From tom at moertel.com Wed May 23 19:17:48 2007 From: tom at moertel.com (Tom Moertel) Date: Wed, 23 May 2007 15:17:48 -0400 Subject: [Fedora-r-devel-list] Package R-Matrix submitted for review Message-ID: <4654935C.6020800@moertel.com> Fellow R-module packagers, I wanted to let you know that I have (finally) submitted the first of my R packages for review: https://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=241052 Please take a look and let me know if there is anything I can do to improve this package. Once all the wrinkles are ironed out and the package is accepted, I will submit my other packages for review. Thanks for your help! Past discussion: https://www.redhat.com/archives/fedora-r-devel-list/2007-April/msg00003.html Cheers, Tom From pingoufc4 at yahoo.fr Wed May 23 20:22:51 2007 From: pingoufc4 at yahoo.fr (pingou) Date: Wed, 23 May 2007 22:22:51 +0200 Subject: [Fedora-r-devel-list] Presentation Message-ID: <4654A29B.6090805@yahoo.fr> Hello, My name is Pierre-Yves Chibon, I am one of the french ambassadors. I have just discovered this mailing list but I am glad to see that I am not the only one using R under Fedora :-) (not lot of french do so) To shortly introduce myself, I am student doing a master in bioinformatics. And i will have to program under R so I have already done the RPMs needed for the software on which I will have to work. These RPMs are Biobase, Multtest, and Maanova (but this one was to try), they are all from the bioconductor website. Biobase and Multtest are waiting for reviews on bugzilla. And I am waiting for their review to make other RPMs :-) I hope to be helpful in what I can do... Sincerely yours, Pierre-Yves ___________________________________________________________________________ Yahoo! Mail r?invente le mail ! D?couvrez le nouveau Yahoo! Mail et son interface r?volutionnaire. http://fr.mail.yahoo.com From tcallawa at redhat.com Wed May 23 20:23:50 2007 From: tcallawa at redhat.com (Tom "spot" Callaway) Date: Wed, 23 May 2007 15:23:50 -0500 Subject: [Fedora-r-devel-list] Presentation In-Reply-To: <4654A29B.6090805@yahoo.fr> References: <4654A29B.6090805@yahoo.fr> Message-ID: <1179951831.6254.328.camel@localhost.localdomain> On Wed, 2007-05-23 at 22:22 +0200, pingou wrote: > Hello, > > My name is Pierre-Yves Chibon, I am one of the french ambassadors. > I have just discovered this mailing list but I am glad to see that I am > not the only one using R under Fedora :-) (not lot of french do so) > > To shortly introduce myself, I am student doing a master in > bioinformatics. And i will have to program under R so I have already > done the RPMs needed for the software on which I will have to work. > These RPMs are Biobase, Multtest, and Maanova (but this one was to try), > they are all from the bioconductor website. > Biobase and Multtest are waiting for reviews on bugzilla. And I am > waiting for their review to make other RPMs :-) > > I hope to be helpful in what I can do... Post the links to the bugzilla tickets? :) ~spot From tcallawa at redhat.com Wed May 23 21:13:54 2007 From: tcallawa at redhat.com (Tom "spot" Callaway) Date: Wed, 23 May 2007 16:13:54 -0500 Subject: [Fedora-r-devel-list] Presentation In-Reply-To: <1179951831.6254.328.camel@localhost.localdomain> References: <4654A29B.6090805@yahoo.fr> <1179951831.6254.328.camel@localhost.localdomain> Message-ID: <1179954834.6254.339.camel@localhost.localdomain> On Wed, 2007-05-23 at 15:23 -0500, Tom "spot" Callaway wrote: > On Wed, 2007-05-23 at 22:22 +0200, pingou wrote: > > Hello, > > > > My name is Pierre-Yves Chibon, I am one of the french ambassadors. > > I have just discovered this mailing list but I am glad to see that I am > > not the only one using R under Fedora :-) (not lot of french do so) > > > > To shortly introduce myself, I am student doing a master in > > bioinformatics. And i will have to program under R so I have already > > done the RPMs needed for the software on which I will have to work. > > These RPMs are Biobase, Multtest, and Maanova (but this one was to try), > > they are all from the bioconductor