From pingou at pingoured.fr Sun Aug 10 18:13:23 2008 From: pingou at pingoured.fr (Pierre-Yves) Date: Sun, 10 Aug 2008 20:13:23 +0200 Subject: [Fedora-r-devel-list] R2spec v2.3 Message-ID: <489F2FC3.4070307@pingoured.fr> Dear all, On the suggestion of Jos? I would like to announce here the new release of my project R2spec. At the end of July I release the version 2 re-designed in OO. I corrected a couple of view bugs or typos up to today where I changed the arguments management. Feed back, tester are more than welcome :) There are the links: * The source http://pingoured.fr/public/R2spec/R2spec-2.3.tar.gz * The spec http://pingoured.fr/public/R2spec/R2spec.spec * The SRPM http://pingoured.fr/public/R2spec/R2spec-2.3-1.fc9.src.rpm * The RPM http://pingoured.fr/public/R2spec/R2spec-2.3-1.fc9.noarch.rpm For more information about the different releases of the version 2 see my blog at: http://pingoured.fr/blog/index.php?post/2008/08/10/R2spec-23 http://pingoured.fr/blog/index.php?post/2008/07/31/R2spec_22 http://pingoured.fr/blog/index.php?post/2008/07/30/R2spec-tester-wanted Best regards, Pierre From jamatos at fc.up.pt Mon Aug 11 09:38:49 2008 From: jamatos at fc.up.pt (=?iso-8859-1?q?Jos=E9_Matos?=) Date: Mon, 11 Aug 2008 10:38:49 +0100 Subject: [Fedora-r-devel-list] useR! 2008 Message-ID: <200808111038.49187.jamatos@fc.up.pt> Hi, I am writing this from Dortmund, at the useR! 2008 conference http://www.statistik.uni-dortmund.de/useR-2008/ I will have a talk tomorrow about the interaction between R and Fedora. It is a 15 minutes session so there is not much time to expand. I will present Fedora and it interacts with R. There are several issues that are common to the relation between Fedora and languages like perl, python, latex or R. I will also take the opportunity to hear feedback from several types of users regarding the state of R in Fedora. If there is anything relevant I will report back to this list. I have asked pingou (I hope I can use this) to write to the list with the new releases of his package as it would be nice that package automatically in Fedora using yum. Regards, PS: In case you are wondering why I took so long to send this message to the list, believe that it is a long story that involves time shortage. :-) -- Jos? Ab?lio From pingou at pingoured.fr Mon Aug 11 11:28:44 2008 From: pingou at pingoured.fr (Pierre-Yves) Date: Mon, 11 Aug 2008 13:28:44 +0200 Subject: [Fedora-r-devel-list] useR! 2008 In-Reply-To: <200808111038.49187.jamatos@fc.up.pt> References: <200808111038.49187.jamatos@fc.up.pt> Message-ID: <48A0226C.6010303@pingoured.fr> Jos? Matos wrote: > Hi, > I am writing this from Dortmund, at the useR! 2008 conference > http://www.statistik.uni-dortmund.de/useR-2008/ Nice :) > > I will have a talk tomorrow about the interaction between R and Fedora. It is > a 15 minutes session so there is not much time to expand. I will present > Fedora and it interacts with R. There are several issues that are common to > the relation between Fedora and languages like perl, python, latex or R. That's great :) Do you have the slides of the presentation ? I would be interested to know how you presented things. > > I will also take the opportunity to hear feedback from several types of users > regarding the state of R in Fedora. If there is anything relevant I will > report back to this list. I would like to know how the think on the difference between suggests and depends dependences of a library. (I still have in my mind the Bioconductor issue). Do they install both ? Do they care about the suggests ? Do they want them ? > > I have asked pingou (I hope I can use this) to write to the list with the new > releases of his package as it would be nice that package automatically in > Fedora using yum. I have asked for a project on the fedorahosted.org, I'll let you know. Thanks, Regards, Pierre From pingou at pingoured.fr Mon Aug 11 15:51:53 2008 From: pingou at pingoured.fr (Pierre-Yves) Date: Mon, 11 Aug 2008 17:51:53 +0200 Subject: [Fedora-r-devel-list] R2spec v2.3 In-Reply-To: <489F2FC3.4070307@pingoured.fr> References: <489F2FC3.4070307@pingoured.fr> Message-ID: <48A06019.8050508@pingoured.fr> Pierre-Yves wrote: > Dear all, > > On the suggestion of Jos? I would like to announce here the new release > of my project R2spec. > At the end of July I release the version 2 re-designed in OO. I > corrected a couple of view bugs or typos up to today where I changed the > arguments management. > > Feed back, tester are more than welcome :) The project is now on trac : https://fedorahosted.org/r2spec/ Thanks you fedora ;) And I created the review : https://bugzilla.redhat.com/show_bug.cgi?id=458685 Regards, Pierre From pingou at pingoured.fr Tue Aug 12 07:23:39 2008 From: pingou at pingoured.fr (Pierre-Yves) Date: Tue, 12 Aug 2008 09:23:39 +0200 Subject: [Fedora-r-devel-list] R package in Fedora Message-ID: <48A13A7B.7040700@pingoured.fr> Dear