From pingou at pingoured.fr Sun Aug 2 16:56:47 2009 From: pingou at pingoured.fr (Pierre-Yves) Date: Sun, 02 Aug 2009 18:56:47 +0200 Subject: [Fedora-r-devel-list] Update the guidelines In-Reply-To: <1237661999.3243.23.camel@localhost.localdomain> References: <1237661999.3243.23.camel@localhost.localdomain> Message-ID: <1249232207.2573.16.camel@red.localdomain> On Sat, 2009-03-21 at 19:59 +0100, Pierre-Yves wrote: > Dear all, > > I would like to propose to update (or mention) some points in the R > packaging guidelines. > > * Mention something about the tex files which are not utf-8 and don't > necessarily have to be converted > see: > https://www.redhat.com/archives/fedora-devel-list/2009-January/msg00741.html > > * Mention something about the -devel package where the headers don't > necessarily have to moved to %{_datadir} since R looks for them in > %{_libdir}. > see: > https://www.redhat.com/archives/fedora-r-devel-list/2009-March/msg00001.html I am planning on writing down a proposal to add those remarks to the guidelines. In addition I though we could also : - Mention about the version which in R might contains '-' which should be replaced in Fedora - Mention R2spec as tool to create spec file - Mention the new sources of library (the two r-forges) Do you see any other points to be added/changed ? I will send to the list the proposal once done. Best regards, Pierre From pingou at pingoured.fr Sun Aug 2 19:50:00 2009 From: pingou at pingoured.fr (Pierre-Yves) Date: Sun, 02 Aug 2009 21:50:00 +0200 Subject: [Fedora-r-devel-list] R2spec v2.5.3 Message-ID: <1249242600.2573.22.camel@red.localdomain> Dear list, As just announced on my blog I released a new version of R2spec and there is the changelog for this version: Version 2.5.3 -- 02nd Aug 2009 - Features added * Prints warning if summary is empty * Prints warning if description is empty * Add support for r-forge.net (option --rforge) * Add support for r-forge.r-project.org (option --rproject) * Add the prefix R- to the list of dependencies with a list of package to ignore (ie: R) * Add a default source0 and url if the bioconductor release is not set - Bugs correction * Does not add the 'Requires:' to the spec if they are empty * Changes the '-' into '.' if the version of the R library contains any '-' Package is available for F-10, F-11, rawhide, EPEL-4 and EPEL-5. Feel free to add some karma if you test it :) Thanks, Best regards, Pierre From pingou at pingoured.fr Tue Aug 4 16:49:51 2009 From: pingou at pingoured.fr (Pierre-Yves) Date: Tue, 04 Aug 2009 18:49:51 +0200 Subject: [Fedora-r-devel-list] Update the guidelines In-Reply-To: <1249232207.2573.16.camel@red.localdomain> References: <1237661999.3243.23.camel@localhost.localdomain> <1249232207.2573.16.camel@red.localdomain> Message-ID: <1249404591.5658.1.camel@red.localdomain> On Sun, 2009-08-02 at 18:56 +0200, Pierre-Yves wrote: > On Sat, 2009-03-21 at 19:59 +0100, Pierre-Yves wrote: > > Dear all, > > > > I would like to propose to update (or mention) some points in the R > > packaging guidelines. > > > > * Mention something about the tex files which are not utf-8 and don't > > necessarily have to be converted > > see: > > https://www.redhat.com/archives/fedora-devel-list/2009-January/msg00741.html > > > > * Mention something about the -devel package where the headers don't > > necessarily have to moved to %{_datadir} since R looks for them in > > %{_libdir}. > > see: > > https://www.redhat.com/archives/fedora-r-devel-list/2009-March/msg00001.html > > I am planning on writing down a proposal to add those remarks to the > guidelines. > > In addition I though we could also : > - Mention about the version which in R might contains '-' which should > be replaced in Fedora > - Mention R2spec as tool to create spec file > - Mention the new sources of library (the two r-forges) > > Do you see any other points to be added/changed ? I put all this together here: https://fedoraproject.org/wiki/ProposalUpdateRGuidelines and also there thus: https://fedoraproject.org/wiki/PackagingDrafts/DraftsTodo I put target date as 'Discuss' waiting to hear from you but there is a meeting tomorrow if we make it on time :) Feel free to react of it :) Best regards, Pierre From pingou at pingoured.fr Sat Aug 8 09:47:37 2009 From: pingou at pingoured.fr (Pierre-Yves) Date: Sat, 08 Aug 2009 11:47:37 +0200 Subject: [Fedora-r-devel-list] version corrected Message-ID: <1249724857.2600.2.camel@red.localdomain> Dear list, Remi and I have patched the website to correct the version number that contained a '-'. You can thus go to [1] to check if you are up-to-date. Let me know if you face an error or a problem :) Best regards, Pierre [1] http://rpms.famillecollet.com/rpmphp/rpm.php?type=R From pingou at pingoured.fr Thu Aug 20 20:20:58 2009 From: pingou at pingoured.fr (Pierre-Yves) Date: Thu, 20 Aug 2009 22:20:58 +0200 Subject: [Fedora-r-devel-list] [Fwd: Re: TeX Live 2009 for Fedora] Message-ID: <1250799658.11515.0.camel@red.localdomain> FYI I will update R2spec to meet the new guidelines soon. Best regards, Pierre -------------- next part -------------- An embedded message was scrubbed... From: Jason L Tibbitts III Subject: Re: TeX Live 2009 for Fedora Date: Thu, 20 Aug 2009 13:26:13 -0500 Size: 4022 URL: From jamatos at fc.up.pt Thu Aug 20 20:34:02 2009 From: jamatos at fc.up.pt (=?utf-8?q?Jos=C3=A9_Matos?=) Date: Thu, 20 Aug 2009 21:34:02 +0100 Subject: [Fedora-r-devel-list] [Fwd: Re: TeX Live 2009 for Fedora] In-Reply-To: <1250799658.11515.0.camel@red.localdomain> References: <1250799658.11515.0.camel@red.localdomain> Message-ID: <200908202134.03638.jamatos@fc.up.pt> On Thursday 20 August 2009 21:20:58 Pierre-Yves wrote: > FYI > > I will update R2spec to meet the new guidelines soon. > > Best regards, > > Pierre The only conflict that I get, for R packages I have installed, when updating the new latex is with R-devel. At the same time as Jason stated the possible complication that comes from the change is the difference between Fedora and EPEL packages. That means one more conditional in the file, perhaps. :-) -- Jos? Ab?lio From pingou at pingoured.fr Thu Aug 20 20:42:17 2009 From: pingou at pingoured.fr (Pierre-Yves) Date: Thu, 20 Aug 2009 22:42:17 +0200 Subject: [Fedora-r-devel-list] [Fwd: Re: TeX Live 2009 for Fedora] In-Reply-To: <200908202134.03638.jamatos@fc.up.pt> References: <1250799658.11515.0.camel@red.localdomain> <200908202134.03638.jamatos@fc.up.pt> Message-ID: <1250800937.11515.16.camel@red.localdomain> On Thu, 2009-08-20 at 21:34 +0100, Jos? Matos wrote: > On Thursday 20 August 2009 21:20:58 Pierre-Yves wrote: > > FYI > > > > I will update R2spec to meet the new guidelines soon. > > > > Best regards, > > > > Pierre > > The only conflict that I get, for R packages I have installed, when updating > the new latex is with R-devel. > > At the same time as Jason stated the possible complication that comes from the > change is the difference between Fedora and EPEL packages. That means one more > conditional in the file, perhaps. :-) > Jindrich replied: > Thanks for updating the packaging guidelines. I will add te tetex-* > provides to be compatible with the legacy packages. I guess this solve the issue, but then I'm curious on whether it makes any difference to change the specs (or did I understand it wrongly ?) Regards, Pierre From ihok at hotmail.com Sun Aug 23 17:11:38 2009 From: ihok at hotmail.com (Jack Tanner) Date: Sun, 23 Aug 2009 13:11:38 -0400 Subject: [Fedora-r-devel-list] RMySQL spec file Message-ID: Hi, here's a spec file in case anyone wants to package up RMySQL. I'm hereby placing it in the public domain, so please modify as necessary, and don't even bother giving me credit. I'm not volunteering to be a maintainer myself. It passes rpmlint, it's tested only