19 Oct 2015 23:09:41 +0200 Subject: [GenABEL-dev] Proposal to move to Github In-Reply-To: <562555FB.7080106@karssen.org> References: <20140428094937.65E8B186FC6@r-forge.r-project.org> <535E2774.6030606@karssen.org> <535E422F.4080402@gmail.com> <535E69D7.1050005@karssen.org> <535E6BDB.3000206@karssen.org> <535EA05E.40201@gmail.com> <535EB58D.6010900@karssen.org> <5362836C.4000105@aices.rwth-aachen.de> <562550A4.5010906@karssen.org> <562555FB.7080106@karssen.org> Message-ID: <56255C15.7050408@karssen.org> Hmm, am I correct that Github allows you to create an 'organisation', but Bitbucket doesn't? I just the GenABEL Project on Github [1] some time ago. Bitbucket seems to have teams, which could work the same way, but if I understand it correctly you need to pay for teams with more than 5 members. That would be a definite plus for GitHub. Lennart. [1] https://github.com/GenABEL-Project On 19-10-15 22:43, L.C. Karssen wrote: > hi Kaiyin, > > On 19-10-15 22:28, K. Zhong wrote: >> Hi, Lennart. >> >> Regarding to (2), it?s possible to start in Bitbucket and then create a >> mirror in Github painlessly (or vice-versa). > > Interesting! I didn't think of that. Thanks for bringing it up. > > I do think that for 'communication' purposes it wouldbe best to have one > 'main/official location' for the packages (either Github or Bitbucket), > to keep possible confusion to a minimum. Now (almost) all development is > done on R-forge's SVN. Nice and clean. Given Git's improvements to the > development process and the fact that Github/Bitucket give a push > towards social coding I have no objections to have both R-forge and a > Git repo, but IMHO spreading packages across three platforms doesn't > sound very good. > >> But for published packages a >> private repo seems unnecessary? > > True. I thought maybe a private repo could be used by packages that are > still under consideration. Or where the authors are not ready yet to > develop 'in broad daylight' yet. Not really in the GenABEL spirit, but > we could be open to that. > > > Lennart. > >> My 2 cents. >> >> >> >> Best regards, >> Kaiyin ZHONG >> ------------------ >> FMB, Erasmus MC >> http://kaiyin.co.vu >> k.zhong at erasmusmc.nl >> kindlychung at gmail.com >> >> >> >> >> >> >> >> >> On 19/10/2015 22:20, "genabel-devel-bounces at lists.r-forge.r-project.org on >> behalf of L.C. Karssen" > on behalf of lennart at karssen.org> wrote: >> >>> Dear list, >>> >>> With this e-mail I'm digging up a conversation from the past (April/May >>> 2014). Back then we discussed (see below) the idea of moving (some of) >>> the GenABEL suite tools to a Git repository like GitHub. >>> >>> Since then I have gained more experience with Git and I love it. So I'm >>> all for giving it a try. This brings up the following questions on which >>> I'd like to hear your opinion: >>> >>> 1) Which package(s) do we migrate first? >>> >>> 2) Where do we migrate to? >>> >>> >>> Regarding 1): I think OmicABEL and OmicABELnoMM are the easiest to start >>> with. They have a linear history (no branches etc.) so conversion is >>> straightforward. I'd love to migrate ProbABEL, but I've spent several >>> hours in vain trying to keep the branches and history correct. More time >>> needed there (if someone has experience in SVN -> Git migration, please >>> let me know). >>> >>> Regarding 2): Either GitHub or BitBucket is an option for me. I have >>> some experience with both. Github is more popular/the de facto standard, >>> but the nice thing about Bitbucket is that it allows private >>> repositories (for up to 5 collaborators) also in their free plan. Not >>> sure if this is of any use for GenABEL. >>> >>> >>> Once we reach agreement on 1 and 2 I volunteer to do the migration. >>> >>> >>> Best, >>> >>> Lennart. >>> >>> >>> On 02-05-14 10:27, Yurii Aulchenko wrote: >>>> On Fri, May 2, 2014 at 12:25 AM, Diego Fabregat >>>> > >>>> wrote: >>>> >>>> I like the idea of moving to git. I have no experience with github, >>>> but I'm using git on an almost daily basis (we have our own git >>>> server in our group for code and papers). I would have no problem in >>>> uploading OmicABEL to a git repo. >>>> >>>> Does dropping R-forge have a (bad) impact on the visibility of the >>>> project or on the user experience (e.g., installation of R >>>> packages)? >>>> >>>> >>>> In my opinion - not really (visibility: I do not think we get many users >>>> because they've found us at r-forge; also we can keep the account and >>>> make links from there; as for installation, the argument partly holds >>>> only for R-packages). What we need to think is of course how we >>>> keep/move all parts such as a) code b) trackers c) project docs such as >>>> code guidelines >>>> >>>> To me it seems that the idea to migrate few packages first is the most >>>> reasonable; few are likely to stay at r-forge for long >>>> >>>> Yurii >>>> >>>> >>>> >>>> On 04/28/2014 10:09 PM, L.C. Karssen wrote: >>>>> Dear Maarten, dear all, >>>>> >>>>> Moving to github... Hmm... That is quite a decision, so I've >>>>> renamed the >>>>> subject to better reflect the discussion. I've also dropped the >>>>> older >>>>> e-mails from the bottom of the thread. >>>>> >>>>> First off, are there any people that have experience with git >>>>> and/or >>>>> github? I've got some git experience (still learning), but no real >>>>> experience with github. >>>>> >>>>> I agree with Maarten that SVN is showing its age. As he indicates >>>>> things >>>>> like branching are much easier in git. Moreover, since I'm >>>>> travelling >>>>> regularly being able to work without internet connection is a pro. >>>>> >>>>> On the other hand, moving to git (whether github or elsewhere) >>>>> means >>>>> leaving R-forge, which is our well-known infrastructure. >>>>> Furthermore, >>>>> such a move operation will cost quite some time, I guess. Moving >>>>> all >>>>> bugs, features, etc... If we decide to move we should plan well >>>>> and not >>>>> rush. And then the current developers will need to learn git if >>>>> they >>>>> don't already know how to use it. >>>>> >>>>> One thing I think we should definitely do is migrate slowly, >>>>> package by >>>>> package. Given that Maarten is positive about such a move and that >>>>> I am >>>>> in a bit of limbo but not fully against, it seems logical that >>>>> ProbABEL >>>>> is the first package