website. > > Biobase and Multtest are waiting for reviews on bugzilla. And I am > > waiting for their review to make other RPMs :-) > > > > I hope to be helpful in what I can do... > > Post the links to the bugzilla tickets? :) OK, so when I looked at R-Biobase: https://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=240500 I noted that it was missing R CMD check in a %check section. Of course, now I remember why. There is a circular "dependency" loop between Biobase, tkWidgets and widgetTools when running R CMD check. Biobase says it needs tkWidgets, tkWidgets says it needs Biobase. Neither is really true, but I'd rather have Biobase running the check than tkWidgets, so thats how I resolved the loop. Occasionally, it is necessary to resolve this "check dependency loop" by not running check on a package. In those cases, please DOCUMENT in the spec file that the check command is commented out, and explain the loop you're breaking. I whipped up the necessary missing packages here: DynDoc: http://www.auroralinux.org/people/spot/review/R-DynDoc-1.14.0-1.fc7.src.rpm http://www.auroralinux.org/people/spot/review/R-DynDoc.spec widgetTools: http://www.auroralinux.org/people/spot/review/R-widgetTools-1.12.0-1.fc7.src.rpm http://www.auroralinux.org/people/spot/review/R-widgetTools.spec tkWidgets: http://www.auroralinux.org/people/spot/review/R-tkWidgets-1.14.0-1.fc7.src.rpm http://www.auroralinux.org/people/spot/review/R-tkWidgets.spec Pingou, if you'd like to own these packages in Fedora, that is fine by me. If not, I'll put them up for review. ~spot From pingoufc4 at yahoo.fr Wed May 23 21:37:07 2007 From: pingoufc4 at yahoo.fr (pingou) Date: Wed, 23 May 2007 23:37:07 +0200 Subject: [Fedora-r-devel-list] Presentation In-Reply-To: <1179954834.6254.339.camel@localhost.localdomain> References: <4654A29B.6090805@yahoo.fr> <1179951831.6254.328.camel@localhost.localdomain> <1179954834.6254.339.camel@localhost.localdomain> Message-ID: <4654B403.1070403@yahoo.fr> Tom "spot" Callaway a ?crit : > On Wed, 2007-05-23 at 15:23 -0500, Tom "spot" Callaway wrote: >> On Wed, 2007-05-23 at 22:22 +0200, pingou wrote: >>> Hello, >>> >>> My name is Pierre-Yves Chibon, I am one of the french ambassadors. >>> I have just discovered this mailing list but I am glad to see that I am >>> not the only one using R under Fedora :-) (not lot of french do so) >>> >>> To shortly introduce myself, I am student doing a master in >>> bioinformatics. And i will have to program under R so I have already >>> done the RPMs needed for the software on which I will have to work. >>> These RPMs are Biobase, Multtest, and Maanova (but this one was to try), >>> they are all from the bioconductor website. >>> Biobase and Multtest are waiting for reviews on bugzilla. And I am >>> waiting for their review to make other RPMs :-) >>> >>> I hope to be helpful in what I can do... >> Post the links to the bugzilla tickets? :) > > OK, so when I looked at R-Biobase: > https://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=240500 > > I noted that it was missing R CMD check in a %check section. > > Of course, now I remember why. There is a circular "dependency" loop > between Biobase, tkWidgets and widgetTools when running R CMD check. > > Biobase says it needs tkWidgets, tkWidgets says it needs Biobase. > Neither is really true, but I'd rather have Biobase running the check > than tkWidgets, so thats how I resolved the loop. > > Occasionally, it is necessary to resolve this "check dependency loop" by > not running check on a package. In those cases, please DOCUMENT in the > spec file that the check command is commented out, and explain the loop > you're breaking. > > I whipped up the necessary missing packages here: > > DynDoc: > http://www.auroralinux.org/people/spot/review/R-DynDoc-1.14.0-1.fc7.src.rpm > http://www.auroralinux.org/people/spot/review/R-DynDoc.spec > > widgetTools: > http://www.auroralinux.org/people/spot/review/R-widgetTools-1.12.0-1.fc7.src.rpm > http://www.auroralinux.org/people/spot/review/R-widgetTools.spec > > tkWidgets: > http://www.auroralinux.org/people/spot/review/R-tkWidgets-1.14.0-1.fc7.src.rpm > http://www.auroralinux.org/people/spot/review/R-tkWidgets.spec > > Pingou, if you'd like to own these packages in Fedora, that is fine by > me. If not, I'll put them up for review. > > ~spot > I do not mind to maintain them as I have no package yet. But it is up to you as you have just made them... (much faster than I did actually :-D) I am checking my others RPMs to see if I have any mistake with the %check Pingou ___________________________________________________________________________ Yahoo! Mail r?invente le mail ! D?couvrez le nouveau Yahoo! Mail et son interface r?volutionnaire. http://fr.mail.yahoo.com From tcallawa at redhat.com Wed May 23 21:43:28 2007 From: tcallawa at redhat.com (Tom "spot" Callaway) Date: Wed, 23 May 2007 16:43:28 -0500 Subject: [Fedora-r-devel-list] Presentation In-Reply-To: <4654B403.1070403@yahoo.fr> References: <4654A29B.6090805@yahoo.fr> <1179951831.6254.328.camel@localhost.localdomain> <1179954834.6254.339.camel@localhost.localdomain> <4654B403.1070403@yahoo.fr> Message-ID: <1179956608.6254.346.camel@localhost.localdomain> On Wed, 2007-05-23 at 23:37 +0200, pingou wrote: > I do not mind to maintain them as I have no package yet. > But it is up to you as you have just made them... (much faster than I > did actually :-D) Well, they're easy packages to make/maintain, since they're all off a basic template. I'll let you own them, as I have enough packages already. Go ahead and put them up for review, and post the bugzilla numbers back to this thread. ~spot From pingoufc4 at yahoo.fr Wed May 23 22:39:24 2007 From: pingoufc4 at yahoo.fr (pingou) Date: Thu, 24 May 2007 00:39:24 +0200 Subject: [Fedora-r-devel-list] Presentation In-Reply-To: <1179956608.6254.346.camel@localhost.localdomain> References: <4654A29B.6090805@yahoo.fr> <1179951831.6254.328.camel@localhost.localdomain> <1179954834.6254.339.camel@localhost.localdomain> <4654B403.1070403@yahoo.fr> <1179956608.6254.346.camel@localhost.localdomain> Message-ID: <4654C29C.5080403@yahoo.fr> Tom "spot" Callaway a ?crit : > Go ahead and put them up for review, and post the bugzilla numbers back > to this thread. > > ~spot > It is done :-) R-DynDoc https://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=241079 R-widgetTools https://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=241081 R-tkWidgets https://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=241082 I have also updated my first package with the %check section (it works) https://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=240497 Pingou (btw I am seeking for a sponsor) ___________________________________________________________________________ Yahoo! Mail r?invente le mail ! D?couvrez le nouveau Yahoo! Mail et son interface r?volutionnaire. http://fr.mail.yahoo.com From tom at moertel.com Fri May 25 16:05:18 2007 From: tom at moertel.com (Tom Moertel) Date: Fri, 25 May 2007 12:05:18 -0400 Subject: [Fedora-r-devel-list] R-Matrix ready for more review [was: Package R-Matrix submitted for review] In-Reply-To: <4654935C.6020800@moertel.com> References: <4654935C.6020800@moertel.com> Message-ID: <4657093E.1090100@moertel.com> Fellow R-module packagers, I believe I have resolved the outstanding problems with the submission of R-Matrix. Please take a look and let me know if there is anything else I ought to do: https://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=241052 Thanks for your help! Cheers, Tom From jamatos at fc.up.pt Fri May 25 16:09:46 2007 From: jamatos at fc.up.pt (=?windows-1252?q?Jos=E9_Matos?