on CentOS 5, and it works for me. YMMV. I'm somewhat unsure about the BuildRequires. By the way, R2spec was a really good starting point, but I had to deviate from its suggestions in a couple of places. You could diff an R2spec-generated file and the one below if you're curious. -- CUT HERE -- %global packname RMySQL %global packrel 1 Name: R-%{packname} Version: 0.7 Release: 4%{?dist} Summary: R interface to the MySQL database Group: Applications/Engineering License: GPLv2 URL: http://cran.r-project.org/web/packages/RMySQL/ Source0: ftp://cran.r-project.org/pub/R/contrib/main/%{packname}_%{version}-%{release}.tar.gz BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n) Requires(post): R Requires(postun): R BuildRequires: R-devel tetex-latex R >= R-2.8.0 R-methods R-DBI >= R-0.2-2 R-utils mysql-devel %description Database interface and MySQL driver for R. This version complies with the database interface definition as implemented in the package DBI 0.2-2. %prep %setup -q -c -n %{packname} %build %install rm -rf %{buildroot} mkdir -p %{buildroot}%{_libdir}/R/library %{_bindir}/R CMD INSTALL -l %{buildroot}%{_libdir}/R/library %{packname} test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so) rm -rf %{buildroot}%{_libdir}/R/library/R.css %check %{_bindir}/R CMD check %{packname} %clean rm -rf %{buildroot} %post %{_R_make_search_index} %postun %{_R_make_search_index} %files %defattr(-, root, root, -) %dir %{_libdir}/R/library/%{packname} %doc %{_libdir}/R/library/%{packname}/latex %doc %{_libdir}/R/library/%{packname}/doc %doc %{_libdir}/R/library/%{packname}/html %doc %{_libdir}/R/library/%{packname}/DESCRIPTION %doc %{_libdir}/R/library/%{packname}/man %doc %{_libdir}/R/library/%{packname}/NEWS %doc %{_libdir}/R/library/%{packname}/GPL %doc %{_libdir}/R/library/%{packname}/GPL %doc %{_libdir}/R/library/%{packname}/INSTALL %doc %{_libdir}/R/library/%{packname}/INSTALL.win %doc %{_libdir}/R/library/%{packname}/README %doc %{_libdir}/R/library/%{packname}/README.windows %doc %{_libdir}/R/library/%{packname}/THANKS %doc %{_libdir}/R/library/%{packname}/TODO %doc %{_libdir}/R/library/%{packname}/WindowsPath.txt %doc %{_libdir}/R/library/%{packname}/newFunctionNames.txt %{_libdir}/R/library/%{packname}/CONTENTS %{_libdir}/R/library/%{packname}/INDEX %{_libdir}/R/library/%{packname}/NAMESPACE %{_libdir}/R/library/%{packname}/Meta %{_libdir}/R/library/%{packname}/R %{_libdir}/R/library/%{packname}/R-ex %{_libdir}/R/library/%{packname}/help %{_libdir}/R/library/%{packname}/FindMySQLhome.R %{_libdir}/R/library/%{packname}/libs/RMySQL.so %changelog * Sun Aug 23 2009 Name 0.7.4-1 - initial package for Fedora From dan.bolser at gmail.com Sun Aug 23 20:26:22 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Sun, 23 Aug 2009 21:26:22 +0100 Subject: [Fedora-r-devel-list] RMySQL spec file In-Reply-To: References: Message-ID: <2c8757af0908231326s63dd83a5v5e707b648442461d@mail.gmail.com> Thanks very much for providing this Jack! 2009/8/23 Jack Tanner : > Hi, here's a spec file in case anyone wants to package up RMySQL. I'm hereby > placing it in the public domain, so please modify as necessary, and don't > even bother giving me credit. I'm not volunteering to be a maintainer > myself. > > It passes rpmlint, it's tested only on CentOS 5, and it works for me. YMMV. > I'm somewhat unsure about the BuildRequires. > > By the way, R2spec was a really good starting point, but I had to deviate > from its suggestions in a couple of places. You could diff an > R2spec-generated file and the one below if you're curious. > > -- CUT HERE -- > > %global packname RMySQL > %global packrel 1 > > Name: R-%{packname} > Version: 0.7 > Release: 4%{?dist} > Summary: R interface to the MySQL database > > Group: Applications/Engineering > License: GPLv2 > URL: http://cran.r-project.org/web/packages/RMySQL/ > Source0: > ftp://cran.r-project.org/pub/R/contrib/main/%{packname}_%{version}-%{release}.tar.gz > BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} > -n) > > Requires(post): R > Requires(postun): R > BuildRequires: R-devel tetex-latex R >= R-2.8.0 R-methods R-DBI >= > R-0.2-2 R-utils mysql-devel > > %description > Database interface and MySQL driver for R. This version complies with the > database interface definition as implemented in the package DBI 0.2-2. > > %prep > %setup -q -c -n %{packname} > > %build > > %install > rm -rf %{buildroot} > mkdir -p %{buildroot}%{_libdir}/R/library > %{_bindir}/R CMD INSTALL -l %{buildroot}%{_libdir}/R/library %{packname} > test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so) > rm -rf %{buildroot}%{_libdir}/R/library/R.css > > %check > %{_bindir}/R CMD check %{packname} > > %clean > rm -rf %{buildroot} > > %post > %{_R_make_search_index} > > %postun > %{_R_make_search_index} > > %files > %defattr(-, root, root, -) > %dir %{_libdir}/R/library/%{packname} > > %doc %{_libdir}/R/library/%{packname}/latex > %doc %{_libdir}/R/library/%{packname}/doc > %doc %{_libdir}/R/library/%{packname}/html > %doc %{_libdir}/R/library/%{packname}/DESCRIPTION > %doc %{_libdir}/R/library/%{packname}/man > %doc %{_libdir}/R/library/%{packname}/NEWS > %doc %{_libdir}/R/library/%{packname}/GPL > %doc %{_libdir}/R/library/%{packname}/GPL > %doc %{_libdir}/R/library/%{packname}/INSTALL > %doc %{_libdir}/R/library/%{packname}/INSTALL.win > %doc %{_libdir}/R/library/%{packname}/README > %doc %{_libdir}/R/library/%{packname}/README.windows > %doc %{_libdir}/R/library/%{packname}/THANKS > %doc %{_libdir}/R/library/%{packname}/TODO > %doc %{_libdir}/R/library/%{packname}/WindowsPath.txt > %doc %{_libdir}/R/library/%{packname}/newFunctionNames.txt > > %{_libdir}/R/library/%{packname}/CONTENTS > %{_libdir}/R/library/%{packname}/INDEX > %{_libdir}/R/library/%{packname}/NAMESPACE > %{_libdir}/R/library/%{packname}/Meta > %{_libdir}/R/library/%{packname}/R > %{_libdir}/R/library/%{packname}/R-ex > %{_libdir}/R/library/%{packname}/help > %{_libdir}/R/library/%{packname}/FindMySQLhome.R > %{_libdir}/R/library/%{packname}/libs/RMySQL.so > > %changelog > * Sun Aug 23 2009 Name 0.7.4-1 > - initial package for Fedora > > _______________________________________________ > Fedora-r-devel-list mailing list > Fedora-r-devel-list at redhat.com > http://www.redhat.com/mailman/listinfo/fedora-r-devel-list > From tcallawa at redhat.com Tue Aug 25 15:27:46 2009 From: tcallawa at redhat.com (Tom "spot" Callaway) Date: Tue, 25 Aug 2009 11:27:46 -0400 Subject: [Fedora-r-devel-list] R 2.9.2 updates are ready Message-ID: <4A9402F2.8020205@redhat.com> Fedora 10: https://admin.fedoraproject.org/updates/rpy-1.0.3-10.fc10,R-2.9.2-1.fc10 Fedora 11: https://admin.fedoraproject.org/updates/rpy-2.0.3-4.fc11,R-2.9.2-1.fc11 (Note: EPEL updates sit in testing for two weeks, or until enough people give them positive karma to push to stable) EL-4: https://admin.fedoraproject.org/updates/R-2.9.2-1.el4 EL-5: https://admin.fedoraproject.org/updates/R-2.9.2-1.el5 ~spot From jamatos at fc.up.pt Thu Aug 27 07:05:47 2009 From: jamatos at fc.up.pt (=?iso-8859-1?q?Jos=E9_Matos?=) Date: Thu, 27 Aug 2009 08:05:47 +0100 Subject: [Fedora-r-devel-list] small issue with yum-presto and R update (config files changed) Message-ID: <200908270805.48473.jamatos@fc.up.pt> While updating to R-2.9.2 I noticed the following in yum: Downloading Packages: Setting up and reading Presto delta metadata updates-testing/prestodelta | 111 kB 00:00 updates/prestodelta | 487 kB 00:01 Processing delta metadata /usr/lib/R/etc/Makeconf: contents have been changed /usr/lib/R/etc/ldpaths: contents have been changed /usr/share/doc/R-2.9.1/html/search/index.txt: contents have been changed delta does not match installed data FWIW I did not change those files other than updating other R packages trough yum. I remember to have the same problem ever