to try such a migration. >>>>> >>>>> >>>>> Looking forward to your comments! >>>>> >>>>> >>>>> Lennart. >>>>> >>>>> >>>>> On 28-04-14 20:39, Maarten Kooyman wrote: >>>>>> Dear all, >>>>>> >>>>>> I think it is easier to use for code review github: >>>>>> >>>>>> Please check to get a impression >>>>>> :https://github.com/jquery/jquery/pull/1241/files >>>>>> >>>>>> I think we should reconsider an other the software version >>>>>> system: the >>>>>> current system is not up to date to current usability. Bug >>>>>> tracking and >>>>>> branching is quite hard in terms of usability. Please have a look >>>>>> at >>>>>> github.com to get a impression what is >>>>>> possible. >>>>>> >>>>>> Kind regards, >>>>>> >>>>>> Maarten >>>>>> >>>>>> >>>>> -- >>>>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* >>>>> 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-dev >>>>> el >>>> >>>> >>>> _______________________________________________ >>>> 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-deve >>>> l >>>> >>>> >>>> >>>> >>>> -- >>>> ----------------------------------------------------- >>>> Yurii S. Aulchenko >>>> >>>> [ LinkedIn ] [ Twitter >>>> ] [ Blog >>>> ] >>>> >>>> >>>> _______________________________________________ >>>> 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-deve >>>> l >>>> >>> >>> -- >>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* >>> 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 >> > > > > _______________________________________________ > 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: From k.zhong at erasmusmc.nl Mon Oct 19 23:12:30 2015 From: k.zhong at erasmusmc.nl (K. Zhong) Date: Mon, 19 Oct 2015 21:12:30 +0000 Subject: [GenABEL-dev] Proposal to move to Github In-Reply-To: <56255C15.7050408@karssen.org> References: <20140428094937.65E8B186FC6@r-forge.r-project.org> <535E2774.6030606@karssen.org> <535E422F.4080402@gmail.com> <535E69D7.1050005@karssen.org> <535E6BDB.3000206@karssen.org> <535EA05E.40201@gmail.com> <535EB58D.6010900@karssen.org> <5362836C.4000105@aices.rwth-aachen.de> <562550A4.5010906@karssen.org> <562555FB.7080106@karssen.org> <56255C15.7050408@karssen.org> Message-ID: You can register for a 5-user team for free on bitbucket. Best regards, Kaiyin ZHONG ------------------ FMB, Erasmus MC http://kspace.co.vu k.zhong at erasmusmc.nl kindlychung at gmail.com On 19/10/2015 23:09, "genabel-devel-bounces at lists.r-forge.r-project.org on behalf of L.C. Karssen" wrote: >Hmm, am I correct that Github allows you to create an 'organisation', >but Bitbucket doesn't? >I just the GenABEL Project on Github [1] some time ago. Bitbucket seems >to have teams, which could work the same way, but if I understand it >correctly you need to pay for teams with more than 5 members. That would >be a definite plus for GitHub. > > >Lennart. > > > >[1] https://github.com/GenABEL-Project > >On 19-10-15 22:43, L.C. Karssen wrote: >> hi Kaiyin, >> >> On 19-10-15 22:28, K. Zhong wrote: >>> Hi, Lennart. >>> >>> Regarding to (2), it?s possible to start in Bitbucket and then create a >>> mirror in Github painlessly (or vice-versa). >> >> Interesting! I didn't think of that. Thanks for bringing it up. >> >> I do think that for 'communication' purposes it wouldbe best to have one >> 'main/official location' for the packages (either Github or Bitbucket), >> to keep possible confusion to a minimum. Now (almost) all development is >> done on R-forge's SVN. Nice and clean. Given Git's improvements to the >> development process and the fact that Github/Bitucket give a push >> towards social coding I have no objections to have both R-forge and a >> Git repo, but IMHO spreading packages across three platforms doesn't >> sound very good. >> >>> But for published packages a >>> private repo seems unnecessary? >> >> True. I thought maybe a private repo could be used by packages that are >> still under consideration. Or where the authors are not ready yet to >> develop 'in broad daylight' yet. Not really in the GenABEL spirit, but >> we could be open to that. >> >> >> Lennart. >> >>> My 2 cents. >>> >>> >>> >>> Best regards, >>> Kaiyin ZHONG >>> ------------------ >>> FMB, Erasmus MC >>> http://kaiyin.co.vu >>> k.zhong at erasmusmc.nl >>> kindlychung at gmail.com >>> >>> >>> >>> >>> >>> >>> >>> >>> On 19/10/2015 22:20, >>>"genabel-devel-bounces at lists.r-forge.r-project.org on >>> behalf of L.C. Karssen" >>>>> on behalf of lennart at karssen.org> wrote: >>> >>>> Dear list, >>>> >>>> With this e-mail I'm digging up a conversation from the past >>>>(April/May >>>> 2014). Back then we discussed (see below) the idea of moving (some of) >>>> the GenABEL suite tools to a Git repository like GitHub. >>>> >>>> Since then I have gained more experience with Git and I love it. So >>>>I'm >>>> all for giving it a try. This brings up the following questions on >>>>which >>>> I'd like to hear your opinion: >>>> >>>> 1) Which package(s) do we migrate first? >>>> >>>> 2) Where do we migrate to? >>>> >>>> >>>> Regarding 1): I think OmicABEL and OmicABELnoMM are the easiest to >>>>start >>>> with. They have a linear history (no branches etc.) so conversion is >>>> straightforward. I'd love to migrate ProbABEL, but I've spent several >>>> hours in vain trying to keep the branches and history correct. More >>>>time >>>> needed there (if someone has experience in SVN -> Git migration, >>>>please >>>> let me know). >>>> >>>> Regarding 2): Either GitHub or BitBucket is an option for me. I have >>>> some experience with both. Github is more popular/the de facto >>>>standard, >>>> but the nice thing about Bitbucket is that it allows private >>>> repositories (for up to 5 collaborators) also in their free plan. Not >>>> sure if this is of any use for GenABEL. >>>> >>>> >>>> Once we reach agreement on 1 and 2 I volunteer to do the migration. >>>> >>>> >>>> Best, >>>> >>>> Lennart. >>>> >>>> >>>> On 02-05-14 10:27, Yurii Aulchenko wrote: >>>>> On Fri, May 2, 2014 at 12:25 AM, Diego Fabregat >>>>> >>>>> >>>>> wrote: >>>>> >>>>> I like the idea of moving to git. I have no experience with >>>>>github, >>>>> but I'm using git on an almost daily basis (we have our own git >>>>> server in our group for code and papers). I would have no >>>>>problem in >>>>> uploading OmicABEL to a git repo. >>>>> >>>>> Does dropping R-forge have a (bad) impact on the visibility of >>>>>the >>>>> project or on the user experience (e.g., installation of R >>>>> packages)? >>>>> >>>>> >>>>> In my opinion - not really (visibility: I do not think we get many >>>>>users >>>>> because they've found us at r-forge; also we can keep the account and >>>>> make links from there; as for installation, the argument partly holds >>>>> only for R-packages). What we need to think is of course how we >>>>> keep/move all parts such as a) code b) trackers c) project docs such >>>>>as >>>>> code guidelines >>>>> >>>>> To me it seems that the idea to migrate few packages first is the >>>>>most >>>>> reasonable; few are likely to stay at r-forge for long >>>>> >>>>> Yurii >>>>> >>>>> >>>>> >>>>> On 04/28/2014 10:09 PM, L.C. Karssen wrote: >>>>>> Dear Maarten, dear all, >>>>>> >>>>>> Moving to github... Hmm... That is quite a decision, so I've >>>>>> renamed the >>>>>> subject to better reflect the discussion. I've also dropped the >>>>>> older >>>>>> e-mails from the bottom of the thread. >>>>>> >>>>>> First off, are there any people that have experience with git >>>>>> and/or >>>>>> github? I've got some git experience (still learning), but no >>>>>>real >>>>>> experience with github. >>>>>> >>>>>> I agree with Maarten that SVN is showing its age. As he >>>>>>indicates >>>>>> things >>>>>> like branching are much easier in git. Moreover, since I'm >>>>>> travelling >>>>>> regularly being able to work without internet connection is a >>>>>>pro. >>>>>> >>>>>> On the other hand, moving to git (whether github or elsewhere) >>>>>> means >>>>>> leaving R-forge, which is our well-known infrastructure. >>>>>> Furthermore, >>>>>> such a move operation will cost quite some time, I guess. Moving >>>>>> all >>>>>> bugs, features, etc... If we decide to move we should plan well >>>>>> and not >>>>>> rush. And then the current developers will need to learn git if >>>>>> they >>>>>> don't already know how to use it. >>>>>> >>>>>> One thing I think we should definitely do is migrate slowly, >>>>>> package by >>>>>> package. Given that Maarten is positive about such a move and >>>>>>that >>>>>> I am >>>>>> in a bit of limbo but not fully against, it seems logical that >>>>>> ProbABEL >>>>>> is the first package to try such a migration. >>>>>> >>>>>> >>>>>> Looking forward to your comments! >>>>>> >>>>>> >>>>>> Lennart. >>>>>> >>>>>> >>>>>> On 28-04-14 20:39, Maarten Kooyman wrote: >>>>>>> Dear all, >>>>>>> >>>>>>> I think it is easier to use for code review github: >>>>>>> >>>>>>> Please check to get a impression >>>>>>> :https://github.com/jquery/jquery/pull/1241/files >>>>>>> >>>>>>> I think we should reconsider an other the software version >>>>>>> system: the >>>>>>> current system is not up to date to current usability. Bug >>>>>>> tracking and >>>>>>> branching is quite hard in terms of usability. Please have a >>>>>>>look >>>>>>> at >>>>>>> github.com to get a impression what is >>>>>>> possible. >>>>>>> >>>>>>> Kind regards, >>>>>>> >>>>>>> Maarten >>>>>>> >>>>>>> >>>>>> -- >>>>>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* >>>>>> 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- >>>>>>dev >>>>>> el >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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-d >>>>>eve >>>>> l >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> ----------------------------------------------------- >>>>> Yurii S. Aulchenko >>>>> >>>>> [ LinkedIn ] [ Twitter >>>>> ] [ Blog >>>>> ] >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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-d >>>>>eve >>>>> l >>>>> >>>> >>>> -- >>>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* >>>> 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-dev >>>el >>> >> >> >> >> _______________________________________________ >> 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-deve >>l >> > >-- >*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* >L.C. Karssen >Utrecht >The Netherlands > >lennart at karssen.org >http://blog.karssen.org >GPG key ID: A88F554A >-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- > From lennart at karssen.org Mon Oct 19 23:21:02 2015 From: lennart at karssen.org (L.C. Karssen) Date: Mon, 19 Oct 2015 23:21:02 +0200 Subject: [GenABEL-dev] Proposal to move to Github In-Reply-To: References: <20140428094937.65E8B186FC6@r-forge.r-project.org> <535E2774.6030606@karssen.org> <535E422F.4080402@gmail.com> <535E69D7.1050005@karssen.org> <535E6BDB.3000206@karssen.org> <535EA05E.40201@gmail.com> <535EB58D.6010900@karssen.org> <5362836C.4000105@aices.rwth-aachen.de> <562550A4.5010906@karssen.org> <562555FB.7080106@karssen.org> <56255C15.7050408@karssen.org> Message-ID: <56255EBE.6000807@karssen.org> On 19-10-15 23:12, K. Zhong wrote: > You can register for a 5-user team for free on bitbucket. Yup, but I guess that would be limiting for some GenABEL packages... Lennart. > > Best regards, > Kaiyin ZHONG > ------------------ > FMB, Erasmus MC > http://kspace.co.vu > k.zhong at erasmusmc.nl > kindlychung at gmail.com > > > > > > > > > On 19/10/2015 23:09, "genabel-devel-bounces at lists.r-forge.r-project.org on > behalf of L.C. Karssen" on behalf of lennart at karssen.org> wrote: > >> Hmm, am I correct that Github allows you to create an 'organisation', >> but Bitbucket doesn't? >> I just the GenABEL Project on Github [1] some time ago. Bitbucket seems >> to have teams, which could work the same way, but if I understand it >> correctly you need to pay for teams with more than 5 members. That would >> be a definite plus for GitHub. >> >> >> Lennart. >> >> >> >> [1] https://github.com/GenABEL-Project >> >> On 19-10-15 22:43, L.C. Karssen wrote: >>> hi Kaiyin, >>> >>> On 19-10-15 22:28, K. Zhong wrote: >>>> Hi, Lennart. >>>> >>>> Regarding to (2), it?s possible to start in Bitbucket and then create a >>>> mirror in Github painlessly (or vice-versa). >>> >>> Interesting! I didn't think of that. Thanks for bringing it up. >>> >>> I do think that for 'communication' purposes it wouldbe best to have one >>> 'main/official location' for the packages (either Github or Bitbucket), >>> to keep possible confusion to a minimum. Now (almost) all development is >>> done on R-forge's SVN. Nice and clean. Given Git's improvements to the >>> development process and the fact that Github/Bitucket give a push >>> towards