=) Date: Fri, 25 May 2007 17:09:46 +0100 Subject: [Fedora-r-devel-list] R-Matrix ready for more review [was: Package R-Matrix submitted for review] In-Reply-To: <4657093E.1090100@moertel.com> References: <4654935C.6020800@moertel.com> <4657093E.1090100@moertel.com> Message-ID: <200705251709.46467.jamatos@fc.up.pt> On Friday 25 May 2007 17:05:18 Tom Moertel wrote: > Fellow R-module packagers, > > I believe I have resolved the outstanding problems with the submission > of R-Matrix. Please take a look and let me know if there is anything > else I ought to do: > > https://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=241052 > > Thanks for your help! I will try to have a look at them next week. I still have to release the first release candidate of lyx 1.5 meanwhile. :-) > Cheers, > Tom -- Jos? Ab?lio From tom at moertel.com Fri May 25 19:21:56 2007 From: tom at moertel.com (Tom Moertel) Date: Fri, 25 May 2007 15:21:56 -0400 Subject: [Fedora-r-devel-list] Which branches should I apply for? FC-6 and F-7? [was: R-Matrix ready for more review] In-Reply-To: <4657093E.1090100@moertel.com> References: <4654935C.6020800@moertel.com> <4657093E.1090100@moertel.com> Message-ID: <46573754.4060101@moertel.com> Fellow R-module packagers, Sorry for all questions. I'm still trying to navigate my away through the nooks and crannies of the submission process. While following the instructions in http://fedoraproject.org/wiki/PackageMaintainers/Join the "Add Package to CVS and Set Owner" step referred me to http://fedoraproject.org/wiki/PackageMaintainers/CVSAdminProcedure I'm presently following the "New Packages" instructions of the second document. They tell me that I must make a Bugzilla comment (presumably to my approved package-review-request ticket), containing the following: New Package CVS Request ======================= Package Name: R-Matrix Short Description: R module, Classes etc. for dense and sparse matrices and matrix ops Owners: tom at moertel.com Branches: FC-6 F-7 InitialCC: tom at moertel.com It's pretty clear to me what ought to go in each of the required fields except Branches. I guessed "FC-6 F-7", but the PackageMaintainers/CVSAdminProcedure page says: Valid branch names currently used for Fedora: FC-5 FC-6 F-7 EL-4 EL-5. Should I list them all? Only the ones for which I have personally tested the package? Some other combination? What's the guiding philosophy here -- more, fewer, or something else? Thanks again for all your help! Cheers, Tom From tcallawa at redhat.com Fri May 25 19:39:14 2007 From: tcallawa at redhat.com (Tom "spot" Callaway) Date: Fri, 25 May 2007 14:39:14 -0500 Subject: [Fedora-r-devel-list] Which branches should I apply for? FC-6 and F-7? [was: R-Matrix ready for more review] In-Reply-To: <46573754.4060101@moertel.com> References: <4654935C.6020800@moertel.com> <4657093E.1090100@moertel.com> <46573754.4060101@moertel.com> Message-ID: <1180121954.6254.389.camel@localhost.localdomain> On Fri, 2007-05-25 at 15:21 -0400, Tom Moertel wrote: > It's pretty clear to me what ought to go in each of the required fields > except Branches. I guessed "FC-6 F-7", but the > PackageMaintainers/CVSAdminProcedure page says: > > Valid branch names currently used for Fedora: > FC-5 FC-6 F-7 EL-4 EL-5. > > Should I list them all? Only the ones for which I have personally > tested the package? Some other combination? What's the guiding > philosophy here -- more, fewer, or something else? Decide which branches you're able to test and maintain. R is pretty consistent across FC-5, FC-6, and F-7. I can't vouch for EL-4, EL-5, as I've never built R there yet. I'll probably end up doing it, as I'm sure there is interest from the .edus. You can always add branches later. ~spot From tom at moertel.com Mon May 28 17:52:10 2007 From: tom at moertel.com (Tom Moertel) Date: Mon, 28 May 2007 13:52:10 -0400 Subject: [Fedora-r-devel-list] Waiting on 'fedorabugs' membership [was: Which branches ... ?] In-Reply-To: <1180121954.6254.389.camel@localhost.localdomain> References: <4654935C.6020800@moertel.com> <4657093E.1090100@moertel.com> <46573754.4060101@moertel.com> <1180121954.6254.389.camel@localhost.localdomain> Message-ID: <465B16CA.8020500@moertel.com> Tom "spot" Callaway wrote: > On Fri, 2007-05-25 at 15:21 -0400, Tom Moertel wrote: > Decide which branches you're able to test and maintain. [...] I'm going for FC-6 and F-7, then. Thanks for your response. Now I'm just waiting for my 'fedorabugs' group membership to clear so I can set the fedora-cvs flag on my ticket in order to get the CVS module created. Thanks again for all your help. Cheers, Tom