all, Remi Collet has done a great job the past days to make these pages: http://rpms.famillecollet.com/rpmphp/ I think you will be interested specially in this one: http://rpms.famillecollet.com/rpmphp/rpm.php?type=R However, helping him to set up the parsers, we have been facing some problem with some package. For example: R-lmtest As you can see here: http://pingoured.fr/cgi-bin/R.py?name=R-lmtest The version have a '-', this leads to a "outdated" mark of the package in this page http://rpms.famillecollet.com/rpmphp/rpm.php?type=R . The question is then, what should we do ? There is nothing on the guideline that mention what we should do about the library that have a '-' on their version name (second exemple: R-pls http://pingoured.fr/cgi-bin/R.py?name=R-pls ). We also faced the problem that at least one library is present in both CRAN and bioconductor repository (R-qvalue http://pingoured.fr/cgi-bin/R.py?name=R-qvalue ). But the version are pretty clear, we kept only the Bioconductor. So I think, when we have a library in CRAN and Bioconductor, we should only keep the Bioconductor version. For the version with a '-', we skipped everything that was after the '-' until now, should we continue ? Thanks for your comments, Regards, Pierre From jamatos at fc.up.pt Tue Aug 12 07:38:09 2008 From: jamatos at fc.up.pt (=?iso-8859-15?q?Jos=E9_Matos?=) Date: Tue, 12 Aug 2008 08:38:09 +0100 Subject: [Fedora-r-devel-list] New CRAN packages in Fedora need reviews In-Reply-To: <1215528554.3214.17.camel@localhost.localdomain> References: <1215528554.3214.17.camel@localhost.localdomain> Message-ID: <200808120838.09382.jamatos@fc.up.pt> On Tuesday 08 July 2008 15:49:14 Tom "spot" Callaway wrote: > I built a few CRAN packages today that looked useful. If anyone wants to > help review these, I'd appreciate it: > > https://bugzilla.redhat.com/show_bug.cgi?id=454439 (R-nws) > https://bugzilla.redhat.com/show_bug.cgi?id=454440 (R-biglm) > https://bugzilla.redhat.com/show_bug.cgi?id=454441 (R-bigmemory) I have been in a tutorial yesterday here these packages have been discussed. Expect a revision next week when I am back home. :-) > Thanks in advance, > > ~spot -- Jos? Ab?lio From pingou at pingoured.fr Tue Aug 12 07:40:23 2008 From: pingou at pingoured.fr (Pierre-Yves) Date: Tue, 12 Aug 2008 09:40:23 +0200 Subject: [Fedora-r-devel-list] New CRAN packages in Fedora need reviews In-Reply-To: <200808120838.09382.jamatos@fc.up.pt> References: <1215528554.3214.17.camel@localhost.localdomain> <200808120838.09382.jamatos@fc.up.pt> Message-ID: <48A13E67.3000500@pingoured.fr> Jos? Matos wrote: > On Tuesday 08 July 2008 15:49:14 Tom "spot" Callaway wrote: >> I built a few CRAN packages today that looked useful. If anyone wants to >> help review these, I'd appreciate it: >> >> https://bugzilla.redhat.com/show_bug.cgi?id=454439 (R-nws) Started >> https://bugzilla.redhat.com/show_bug.cgi?id=454440 (R-biglm) Done >> https://bugzilla.redhat.com/show_bug.cgi?id=454441 (R-bigmemory) Waiting :) Regards, Pierre From alexl at users.sourceforge.net Tue Aug 12 11:05:37 2008 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Tue, 12 Aug 2008 04:05:37 -0700 Subject: [Fedora-r-devel-list] Re: R package in Fedora In-Reply-To: <48A13A7B.7040700@pingoured.fr> (Pierre-Yves's message of "Tue\, 12 Aug 2008 09\:23\:39 +0200") References: <48A13A7B.7040700@pingoured.fr> Message-ID: >>>>> "P" == Pierre-Yves writes: P> Dear all, Remi Collet has done a great job the past days to make P> these pages: http://rpms.famillecollet.com/rpmphp/ P> I think you will be interested specially in this one: P> http://rpms.famillecollet.com/rpmphp/rpm.php?type=R Hey Pierre-Yves, This looks great! I wonder if you could also integrate Chris Weyl's Perl CPAN tracking tool, e.g.: http://fedora.biggerontheinside.net/perl/alexlan.html P> However, helping him to set up the parsers, we have been facing P> some problem with some package. For example: R-lmtest As you can P> see here: http://pingoured.fr/cgi-bin/R.py?name=R-lmtest The P> version have a '-', this leads to a "outdated" mark of the package P> in this page http://rpms.famillecollet.com/rpmphp/rpm.php?type=R . P> The question is then, what should we do ? There is nothing on the P> guideline that mention what we should do about the library that P> have a '-' on their version name (second exemple: R-pls P> http://pingoured.fr/cgi-bin/R.py?name=R-pls ). P> We also faced the problem that at least one library is present in P> both CRAN and bioconductor repository (R-qvalue P> http://pingoured.fr/cgi-bin/R.py?name=R-qvalue ). But the version P> are pretty clear, we kept only the Bioconductor. P> So I think, when we have a library in CRAN and Bioconductor, we P> should only keep the Bioconductor version. P> For the version with a '-', we skipped everything that was after P> the -' until now, should we continue ? On the R libraries issue. Not sure about that