social coding I have no objections to have both R-forge and a >>> Git repo, but IMHO spreading packages across three platforms doesn't >>> sound very good. >>> >>>> But for published packages a >>>> private repo seems unnecessary? >>> >>> True. I thought maybe a private repo could be used by packages that are >>> still under consideration. Or where the authors are not ready yet to >>> develop 'in broad daylight' yet. Not really in the GenABEL spirit, but >>> we could be open to that. >>> >>> >>> Lennart. >>> >>>> My 2 cents. >>>> >>>> >>>> >>>> Best regards, >>>> Kaiyin ZHONG >>>> ------------------ >>>> FMB, Erasmus MC >>>> http://kaiyin.co.vu >>>> k.zhong at erasmusmc.nl >>>> kindlychung at gmail.com >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> On 19/10/2015 22:20, >>>> "genabel-devel-bounces at lists.r-forge.r-project.org on >>>> behalf of L.C. Karssen" >>>> >>> on behalf of lennart at karssen.org> wrote: >>>> >>>>> Dear list, >>>>> >>>>> With this e-mail I'm digging up a conversation from the past >>>>> (April/May >>>>> 2014). Back then we discussed (see below) the idea of moving (some of) >>>>> the GenABEL suite tools to a Git repository like GitHub. >>>>> >>>>> Since then I have gained more experience with Git and I love it. So >>>>> I'm >>>>> all for giving it a try. This brings up the following questions on >>>>> which >>>>> I'd like to hear your opinion: >>>>> >>>>> 1) Which package(s) do we migrate first? >>>>> >>>>> 2) Where do we migrate to? >>>>> >>>>> >>>>> Regarding 1): I think OmicABEL and OmicABELnoMM are the easiest to >>>>> start >>>>> with. They have a linear history (no branches etc.) so conversion is >>>>> straightforward. I'd love to migrate ProbABEL, but I've spent several >>>>> hours in vain trying to keep the branches and history correct. More >>>>> time >>>>> needed there (if someone has experience in SVN -> Git migration, >>>>> please >>>>> let me know). >>>>> >>>>> Regarding 2): Either GitHub or BitBucket is an option for me. I have >>>>> some experience with both. Github is more popular/the de facto >>>>> standard, >>>>> but the nice thing about Bitbucket is that it allows private >>>>> repositories (for up to 5 collaborators) also in their free plan. Not >>>>> sure if this is of any use for GenABEL. >>>>> >>>>> >>>>> Once we reach agreement on 1 and 2 I volunteer to do the migration. >>>>> >>>>> >>>>> Best, >>>>> >>>>> Lennart. >>>>> >>>>> >>>>> On 02-05-14 10:27, Yurii Aulchenko wrote: >>>>>> On Fri, May 2, 2014 at 12:25 AM, Diego Fabregat >>>>>> >>>>> > >>>>>> wrote: >>>>>> >>>>>> I like the idea of moving to git. I have no experience with >>>>>> github, >>>>>> but I'm using git on an almost daily basis (we have our own git >>>>>> server in our group for code and papers). I would have no >>>>>> problem in >>>>>> uploading OmicABEL to a git repo. >>>>>> >>>>>> Does dropping R-forge have a (bad) impact on the visibility of >>>>>> the >>>>>> project or on the user experience (e.g., installation of R >>>>>> packages)? >>>>>> >>>>>> >>>>>> In my opinion - not really (visibility: I do not think we get many >>>>>> users >>>>>> because they've found us at r-forge; also we can keep the account and >>>>>> make links from there; as for installation, the argument partly holds >>>>>> only for R-packages). What we need to think is of course how we >>>>>> keep/move all parts such as a) code b) trackers c) project docs such >>>>>> as >>>>>> code guidelines >>>>>> >>>>>> To me it seems that the idea to migrate few packages first is the >>>>>> most >>>>>> reasonable; few are likely to stay at r-forge for long >>>>>> >>>>>> Yurii >>>>>> >>>>>> >>>>>> >>>>>> On 04/28/2014 10:09 PM, L.C. Karssen wrote: >>>>>>> Dear Maarten, dear all, >>>>>>> >>>>>>> Moving to github... Hmm... That is quite a decision, so I've >>>>>>> renamed the >>>>>>> subject to better reflect the discussion. I've also dropped the >>>>>>> older >>>>>>> e-mails from the bottom of the thread. >>>>>>> >>>>>>> First off, are there any people that have experience with git >>>>>>> and/or >>>>>>> github? I've got some git experience (still learning), but no >>>>>>> real >>>>>>> experience with github. >>>>>>> >>>>>>> I agree with Maarten that SVN is showing its age. As he >>>>>>> indicates >>>>>>> things >>>>>>> like branching are much easier in git. Moreover, since I'm >>>>>>> travelling >>>>>>> regularly being able to work without internet connection is a >>>>>>> pro. >>>>>>> >>>>>>> On the other hand, moving to git (whether github or elsewhere) >>>>>>> means >>>>>>> leaving R-forge, which is our well-known infrastructure. >>>>>>> Furthermore, >>>>>>> such a move operation will cost quite some time, I guess. Moving >>>>>>> all >>>>>>> bugs, features, etc... If we decide to move we should plan well >>>>>>> and not >>>>>>> rush. And then the current developers will need to learn git if >>>>>>> they >>>>>>> don't already know how to use it. >>>>>>> >>>>>>> One thing I think we should definitely do is migrate slowly, >>>>>>> package by >>>>>>> package. Given that Maarten is positive about such a move and >>>>>>> that >>>>>>> I am >>>>>>> in a bit of limbo but not fully against, it seems logical that >>>>>>> ProbABEL >>>>>>> is the first package to try such a migration. >>>>>>> >>>>>>> >>>>>>> Looking forward to your comments! >>>>>>> >>>>>>> >>>>>>> Lennart. >>>>>>> >>>>>>> >>>>>>> On 28-04-14 20:39, Maarten Kooyman wrote: >>>>>>>> Dear all, >>>>>>>> >>>>>>>> I think it is easier to use for code review github: >>>>>>>> >>>>>>>> Please check to get a impression >>>>>>>> :https://github.com/jquery/jquery/pull/1241/files >>>>>>>> >>>>>>>> I think we should reconsider an other the software version >>>>>>>> system: the >>>>>>>> current system is not up to date to current usability. Bug >>>>>>>> tracking and >>>>>>>> branching is quite hard in terms of usability. Please have a >>>>>>>> look >>>>>>>> at >>>>>>>> github.com to get a impression what is >>>>>>>> possible. >>>>>>>> >>>>>>>> Kind regards, >>>>>>>> >>>>>>>> Maarten >>>>>>>> >>>>>>>> >>>>>>> -- >>>>>>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* >>>>>>> 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- >>>>>>> dev >>>>>>> el >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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-d >>>>>> eve >>>>>> l >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> ----------------------------------------------------- >>>>>> Yurii S. Aulchenko >>>>>> >>>>>> [ LinkedIn ] [ Twitter >>>>>> ] [ Blog >>>>>> ] >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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-d >>>>>> eve >>>>>> l >>>>>> >>>>> >>>>> -- >>>>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* >>>>> 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-dev >>>> el >>>> >>> >>> >>> >>> _______________________________________________ >>> 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-deve >>> l >>> >> >> -- >> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* >> L.C. Karssen >> Utrecht >> The Netherlands >> >> lennart at karssen.org >> http://blog.karssen.org >> GPG key ID: A88F554A >> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- >> > -- *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* 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: From lennart at karssen.org Sat Oct 24 05:27:17 2015 From: lennart at karssen.org (L.C. Karssen) Date: Sat, 24 Oct 2015 06:27:17 +0300 Subject: [GenABEL-dev] Proposal to move to Github In-Reply-To: <562550A4.5010906@karssen.org> References: <20140428094937.65E8B186FC6@r-forge.r-project.org> <535E2774.6030606@karssen.org> <535E422F.4080402@gmail.com> <535E69D7.1050005@karssen.org> <535E6BDB.3000206@karssen.org> <535EA05E.40201@gmail.com> <535EB58D.6010900@karssen.org> <5362836C.4000105@aices.rwth-aachen.de> <562550A4.5010906@karssen.org> Message-ID: <562AFA95.3010601@karssen.org> Dear all, Looking at the discussion we had on this topic both in the past week and back in 2014 I propose the following: 1) I will migrate OmicABEL and OmicABELnoMM These two projects have a simple history (no tags, no branches) and converting them proved to be easy. Moreover, I seem to be the de facto maintainer of OmicABELnoMM and in last year's discussion Diego said he liked the idea of moving to Github. Finally, neither of these tools has had any bugs filed, so no work needs to be done on that front. 2) The new location will be Github. My reason for choosing Github over Bitbucket is mainly based on the popularity/dominance of Github. Please let me know of any objections. If I don't receive and objections in the next couple days I will upload the two Git repositories to Github under the GenABEL project flag, starting with OmicABELnoMM. Once that has been done and shown to work, we should somehow indicate in the SVN repo that the code has moved. I was thinking of simply removing the code in the /pkg/OmicABEL{,noMM} and replace it with a README that points to the Github locations. Of course, other suggestions are welcome. Best, Lennart. On 19-10-15 23:20, L.C. Karssen wrote: > Dear list, > > With this e-mail I'm digging up a conversation from the past (April/May > 2014). Back then we discussed (see below) the idea of moving (some of) > the GenABEL suite tools to a Git repository like GitHub. > > Since then I have gained more experience with Git and I love it. So I'm > all for giving it a try. This brings up the following questions on which > I'd like to hear your opinion: > > 1) Which package(s) do we migrate first? > > 2) Where do we migrate to? > > > Regarding 1): I think OmicABEL and OmicABELnoMM are the easiest to start > with. They have a linear history (no branches etc.) so conversion is > straightforward. I'd love to migrate ProbABEL, but I've spent several > hours in vain trying to keep the branches and history correct. More time > needed there (if someone has experience in SVN -> Git migration, please > let me know). > > Regarding 2): Either GitHub or BitBucket is an option for me. I have > some experience with both. Github is more popular/the de facto standard, > but the nice thing about Bitbucket is that it allows private > repositories (for up to 5 collaborators) also in their free plan. Not > sure if this is of any use for GenABEL. > > > Once we reach agreement on 1 and 2 I volunteer to do the migration. > > > Best, > > Lennart. > > > On 02-05-14 10:27, Yurii Aulchenko wrote: >> On Fri, May 2, 2014 at 12:25 AM, Diego Fabregat >> > >> wrote: >> >> I like the idea of moving to git. I have no experience with github, >> but I'm using git on an almost daily basis (we have our own git >> server in our group for code and papers). I would have no problem in >> uploading OmicABEL to a git repo. >> >> Does dropping R-forge have a (bad) impact on the visibility of the >> project or on the user experience (e.g., installation of R packages)? >> >> >> In my opinion - not really (visibility: I do not think we get many users >> because they've found us at r-forge; also we can keep the account and >> make links from there; as for installation, the argument partly holds >> only for R-packages). What we need to think is of course how we >> keep/move all parts such as a) code b) trackers c) project docs such as >> code guidelines >> >> To me it seems that the idea to migrate few packages first is the most >> reasonable; few are likely to stay at r-forge for long >> >> Yurii >> >> >> >> On 04/28/2014 10:09 PM, L.C. Karssen wrote: >>> Dear Maarten, dear all, >>> >>> Moving to github... Hmm... That is quite a decision, so I've renamed the >>> subject to better reflect the discussion. I've also dropped the older >>> e-mails from the bottom of the thread. >>> >>> First off, are there any people that have experience with git and/or >>> github? I've got some git experience (still learning), but no real >>> experience with github. >>> >>> I agree with Maarten that SVN is showing its age. As he indicates things >>> like branching are much easier in git. Moreover, since I'm travelling >>> regularly being able to work without internet connection is a pro. >>> >>> On the other hand, moving to git (whether github or elsewhere) means >>> leaving R-forge, which is our well-known infrastructure. Furthermore, >>> such a move operation will cost quite some time, I guess. Moving all >>> bugs, features, etc... If we decide to move we should plan well and not >>> rush. And then the current developers will need to learn git if they >>> don't already know how to use it. >>> >>> One thing I think we should definitely do is migrate slowly, package by >>> package. Given that Maarten is positive about such a move and that I am >>> in a bit of limbo but not fully against, it seems logical