since I have installed yum- presto when updating R. Is it possible to solve this in the spec file? Should I report this to bugzilla? Regards, -- Jos? Ab?lio From martyn.plummer at r-project.org Fri Aug 28 15:45:38 2009 From: martyn.plummer at r-project.org (Martyn Plummer) Date: Fri, 28 Aug 2009 17:45:38 +0200 Subject: [Fedora-r-devel-list] R 2.9.2 updates are ready In-Reply-To: <1251453428.2585.6.camel@seurat.iarc.fr> References: <4A9402F2.8020205@redhat.com> <1251453428.2585.6.camel@seurat.iarc.fr> Message-ID: <1251474338.5903.29.camel@seurat.iarc.fr> Up until now we have been building our own R RPMS for EL4 and EL5 for distribution via CRAN. To be precise, Bob Kinney at Harvard (cc'ed) has been building them. Lately I stepped in to rebuild the 32-bit EL4/5 RPMS using mock. With R 2.9.1 and R 2.9.2 you have built EPEL RPMS for R at the same time as the Fedora ones. Does this mean we can give up building our own? Is it OK for me to grab the EPEL RPMS and put them on CRAN before they get pushed to stable? Thanks Martyn On Tue, 2009-08-25 at 11:27 -0400, Tom "spot" Callaway wrote: > Fedora 10: > https://admin.fedoraproject.org/updates/rpy-1.0.3-10.fc10,R-2.9.2-1.fc10 > Fedora 11: > https://admin.fedoraproject.org/updates/rpy-2.0.3-4.fc11,R-2.9.2-1.fc11 > > (Note: EPEL updates sit in testing for two weeks, or until enough people > give them positive karma to push to stable) > EL-4: https://admin.fedoraproject.org/updates/R-2.9.2-1.el4 > EL-5: https://admin.fedoraproject.org/updates/R-2.9.2-1.el5 > > ~spot ----------------------------------------------------------------------- This message and its attachments are strictly confidential. If you are not the intended recipient of this message, please immediately notify the sender and delete it. Since its integrity cannot be guaranteed, its content cannot involve the sender's responsibility. Any misuse, any disclosure or publication of its content, either whole or partial, is prohibited, exception made of formally approved use ----------------------------------------------------------------------- From tcallawa at redhat.com Fri Aug 28 17:58:39 2009 From: tcallawa at redhat.com (Tom "spot" Callaway) Date: Fri, 28 Aug 2009 13:58:39 -0400 Subject: [Fedora-r-devel-list] R 2.9.2 updates are ready In-Reply-To: <1251474338.5903.29.camel@seurat.iarc.fr> References: <4A9402F2.8020205@redhat.com> <1251453428.2585.6.camel@seurat.iarc.fr> <1251474338.5903.29.camel@seurat.iarc.fr> Message-ID: <4A981ACF.3060803@redhat.com> On 08/28/2009 11:45 AM, Martyn Plummer wrote: > Up until now we have been building our own R RPMS for EL4 and EL5 for > distribution via CRAN. To be precise, Bob Kinney at Harvard (cc'ed) has > been building them. Lately I stepped in to rebuild the 32-bit EL4/5 RPMS > using mock. > > With R 2.9.1 and R 2.9.2 you have built EPEL RPMS for R at the same time > as the Fedora ones. Does this mean we can give up building our own? Sure. It doesn't really take much time for me to do these additional targets. > Is it OK for me to grab the EPEL RPMS and put them on CRAN before they > get pushed to stable? Sure, assuming you see no problems with them (and if you do, please let me know). ~tom From ihok at hotmail.com Sat Aug 29 02:10:54 2009 From: ihok at hotmail.com (Jack Tanner) Date: Fri, 28 Aug 2009 22:10:54 -0400 Subject: [Fedora-r-devel-list] collaborating on ggplot2 ? Message-ID: Howdy, I'd like to get the ggplot2 library package-able. I cannot sign up as a maintainer, but I can work on spec files. ggplot2 has a whole bunch of dependencies: According to http://cran.r-project.org/web/packages/ggplot2/ , Imports: reshape (? 0.8.0), plyr (? 0.1.6), splines, MASS , RColorBrewer , grid, proto Suggests: quantreg , Hmisc , mapproj , maps , digest , colorspace , hexbin , gpclib , maptools Would anyone be interested in taking this on with me and writing spec files for some of the ggplot2 prereqs?