problem, that's a bit of pain. Have to think about that one. Alex From pingou at pingoured.fr Tue Aug 12 11:08:51 2008 From: pingou at pingoured.fr (Pierre-Yves) Date: Tue, 12 Aug 2008 13:08:51 +0200 Subject: [Fedora-r-devel-list] Re: R package in Fedora In-Reply-To: References: <48A13A7B.7040700@pingoured.fr> Message-ID: <48A16F43.50506@pingoured.fr> Alex Lancaster wrote: >>>>>> "P" == Pierre-Yves writes: > > P> Dear all, Remi Collet has done a great job the past days to make > P> these pages: http://rpms.famillecollet.com/rpmphp/ > P> I think you will be interested specially in this one: > P> http://rpms.famillecollet.com/rpmphp/rpm.php?type=R > > Hey Pierre-Yves, > > This looks great! I wonder if you could also integrate Chris Weyl's > Perl CPAN tracking tool, e.g.: > > http://fedora.biggerontheinside.net/perl/alexlan.html Remi contacted Chris in order to integrate both work. ;) He actually partly based his work from this page. > P> For the version with a '-', we skipped everything that was after > P> the -' until now, should we continue ? > > On the R libraries issue. Not sure about that problem, that's a bit > of pain. Have to think about that one. Let us know :) Thanks, Regards, Pierre From jamatos at fc.up.pt Tue Aug 19 15:41:16 2008 From: jamatos at fc.up.pt (=?iso-8859-1?q?Jos=E9_Matos?=) Date: Tue, 19 Aug 2008 16:41:16 +0100 Subject: [Fedora-r-devel-list] useR! 2008 status report Message-ID: <200808191641.16517.jamatos@fc.up.pt> Hi all, after a busy week I am finally starting to get back to some kind of normality (no pun intended :-) ). At useR! 2008 I had Martin Plummer, Marc Schwartz and Peter Dalgaard in the audience. The talk went well and it was a fun to do. The room was small for the attendance and in my (biased) view it seemed that I had people coming on purpose for the talk. :-) After the session ended I had a friendly discussion with Martin and Marc regarding Fedora and R relationship. :-) Some of the topics covered were (in no particular order other than my notes). 1) The redundancy between the two mailing lists devoted to R and Fedora (this and SIG list). Actually at that time I forgot the SIG mailing list (my bad). I always keep forgetting about the different purpose of both lists. 2) Martin and Marc suggested one scenario that involved the removal of all R packages from Fedora where the only remaining installed package would be the R core package. Then using some kind of package, the better analogy that I found was a backend to PackageKit providing automatic installs from CRAN. My opinion (that I have also expressed back then) was that this would be a no go for Fedora for two reasons, first the packages dependency outside of CRAN would be hard to get right (think about packages like R-hdf5 that require linking with an external package). The second and probably the most important issue from our (Fedora) point of view would be the liability issue. We would be connecting to a repository that we have no control about, I tried to express the different reasons why this is not possible. 3) There are discussions at R about the next generation CRAN meta-information (improved DESCRIPTION format) and the opinions of distributions are welcome. 4) Is there a link in fedora bugzilla to connect upstream for R bugs reported to Fedora? I am not sure if this is possible with the new bugzilla but I suppose that there are not so many bugs like that reported at Fedora. 5) One problem usually reported in the R users mailing list is the installation procedure used to install R packages (not in Fedora) using the R interface. This problem has been reported again this weekend FWIW. Instead of providing R-devel in the R package as Martin and Marc have suggested I think that we could create a FAQ for R in Fedora. Something like: *********************** Draft to R - Fedora FAQ ************************** Q: I tried to install the following R package in Fedora but R failed with horrendous error messages, what should I do? A: Look to the content of the R package you are trying to install (link to CRAN). 1) Does it contains C or C++ files (.c or .cpp ending filenames)? If yes then install R-devel if it is not yet installed. [Instructions how to install R-devel using yum or packagekit] 2) Does it contains Fortran files (.f or .F ending filenames)? If yes then install gcc-gfortran if it is not yet installed. [Instructions how to install R-devel using yum or packagekit] 3) If the steps above are not enough and the package depends on an external library you need to guarantee that you have installed the files necessary to compile the package. Do not forget that the -devel subpackages are required to be installed to compile and link with the external libraries. ****************************************************************************** This is my fable attempt to document some of the possible of the problems found by our users. :-) We could then expand the FAQ content to other topics like how to search Fedora R packages. The target of the FAQ would be naturally the users and not just the developers. Comments are welcome to all the points above, -- Jos? Ab?lio From jamatos at fc.up.pt Tue Aug 19 17:01:28 2008 From: jamatos at fc.up.pt (=?iso-8859-1?q?Jos=E9_Matos?