that ProbABEL >>> is the first package to try such a migration. >>> >>> >>> Looking forward to your comments! >>> >>> >>> Lennart. >>> >>> >>> On 28-04-14 20:39, Maarten Kooyman wrote: >>>> Dear all, >>>> >>>> I think it is easier to use for code review github: >>>> >>>> Please check to get a impression >>>> :https://github.com/jquery/jquery/pull/1241/files >>>> >>>> I think we should reconsider an other the software version system: the >>>> current system is not up to date to current usability. Bug tracking and >>>> branching is quite hard in terms of usability. Please have a look at >>>> github.com to get a impression what is possible. >>>> >>>> Kind regards, >>>> >>>> Maarten >>>> >>>> >>> -- >>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* >>> 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 >> >> >> _______________________________________________ >> 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 >> >> >> >> >> -- >> ----------------------------------------------------- >> Yurii S. Aulchenko >> >> [ LinkedIn ] [ Twitter >> ] [ Blog >> ] >> >> >> _______________________________________________ >> 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 >> > > > > _______________________________________________ > 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: From fabregat at aices.rwth-aachen.de Sat Oct 24 15:07:08 2015 From: fabregat at aices.rwth-aachen.de (Diego Fabregat) Date: Sat, 24 Oct 2015 15:07:08 +0200 Subject: [GenABEL-dev] Proposal to move to Github In-Reply-To: <562AFA95.3010601@karssen.org> References: <20140428094937.65E8B186FC6@r-forge.r-project.org> <535E2774.6030606@karssen.org> <535E422F.4080402@gmail.com> <535E69D7.1050005@karssen.org> <535E6BDB.3000206@karssen.org> <535EA05E.40201@gmail.com> <535EB58D.6010900@karssen.org> <5362836C.4000105@aices.rwth-aachen.de> <562550A4.5010906@karssen.org> <562AFA95.3010601@karssen.org> Message-ID: <562B827C.80903@aices.rwth-aachen.de> Hi Lennart (and the others :), sorry for not replying earlier. As you said, I am perfectly fine with the idea of migrating OmicABEL to github :) Best, Diego On 24.10.2015 05:27, L.C. Karssen wrote: > Dear all, > > Looking at the discussion we had on this topic both in the past week and > back in 2014 I propose the following: > > 1) I will migrate OmicABEL and OmicABELnoMM > > These two projects have a simple history (no tags, no branches) and > converting them proved to be easy. Moreover, I seem to be the de facto > maintainer of OmicABELnoMM and in last year's discussion Diego said he > liked the idea of moving to Github. Finally, neither of these tools has > had any bugs filed, so no work needs to be done on that front. > > 2) The new location will be Github. > > My reason for choosing Github over Bitbucket is mainly based on the > popularity/dominance of Github. > > > > Please let me know of any objections. If I don't receive and objections > in the next couple days I will upload the two Git repositories to Github > under the GenABEL project flag, starting with OmicABELnoMM. > > Once that has been done and shown to work, we should somehow indicate in > the SVN repo that the code has moved. I was thinking of simply removing > the code in the /pkg/OmicABEL{,noMM} and replace it with a README that > points to the Github locations. > Of course, other suggestions are welcome. > > > Best, > > Lennart. > > On 19-10-15 23:20, L.C. Karssen wrote: >> Dear list, >> >> With this e-mail I'm digging up a conversation from the past (April/May >> 2014). Back then we discussed (see below) the idea of moving (some of) >> the GenABEL suite tools to a Git repository like GitHub. >> >> Since then I have gained more experience with Git and I love it. So I'm >> all for giving it a try. This brings up the following questions on which >> I'd like to hear your opinion: >> >> 1) Which package(s) do we migrate first? >> >> 2) Where do we migrate to? >> >> >> Regarding 1): I think OmicABEL and OmicABELnoMM are the easiest to start >> with. They have a linear history (no branches etc.) so conversion is >> straightforward. I'd love to migrate ProbABEL, but I've spent several >> hours in vain trying to keep the branches and history correct. More time >> needed there (if someone has experience in SVN -> Git migration, please >> let me know). >> >> Regarding 2): Either GitHub or BitBucket is an option for me. I have >> some experience with both. Github is more popular/the de facto standard, >> but the nice thing about Bitbucket is that it allows private >> repositories (for up to 5 collaborators) also in their free plan. Not >> sure if this is of any use for GenABEL. >> >> >> Once we reach agreement on 1 and 2 I volunteer to do the migration. >> >> >> Best, >> >> Lennart. >> >> >> On 02-05-14 10:27, Yurii Aulchenko wrote: >>> On Fri, May 2, 2014 at 12:25 AM, Diego Fabregat >>> > >>> wrote: >>> >>> I like the idea of moving to git. I have no experience with github, >>> but I'm using git on an almost daily basis (we have our own git >>> server in our group for code and papers). I would have no problem in >>> uploading OmicABEL to a git repo. >>> >>> Does dropping R-forge have a (bad) impact on the visibility of the >>> project or on the user experience (e.g., installation of R packages)? >>> >>> >>> In my opinion - not really (visibility: I do not think we get many users >>> because they've found us at r-forge; also we can keep the account and >>> make links from there; as for installation, the argument partly holds >>> only for R-packages). What we need to think is of course how we >>> keep/move all parts such as a) code b) trackers c) project docs such as >>> code guidelines >>> >>> To me it seems that the idea to migrate few packages first is the most >>> reasonable; few are likely to stay at r-forge for long >>> >>> Yurii >>> >>> >>> >>> On 04/28/2014 10:09 PM, L.C. Karssen wrote: >>>> Dear Maarten, dear all, >>>> >>>> Moving to github... Hmm... That is quite a decision, so I've renamed the >>>> subject to better reflect the discussion. I've also dropped the older >>>> e-mails from the bottom of the thread. >>>> >>>> First off, are there any people that have experience with git and/or >>>> github? I've got some git experience (still learning), but no real >>>> experience with github. >>>> >>>> I agree with Maarten that SVN is showing its age. As he indicates things >>>> like branching are much easier in git. Moreover, since I'm travelling >>>> regularly being able to work without internet connection is a pro. >>>> >>>> On the other hand, moving to git (whether github or elsewhere) means >>>> leaving R-forge, which is our well-known infrastructure. Furthermore, >>>> such a move operation will cost quite some time, I guess. Moving all >>>> bugs, features, etc... If we decide to move we should plan well and not >>>> rush. And then the current developers will need to learn git if they >>>> don't already know how to use it. >>>> >>>> One thing I think we should definitely do is migrate slowly, package by >>>> package. Given that Maarten is positive about such a move and that I am >>>> in a bit of limbo but not fully against, it seems logical that ProbABEL >>>> is the first package to try such a migration. >>>> >>>> >>>> Looking forward to your comments! >>>> >>>> >>>> Lennart. >>>> >>>> >>>> On 28-04-14 20:39, Maarten Kooyman wrote: >>>>> Dear all, >>>>> >>>>> I think it is easier to use for code review github: >>>>> >>>>> Please check to get a impression >>>>> :https://github.com/jquery/jquery/pull/1241/files >>>>> >>>>> I think we should reconsider an other the software version system: the >>>>> current system is not up to date to current usability. Bug tracking and >>>>> branching is quite hard in terms of usability. Please have a look at >>>>> github.com to get a impression what is possible. >>>>> >>>>> Kind regards, >>>>> >>>>> Maarten >>>>> >>>>> >>>> -- >>>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* >>>> 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 >>> >>> _______________________________________________ >>> 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 >>> >>> >>> >>> >>> -- >>> ----------------------------------------------------- >>> Yurii S. Aulchenko >>> >>> [ LinkedIn ] [ Twitter >>> ] [ Blog >>> ] >>> >>> >>> _______________________________________________ >>> 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 >>> >> >> >> _______________________________________________ >> 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 >> > > > _______________________________________________ > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From lennart at karssen.org Sun Oct 25 07:25:20 2015 From: lennart at karssen.org (L.C. Karssen) Date: Sun, 25 Oct 2015 12:25:20 +0600 Subject: [GenABEL-dev] Proposal to move to Github In-Reply-To: <562B827C.80903@aices.rwth-aachen.de> References: <20140428094937.65E8B186FC6@r-forge.r-project.org> <535E2774.6030606@karssen.org> <535E422F.4080402@gmail.com> <535E69D7.1050005@karssen.org> <535E6BDB.3000206@karssen.org> <535EA05E.40201@gmail.com> <535EB58D.6010900@karssen.org> <5362836C.4000105@aices.rwth-aachen.de> <562550A4.5010906@karssen.org> <562AFA95.3010601@karssen.org> <562B827C.80903@aices.rwth-aachen.de> Message-ID: <562C75D0.3010700@karssen.org> Hi Diego, On 24-10-15 19:07, Diego Fabregat wrote: > Hi Lennart (and the others :), > > sorry for not replying earlier. As you said, I am perfectly fine > with the idea of migrating OmicABEL to github :) Thanks for the confirmation! I'll set things in motion later this week. Best, Lennart. > > Best, > Diego > > On 24.10.2015 05:27, L.C. Karssen wrote: >> Dear all, >> >> Looking at the discussion we had on this topic both in the past week and >> back in 2014 I propose the following: >> >> 1) I will migrate OmicABEL and OmicABELnoMM >> >> These two projects have a simple history (no tags, no branches) and >> converting them proved to be easy. Moreover, I seem to be the de facto >> maintainer of OmicABELnoMM and in last year's discussion Diego said he >> liked the idea of moving to Github. Finally, neither of these tools has >> had any bugs filed, so no work needs to be done on that front. >> >> 2) The new location will be Github. >> >> My reason for choosing Github over Bitbucket is mainly based on the >> popularity/dominance of Github. >> >> >> >> Please let me know of any objections. If I don't receive and objections >> in the next couple days I will upload the two Git repositories to Github >> under the GenABEL project flag, starting with OmicABELnoMM. >> >> Once that has been done and shown to work, we should somehow indicate in >> the SVN repo that the code has moved. I was thinking of simply removing >> the code in the /pkg/OmicABEL{,noMM} and replace it with a README that >> points to the Github locations. >> Of course, other suggestions are welcome. >> >> >> Best, >> >> Lennart. >> >> On 19-10-15 23:20, L.C. Karssen wrote: >>> Dear list, >>> >>> With this e-mail I'm digging up a conversation from the past (April/May >>> 2014). Back then we discussed (see below) the idea of moving (some of) >>> the GenABEL suite tools to a Git repository like GitHub. >>> >>> Since then I have gained more experience with Git and I love it. So I'm >>> all for giving it a try. This brings up the following questions on which >>> I'd like to hear your opinion: >>> >>> 1) Which package(s) do we migrate first? >>> >>> 2) Where do we migrate to? >>> >>> >>> Regarding 1): I think OmicABEL and OmicABELnoMM are the easiest to start >>> with. They have a linear history (no branches etc.) so conversion is >>> straightforward. I'd love to migrate ProbABEL, but I've spent several >>> hours in vain trying to keep the branches and history correct. More time >>> needed there (if someone has experience in SVN -> Git migration, please >>> let me know). >>> >>> Regarding 2): Either GitHub or BitBucket is an option for me. I have >>> some experience with both. Github is more popular/the de facto standard, >>> but the nice thing about Bitbucket is that it allows private >>> repositories (for up to 5 collaborators) also in their free plan. Not >>> sure if this is of any use for GenABEL. >>> >>> >>> Once we reach agreement on 1 and 2 I volunteer to do the migration. >>> >>> >>> Best, >>> >>> Lennart. >>> >>> >>> On 02-05-14 10:27, Yurii Aulchenko wrote: >>>> On Fri, May 2, 2014 at 12:25 AM, Diego Fabregat >>>> > >>>> wrote: >>>> >>>> I like the idea of moving to git. I have no experience with github, >>>> but I'm using git on an almost daily basis (we have our own git >>>> server in our group for code and papers). I would have no problem in >>>> uploading OmicABEL to a git repo. >>>> >>>> Does dropping R-forge have a (bad) impact