=) Date: Tue, 19 Aug 2008 18:01:28 +0100 Subject: [Fedora-r-devel-list] useR! 2008 status report In-Reply-To: <200808191641.16517.jamatos@fc.up.pt> References: <200808191641.16517.jamatos@fc.up.pt> Message-ID: <200808191801.29240.jamatos@fc.up.pt> FWIW, as promised, the talk slides can be found here: http://jamatos.fedorapeople.org/talk-user2008.pdf I am aware that there are some typos. The thesis of the talk was that the relation between Fedora and R can placed in a more general context, in this case between linux software distributions and free software script languages. The free languages like perl, python, tex, php and R (among others) have developed a set of procedures to cope with installation and updating in different operating systems. On the other hand in Fedora (and other linux distributions) we have to deal with different packaging models of open source languages and that give us a different view point regarding the problem of installing and updating the language and its libraries. As you can see there is nothing earth shattering here. :-) -- Jos? Ab?lio From tcallawa at redhat.com Tue Aug 19 17:04:37 2008 From: tcallawa at redhat.com (Tom "spot" Callaway) Date: Tue, 19 Aug 2008 13:04:37 -0400 Subject: [Fedora-r-devel-list] useR! 2008 status report In-Reply-To: <200808191641.16517.jamatos@fc.up.pt> References: <200808191641.16517.jamatos@fc.up.pt> Message-ID: <1219165477.3401.16.camel@localhost.localdomain> On Tue, 2008-08-19 at 16:41 +0100, Jos? Matos wrote: > Q: I tried to install the following R package in Fedora but R failed > with > horrendous error messages, what should I do? A much much more intelligent fix would be for R to check for the devel files that it needs before attempting a build operation, then failing gracefully with an explanation that suggests the user look for a -devel package if they're using R from the distribution. ~spot From pingou at pingoured.fr Tue Aug 19 17:38:33 2008 From: pingou at pingoured.fr (Pierre-Yves) Date: Tue, 19 Aug 2008 19:38:33 +0200 Subject: [Fedora-r-devel-list] useR! 2008 status report In-Reply-To: <200808191641.16517.jamatos@fc.up.pt> References: <200808191641.16517.jamatos@fc.up.pt> Message-ID: <48AB0519.70907@pingoured.fr> Jos? Matos wrote: > Hi all, > after a busy week I am finally starting to get back to some kind of normality > (no pun intended :-) ). > > At useR! 2008 I had Martin Plummer, Marc Schwartz and Peter Dalgaard in the > audience. The talk went well and it was a fun to do. The room was small for > the attendance and in my (biased) view it seemed that I had people coming on > purpose for the talk. :-) > > After the session ended I had a friendly discussion with Martin and Marc > regarding Fedora and R relationship. :-) > > Some of the topics covered were (in no particular order other than my notes). > > 1) The redundancy between the two mailing lists devoted to R and Fedora (this > and SIG list). Actually at that time I forgot the SIG mailing list (my bad). I > always keep forgetting about the different purpose of both lists. /me notes to subscribe to this list... > 2) Martin and Marc suggested one scenario that involved the removal of all R > packages from Fedora where the only remaining installed package would be the R > core package. Then using some kind of package, the better analogy that I found > was a backend to PackageKit providing automatic installs from CRAN. > > My opinion (that I have also expressed back then) was that this would be a no > go for Fedora for two reasons, first the packages dependency outside of CRAN > would be hard to get right (think about packages like R-hdf5 that require > linking with an external package). I have a couple of other example with the same issue, it is definitely something against such principle. > The second and probably the most important > issue from our (Fedora) point of view would be the liability issue. We would > be connecting to a repository that we have no control about, I tried to > express the different reasons why this is not possible. I (as packager) have also faced problem concerning the quality of some packages (pages not in UTF8, files put in the wrong part of the FS...). RPMs avoid these problems and make sure that the FS is kept clear. Do you know if there is a place where such cross distro issues are/could be discussed ? > 4) Is there a link in fedora bugzilla to connect upstream for R bugs reported > to Fedora? I am not sure if this is possible with the new bugzilla but I > suppose that there are not so many bugs like that reported at Fedora. Spot, do you have many bugs reported against R ? > > 5) One problem usually reported in the R users mailing list is the > installation procedure used to install R packages (not in Fedora) using the R > interface. > > This problem has been reported again this weekend FWIW. Instead of providing > R-devel in the R package as Martin and Marc have suggested I think that we > could create a FAQ for R in Fedora. Something like: > > *********************** Draft to R - Fedora FAQ ************************** > > Q: I tried to install the following R package in Fedora but R failed with > horrendous error messages, what should I do? > > A: Look to the content of the R package you are trying to install (link to > CRAN). > > 1) Does it contains C or C++ files (.c or .cpp ending filenames)? If yes > then install R-devel if it is not yet installed. > > [Instructions how to install R-devel using yum or packagekit] > > 2) Does it contains Fortran files (.f or .F ending filenames)? If yes then > install gcc-gfortran if it is not yet installed. > > [Instructions how to install R-devel using yum or packagekit] If the solution proposed by spot does not work (or before it works) I think a simple: find ./source/ -name "*.py" -o -name "*.c" -o -name "*.cp" -o -name "*.f" -o -name "*.F" If it returns something then install the -devel... > 3) If the steps above are not enough and the package depends on an external > library you need to guarantee that you have installed the files necessary to > compile the package. Do not forget that the -devel subpackages are required to > be installed to compile and link with the external libraries. > I went briefly through your presentation, nice :) I hope you had good time there. Regards, Pierre From tcallawa at redhat.com Tue Aug 19 17:47:30 2008 From: tcallawa at redhat.com (Tom "spot" Callaway) Date: Tue, 19 Aug 2008 13:47:30 -0400 Subject: [Fedora-r-devel-list] useR! 2008 status report In-Reply-To: <48AB0519.70907@pingoured.fr> References: <200808191641.16517.jamatos@fc.up.pt> <48AB0519.70907@pingoured.fr> Message-ID: <1219168050.3401.23.camel@localhost.localdomain> On Tue, 2008-08-19 at 19:38 +0200, Pierre-Yves wrote: > Spot, do you have many bugs reported against R ? One at the moment (it is a Fedora specific issue, just need to enable support for alpha systems): https://admin.fedoraproject.org/pkgdb/packages/bugs/R Historically, we get very few bugs filed against R. ~spot From gnwiii at gmail.com Wed Aug 20 21:04:09 2008 From: gnwiii at gmail.com (George N. White III) Date: Wed, 20 Aug 2008 18:04:09 -0300 (ADT) Subject: [Fedora-r-devel-list] Re: useR! 2008 status report In-Reply-To: <200808191801.29240.jamatos@fc.up.pt> References: <200808191641.16517.jamatos@fc.up.pt> <200808191801.29240.jamatos@fc.up.pt> Message-ID: On Tue, 19 Aug 2008, Jos? Matos wrote: > FWIW, as promised, the talk slides can be found here: > http://jamatos.fedorapeople.org/talk-user2008.pdf > > I am aware that there are some typos. > > The thesis of the talk was that the relation between Fedora and R can placed > in a more general context, in this case between linux software distributions > and free software script languages. > > The free languages like perl, python, tex, php and R (among others) have > developed a set of procedures to cope with installation and updating in > different operating systems. > > On the other hand in Fedora (and other linux distributions) we have to deal > with different packaging models of open source languages and that give us a > different view point regarding the problem of installing and updating the > language and its libraries. > > As you can see there is nothing earth shattering here. :-) Well, big changes sometimes occur from modest beginnings. There is a growing problem with the common perception that packages can only be installed with root privileges. Many end-user applications like R can exist and run very nicely without special privileges. There are really only two reasons root privileges are needed to install the majority of end-user apps: 1. to update a global database of installed packages 2. to guard against a malicious user installing a trojan on multi-user machines. As you note, many apps have app-specific package systems, so you can end up installing in a way that fails to update the global database. In practice, those of us who work in environments where root privileges are in short supply (and asking to have them invoked often results in real $ charges to your budget) tend to use the app-specific packaging when we can, but then there can be confusion (user a gets result X from the package installed by the administrator, while user b gets result Y from the package installed from CXAN). We are starting to see tools to manipulate packages, e.g., to create rpm .spec files from the TeX Live packages, to create null rpm .spec files for installation into personal rpm databases so prerequisites will be satisfied without forcing the install. One of the difficulties in discussing these issues is that no one person is likely to encounter the full range of environments that need to be supported. There are very different security and control problems for a server running R to produce offical statistics than for a student's personal workstation. Certainly security can be enhanced if we minimize the use of root to manage end-user apps. This says we need to move to a multi-level packaging approach that supports packaged installs under user/group control without root privileges. -- George N. White III From jamatos at fc.up.pt Fri Aug 22 10:25:50 2008 From: jamatos at fc.up.pt (=?utf-8?q?Jos=C3=A9_Matos?=) Date: Fri, 22 Aug 2008 11:25:50 +0100 Subject: [Fedora-r-devel-list] useR! 2008 status report In-Reply-To: <1219165477.3401.16.camel@localhost.localdomain> References: <200808191641.16517.jamatos@fc.up.pt> <1219165477.3401.16.camel@localhost.localdomain> Message-ID: <200808221125.50523.jamatos@fc.up.pt> On Tuesday 19 August 2008 18:04:37 Tom "spot" Callaway wrote: > A much much more intelligent fix would be for R to check for the devel > files that it needs before attempting a build operation, then failing > gracefully with an explanation that suggests the user look for a -devel > package if they're using R from the distribution. Not necessarily an easy thing to do for every platform they support. :-) Do you know any language that does this successfully? (I really mean this as a question not any rhetoric). On the other hand we are trying to be good neighbours. ;-) I am sure they would not mind if he had some kind of hook to that specifically for Fedora. > ~spot -- Jos? Ab?lio From jamatos at fc.up.pt Fri Aug 22 10:44:10 2008 From: jamatos at fc.up.pt (=?utf-8?q?Jos=C3=A9_Matos?=) Date: Fri, 22 Aug 2008 11:44:10 +0100 Subject: [Fedora-r-devel-list] Re: useR! 2008 status report In-Reply-To: References: <200808191641.16517.jamatos@fc.up.pt> <200808191801.29240.jamatos@fc.up.pt> Message-ID: <200808221144.10279.jamatos@fc.up.pt> On Wednesday 20 August 2008 22:04:09 George N. White III wrote: > One of the difficulties in discussing these issues is that no > one person is likely to encounter the full range of environments > that need to be supported. ?There are very different security and > control problems for a server running R to produce offical statistics > than for a student's personal workstation. ?Certainly security can > be enhanced if we minimize the use of root to manage end-user apps. This is an issue with lots of gray shadings. If we place virtualization on the board we have another level. :-) > This says we need to move to a multi-level packaging approach that > supports packaged installs under user/group control without root > privileges. Well this is easier said than done. :-) Although I agree that you right and that there are bigger fishes to fry, my interest was just to place Fedora and R in a context that allowed us to have more R packages in Fedora done and at the same time not forgetting the lessons that were learned from packaging other languages (specifically Perl and Python). -- Jos? Ab?lio From jamatos at fc.up.pt Fri Aug 22 10:53:31 2008 From: jamatos at fc.up.pt (=?iso-8859-1?q?Jos=E9_Matos?=) Date: Fri, 22 Aug 2008 11:53:31 +0100 Subject: [Fedora-r-devel-list] useR! 2008 status report In-Reply-To: <48AB0519.70907@pingoured.fr> References: <200808191641.16517.jamatos@fc.up.pt> <48AB0519.70907@pingoured.fr> Message-ID: <200808221153.31981.jamatos@fc.up.pt> On Tuesday 19 August 2008 18:38:33 Pierre-Yves wrote: > If the solution proposed by spot does not work (or before it works) > I think a simple: > find ./source/ -name "*.py" -o -name "*.c" -o -name "*.cp" ?-o -name > "*.f" ?-o -name "*.F" > If it returns something then install the -devel... Actually we can develop that as it will be useful for R2spec as well. It would be interesting because the common problems are the same. :-) > > ? 3) If the steps above are not enough and the package depends on an > > external library you need to guarantee that you have installed the files > > necessary to compile the package. Do not forget that the -devel > > subpackages are required to be installed to compile and link with the > > external libraries. > > I went briefly through your presentation, nice :) > I hope you had good time there. It was a nice conference, with an optimum number of participants (around 400). It was nice to meet there some people that I only knew from the mailing lists like some of the Debian guys. It was also interesting to notice that there are some issues related to the community growth that are being dealt in the same way both in Fedora and R. R-Forge for example is a project under the R Core umbrella where space and infrastructural tools are given to authors to develop their packages before they are place in CRAN. R-Forge is thus the analogue of fedorahosted. :-) > Regards, > Pierre -- Jos? Ab?lio From tcallawa at redhat.com Fri Aug 29 16:08:11 2008 From: tcallawa at redhat.com (Tom "spot" Callaway) Date: Fri, 29 Aug 2008 12:08:11 -0400 Subject: [Fedora-r-devel-list] R 2.7.2 Message-ID: <1220026091.3606.44.camel@localhost.localdomain> R 2.7.2 is coming! Builds are going for EL-4, EL-5, F-8, F-9, and devel. I'll need to rebuild rpy and push updates, so this won't happen overnight, but this is your official "heads-up". Thanks, ~spot From pingou at pingoured.fr Sun Aug 31 11:36:46 2008 From: pingou at pingoured.fr (Pierre-Yves) Date: Sun, 31 Aug 2008 13:36:46 +0200 Subject: [Fedora-r-devel-list] R2spec new release Message-ID: <48BA824E.9090705@pingoured.fr> Dear all As agreed with Jos? there is the news of the new release of R2spec. Have a nice sunday Best regards, Pierre ====================================================================== There is the latest version of R2spec, I have been working quite a bit on it with the suggestion of faceface from #R on irc.freenode.net to improve this software. Therefore the changelog for this new release is quite long and the list of features added seems also important. The principle is still the same: make R packages as simple as possible. Seems there are mainly two sources of libraries for R (Bioconductor and the CRAN) I added two options (--bioc and --cran) that add the Source0 and the URL in the spec file if it has not been defined by the --url option. From that I aslo considered the case of the noarch packages, it now looks for *.c, *.C, *.cp, *.cpp, *.f and *.F files, if it does not find any it consider the package as noarch and thus adapt the specfile for that. It also offers the possibility to move the source to %_topdir (defined in ~/.rpmmacros) so that you can directly run the rpmbuild -ba once you have made the small correction advised on the spec file. That's the main features added, you can see below the changelog for this new release and you can always test and give feed back, report bugs and suggest enhancement on the trac of the R2spec project [1]. The RPMs and sources are available on the git of the R2spec project [2]. Thanks for your attention :-) [1] https://fedorahosted.org/r2spec [2] https://fedorahosted.org/r2spec/browse From dan.bolser at gmail.com Sun Aug 31 12:35:55 2008 From: dan.bolser at gmail.com (Dan Bolser) Date: Sun, 31 Aug 2008 13:35:55 +0100 Subject: [Fedora-r-devel-list] R2spec new release In-Reply-To: <48BA824E.9090705@pingoured.fr> References: <48BA824E.9090705@pingoured.fr> Message-ID: <2c8757af0808310535y560c19d3gcfe3da9847a2a70a@mail.gmail.com> Hey Pierre, That looks like a great list of changes! Hello list! I have been using R (and Fedora) for several years, but I have only just started to look at the R-Repo stuff (thanks to Pierre!). I have only recently used R2Spec, but I found it very convenient and easy to use. One question that I raised with Pierre previously (and he suggested that I raise it here on list) is the issue of getting the R-library manager to some how 'talk to' the Yum package manager. I think the first step would be to build a dummy RPM that includes all the R-libraries that come by default with R. Such things as base, lattice, stats, etc., etc. All these libraries could (?) be rolled into an RPM called R-libs (or something), and then when packaging an R-library that depends on 'stats', for example, the dependency would be satisfied by R-libs... Is that possible? It would be good to know what libraries comes with each version of R by default, and it seems natural to put that information into a specific RPM. Not sure if that makes sense... All the best, Dan. 2008/8/31 Pierre-Yves > Dear all > > As agreed with Jos? there is the news of the new release of R2spec. > > Have a nice sunday > > Best regards, > Pierre > > ====================================================================== > > There is the latest version of R2spec, I have been working quite a bit on > it with the suggestion of faceface from #R on irc.freenode.net to improve > this software. Therefore the changelog for this new release is quite long > and the list of features added seems also important. > > The principle is still the same: make R packages as simple as possible. > > Seems there are mainly two sources of libraries for R (Bioconductor and the > CRAN) I added two options (--bioc and --cran) that add the Source0 and the > URL in the spec file if it has not been defined by the --url option. > > From that I aslo considered the case of the noarch packages, it now looks > for *.c, *.C, *.cp, *.cpp, *.f and *.F files, if it does not find any it > consider the package as noarch and thus adapt the specfile for that. > > It also offers the possibility to move the source to %_topdir (defined in > ~/.rpmmacros) so that you can directly run the rpmbuild -ba once you have > made the small correction advised on the spec file. > > That's the main features added, you can see below the changelog for this > new release and you can always test and give feed back, report bugs and > suggest enhancement on the trac of the R2spec project [1]. > > The RPMs and sources are available on the git of the R2spec project [2]. > > Thanks for your attention :-) > > [1] https://fedorahosted.org/r2spec > [2] https://fedorahosted.org/r2spec/browse > > _______________________________________________ > Fedora-r-devel-list mailing list > Fedora-r-devel-list at redhat.com > http://www.redhat.com/mailman/listinfo/fedora-r-devel-list > -- hello -------------- next part -------------- An HTML attachment was scrubbed... URL: From tcallawa at redhat.com Sun Aug 31 13:14:10 2008 From: tcallawa at redhat.com (Tom "spot" Callaway) Date: Sun, 31 Aug 2008 09:14:10 -0400 Subject: [Fedora-r-devel-list] R2spec new release In-Reply-To: <2c8757af0808310535y560c19d3gcfe3da9847a2a70a@mail.gmail.com> References: <48BA824E.9090705@pingoured.fr> <2c8757af0808310535y560c19d3gcfe3da9847a2a70a@mail.gmail.com> Message-ID: <1220188450.17883.12.camel@localhost.localdomain> On Sun, 2008-08-31 at 13:35 +0100, Dan Bolser wrote: > I think the first step would be to build a dummy RPM that includes all > the R-libraries that come by default with R. Such things as base, > lattice, stats, etc., etc. All these libraries could (?) be rolled > into an RPM called R-libs (or something), and then when packaging an > R-library that depends on 'stats', for example, the dependency would > be satisfied by R-libs... Is that possible? The R package already does this: Provides: R-base = %{version} Provides: R-boot = 1.2 Provides: R-class = 7.2 Provides: R-cluster = 1.11.11 Provides: R-codetools = 0.2 Provides: R-datasets = %{version} Provides: R-foreign = 0.8 Provides: R-graphics = %{version} Provides: R-grDevices = %{version} Provides: R-grid = %{version} Provides: R-KernSmooth = 2.22 Provides: R-lattice = 0.17 Provides: R-MASS = 7.2 Provides: R-methods = %{version} Provides: R-mgcv = 1.4 Provides: R-nlme = 3.1 Provides: R-nnet = 7.2 Provides: R-rpart = 3.1 Provides: R-spatial = 7.2 Provides: R-splines = %{version} Provides: R-stats = %{version} Provides: R-stats4 = %{version} Provides: R-survival = 2.34 Provides: R-tcltk = %{version} Provides: R-tools = %{version} Provides: R-utils = %{version} Provides: R-VR = 7.2 %{version} is the version of R, in this case, 2.7.2. ~spot From dan.bolser at gmail.com Sun Aug 31 17:12:35 2008 From: dan.bolser at gmail.com (Dan Bolser) Date: Sun, 31 Aug 2008 18:12:35 +0100 Subject: [Fedora-r-devel-list] R2spec new release In-Reply-To: <1220188450.17883.12.camel@localhost.localdomain> References: <48BA824E.9090705@pingoured.fr> <2c8757af0808310535y560c19d3gcfe3da9847a2a70a@mail.gmail.com> <1220188450.17883.12.camel@localhost.localdomain> Message-ID: <2c8757af0808311012m5f6c4d1dm26a929c949d58c9c@mail.gmail.com> 2008/8/31 Tom spot Callaway : > On Sun, 2008-08-31 at 13:35 +0100, Dan Bolser wrote: >> I think the first step would be to build a dummy RPM that includes all >> the R-libraries that come by default with R. Such things as base, >> lattice, stats, etc., etc. All these libraries could (?) be rolled >> into an RPM called R-libs (or something), and then when packaging an >> R-library that depends on 'stats', for example, the dependency would >> be satisfied by R-libs... Is that possible? > > The R package already does this: > > Provides: R-base = %{version} > Provides: R-boot = 1.2 > Provides: R-class = 7.2 > Provides: R-cluster = 1.11.11 > Provides: R-codetools = 0.2 > Provides: R-datasets = %{version} > Provides: R-foreign = 0.8 > Provides: R-graphics = %{version} > Provides: R-grDevices = %{version} > Provides: R-grid = %{version} > Provides: R-KernSmooth = 2.22 > Provides: R-lattice = 0.17 > Provides: R-MASS = 7.2 > Provides: R-methods = %{version} > Provides: R-mgcv = 1.4 > Provides: R-nlme = 3.1 > Provides: R-nnet = 7.2 > Provides: R-rpart = 3.1 > Provides: R-spatial = 7.2 > Provides: R-splines = %{version} > Provides: R-stats = %{version} > Provides: R-stats4 = %{version} > Provides: R-survival = 2.34 > Provides: R-tcltk = %{version} > Provides: R-tools = %{version} > Provides: R-utils = %{version} > Provides: R-VR = 7.2 > > %{version} is the version of R, in this case, 2.7.2. That is excellent. Thanks for the info. Now is there any way to cross check these against what R actually has installed? I am trying to think about ways that the R-installer could be used in combination with the packages... or is the idea to package the whole of CRAN? Where would such a repo be maintained? How would it be kept in sync with CRAN? Please just point me at the relevant docs if I am asking questions that have been covered before ;-) Cheers, Dan. > > ~spot > > _______________________________________________ > Fedora-r-devel-list mailing list > Fedora-r-devel-list at redhat.com > http://www.redhat.com/mailman/listinfo/fedora-r-devel-list > -- http://network.nature.com/profile/dan