on the visibility of the >>>> project or on the user experience (e.g., installation of R packages)? >>>> >>>> >>>> In my opinion - not really (visibility: I do not think we get many users >>>> because they've found us at r-forge; also we can keep the account and >>>> make links from there; as for installation, the argument partly holds >>>> only for R-packages). What we need to think is of course how we >>>> keep/move all parts such as a) code b) trackers c) project docs such as >>>> code guidelines >>>> >>>> To me it seems that the idea to migrate few packages first is the most >>>> reasonable; few are likely to stay at r-forge for long >>>> >>>> Yurii >>>> >>>> >>>> >>>> On 04/28/2014 10:09 PM, L.C. Karssen wrote: >>>>> Dear Maarten, dear all, >>>>> >>>>> Moving to github... Hmm... That is quite a decision, so I've renamed the >>>>> subject to better reflect the discussion. I've also dropped the older >>>>> e-mails from the bottom of the thread. >>>>> >>>>> First off, are there any people that have experience with git and/or >>>>> github? I've got some git experience (still learning), but no real >>>>> experience with github. >>>>> >>>>> I agree with Maarten that SVN is showing its age. As he indicates things >>>>> like branching are much easier in git. Moreover, since I'm travelling >>>>> regularly being able to work without internet connection is a pro. >>>>> >>>>> On the other hand, moving to git (whether github or elsewhere) means >>>>> leaving R-forge, which is our well-known infrastructure. Furthermore, >>>>> such a move operation will cost quite some time, I guess. Moving all >>>>> bugs, features, etc... If we decide to move we should plan well and not >>>>> rush. And then the current developers will need to learn git if they >>>>> don't already know how to use it. >>>>> >>>>> One thing I think we should definitely do is migrate slowly, package by >>>>> package. Given that Maarten is positive about such a move and that I am >>>>> in a bit of limbo but not fully against, it seems logical that ProbABEL >>>>> is the first package to try such a migration. >>>>> >>>>> >>>>> Looking forward to your comments! >>>>> >>>>> >>>>> Lennart. >>>>> >>>>> >>>>> On 28-04-14 20:39, Maarten Kooyman wrote: >>>>>> Dear all, >>>>>> >>>>>> I think it is easier to use for code review github: >>>>>> >>>>>> Please check to get a impression >>>>>> :https://github.com/jquery/jquery/pull/1241/files >>>>>> >>>>>> I think we should reconsider an other the software version system: the >>>>>> current system is not up to date to current usability. Bug tracking and >>>>>> branching is quite hard in terms of usability. Please have a look at >>>>>> github.com to get a impression what is possible. >>>>>> >>>>>> Kind regards, >>>>>> >>>>>> Maarten >>>>>> >>>>>> >>>>> -- >>>>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* >>>>> 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 >>>> >>>> _______________________________________________ >>>> 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 >>>> >>>> >>>> >>>> >>>> -- >>>> ----------------------------------------------------- >>>> Yurii S. Aulchenko >>>> >>>> [ LinkedIn ] [ Twitter >>>> ] [ Blog >>>> ] >>>> >>>> >>>> _______________________________________________ >>>> 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 >>>> >>> >>> >>> _______________________________________________ >>> 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 >>> >> >> >> _______________________________________________ >> 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 > > > > _______________________________________________ > 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: From lennart at karssen.org Thu Oct 29 13:25:24 2015 From: lennart at karssen.org (L.C. Karssen) Date: Thu, 29 Oct 2015 18:25:24 +0600 Subject: [GenABEL-dev] OmicABEL and OmicABELnoMM moved to Github Message-ID: <56321034.8070801@karssen.org> Dear list, I have converted the SVN repo for OmicABEL and OmicABELnoMM to Git and uploaded them to Github [1,2]. All in all the transition went smoothly. Only for OmicABELnoMM I had to remove the examples/Y.fvd file since it was larger then 100MB, which GitHub doesn't allow. Since the examples/CreateData.R recreates the example files, this was not really a problem. Neither of these two projects had bug reports/feature requests associated with them in the Bug tracker. Diego, since you're the OmicABEL maintainer, can you send me your github username so I can give you the correct permissions. As a side note: on the GenABEL Project Github webpage you can also see ProbABEL and filevector, those two are in principle ok, but existing bugs and feature requests have not been lifted over to Github yet. Best, Lennart. [1] https://github.com/GenABEL-Project/OmicABEL [2] https://github.com/GenABEL-Project/OmicABELnoMM -- *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* 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: From lennart at karssen.org Thu Oct 29 13:26:37 2015 From: lennart at karssen.org (L.C. Karssen) Date: Thu, 29 Oct 2015 18:26:37 +0600 Subject: [GenABEL-dev] OmicABEL and OmicABELnoMM moved to Github Message-ID: <5632107D.6070307@karssen.org> Dear list, I have converted the SVN repo for OmicABEL and OmicABELnoMM to Git and uploaded them to Github [1,2]. All in all the transition went smoothly. Only for OmicABELnoMM I had to remove the examples/Y.fvd file since it was larger then 100MB, which GitHub doesn't allow. Since the examples/CreateData.R recreates the example files, this was not really a problem. Neither of these two projects had bug reports/feature requests associated with them in the Bug tracker. As for cleaning up SVN: I will remove the files from the OmicABEL and OmicABELnoMM directories and put in a README file pointing to the GitHub pages. Diego, since you're the OmicABEL maintainer, can you send me your github username so I can give you the correct permissions. As a side note: on the GenABEL Project Github webpage you can also see ProbABEL and filevector, those two are in principle ok, but existing bugs and feature requests have not been lifted over to Github yet. Best, Lennart. [1] https://github.com/GenABEL-Project/OmicABEL [2] https://github.com/GenABEL-Project/OmicABELnoMM -- *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* 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: