From pingou at pingoured.fr Wed Oct 8 08:01:45 2008 From: pingou at pingoured.fr (Pierre-Yves) Date: Wed, 08 Oct 2008 10:01:45 +0200 Subject: [Fedora-r-devel-list] R2spec version 2.5.1 Message-ID: <48EC68E9.6090500@pingoured.fr> Dear list, As previously I am announcing here the new release of R2spec, the version 2.5.1. Here is the changelog for this version: # Version 2.5.1 -- 07th Oct 2008 # -Features added # * Add the summary from Title in the DESCRIPTION file # * Add the possibility to have a ~/.R2spec.conf which overrides the /etc/R2spec.conf # -Bugs correction # * Correct a typo SOURCES != SOURCE # * Copy from ./ to ~/rpmbuild and not ../ Bug #1 # * Change "summary should be not be longer than that" to "summary should be not be longer than this" # * Create the function finishName in the spec class to avoid redundancy in the code # * Move the check of the specfile to Package.py to avoid redundancy in the code # * Change some layout in the output Feed back, bugs and suggestions welcome here or in : https://fedorahosted.org/r2spec Thanks, Have a nice day, Pierre From dan.bolser at gmail.com Wed Oct 8 09:00:46 2008 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 8 Oct 2008 10:00:46 +0100 Subject: [Fedora-r-devel-list] R2spec version 2.5.1 In-Reply-To: <48EC68E9.6090500@pingoured.fr> References: <48EC68E9.6090500@pingoured.fr> Message-ID: <2c8757af0810080200s1205dccak37094cce9224b494@mail.gmail.com> 2008/10/8 Pierre-Yves : > Dear list, > > As previously I am announcing here the new release of R2spec, the version > 2.5.1. > > Here is the changelog for this version: Also the web page - https://fedorahosted.org/r2spec - has been greatly improved (much more information on how to use R2spec)! All the best, Dan. > # Version 2.5.1 -- 07th Oct 2008 > # -Features added > # * Add the summary from Title in the DESCRIPTION file > # * Add the possibility to have a ~/.R2spec.conf which overrides the > /etc/R2spec.conf > # -Bugs correction > # * Correct a typo SOURCES != SOURCE > # * Copy from ./ to ~/rpmbuild and not ../ Bug #1 > # * Change "summary should be not be longer than that" to "summary should > be not be longer than this" > # * Create the function finishName in the spec class to avoid redundancy > in the code > # * Move the check of the specfile to Package.py to avoid redundancy in > the code > # * Change some layout in the output > > Feed back, bugs and suggestions welcome here or in : > https://fedorahosted.org/r2spec > > Thanks, > Have a nice day, > > Pierre > > _______________________________________________ > 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 From pingou at pingoured.fr Wed Oct 8 09:12:02 2008 From: pingou at pingoured.fr (Pierre-Yves) Date: Wed, 08 Oct 2008 11:12:02 +0200 Subject: [Fedora-r-devel-list] R2spec version 2.5.1 In-Reply-To: <2c8757af0810080200s1205dccak37094cce9224b494@mail.gmail.com> References: <48EC68E9.6090500@pingoured.fr> <2c8757af0810080200s1205dccak37094cce9224b494@mail.gmail.com> Message-ID: <48EC7962.9000109@pingoured.fr> Dan Bolser wrote: > 2008/10/8 Pierre-Yves : >> Dear list, >> >> As previously I am announcing here the new release of R2spec, the version >> 2.5.1. >> >> Here is the changelog for this version: > > Also the web page - https://fedorahosted.org/r2spec - has been greatly > improved (much more information on how to use R2spec)! > Thanks to you for a good part :) Regards, Pierre From tcallawa at redhat.com Thu Oct 23 13:55:08 2008 From: tcallawa at redhat.com (Tom "spot" Callaway) Date: Thu, 23 Oct 2008 09:55:08 -0400 Subject: [Fedora-r-devel-list] R-devel going away Message-ID: <1224770108.3601.40.camel@localhost.localdomain> This email serves as an announcement that I plan to swallow up R-devel into the base R package. Why? * It is causing no end of user complaints. The typical R user expects to be able to do a "CPAN" (really, I should say "CRAN") style package install through the R interface: install.packages("RSQLite") This doesn't work unless you have R-devel installed. The average R user is a professor or a student, and neither of them are going to necessarily possess the necessary Linux/Fedora knowledge to be able to understand why this doesn't work like the R documentation says it should. * The size of the R-devel is tiny, about 440K installed. It will not bloat the main package to absorb the .h files and a .pc file into the main package. There are no libraries in the R-devel package. * The primary users of R-devel are R addon packages. They can continue to BuildRequires: R-devel safely (hooray for Provides/Requires). * libRmath (the R shared library) will still be a separate package. libRmath-devel will still be a separate package. As far as I know, nothing in Fedora uses libRmath, nor is libRmath-devel necessary for building R addons. Now, I recognize that this is a violation of the Fedora Packaging Guidelines, and I've given a lot of thought to this over the last few days, and technically, this is a reversal of my earlier stance (which is to stick to the guidelines). However, I think this is a key functionality that Fedora R users expect to just work, and I want to try to make sure that they get the best R experience out of the box that they can. As Martyn Plummer pointed out: There are currently 1533 packages/bundles on CRAN, not counting the recommended packages that are already distributed with R. Of these packages, 420 require to the R headers. Fedora only supplies RPMs for 9 of them. I'm not entirely sure if I need FESCo or FPC approval to take this action, if so, this is my notice of requesting it. ;) I'm also looking for feedback and comments, of course. Thanks, ~spot (Fedora R maintainer) From tcallawa at redhat.com Thu Oct 23 14:42:19 2008 From: tcallawa at redhat.com (Tom "spot" Callaway) Date: Thu, 23 Oct 2008 10:42:19 -0400 Subject: [Fedora-r-devel-list] Re: R-devel going away In-Reply-To: <87mygvcrd0.fsf@fc5.bigo.ensc.de> References: <1224770108.3601.40.camel@localhost.localdomain> <87mygvcrd0.fsf@fc5.bigo.ensc.de> Message-ID: <1224772939.3601.54.camel@localhost.localdomain> On Thu, 2008-10-23 at 16:34 +0200, Enrico Scholz wrote: > Better solutions: > > * add it to comps.xml > * move 'R' to R-core, and add 'R' which depends on 'R-core' + > 'R-devel' > > > > * The size of the R-devel is tiny, about 440K installed. > > You miss its dependencies: > > bzip2-devel > gcc-c++ > gcc-gfortran > libICE-devel > libSM-devel > libX11-devel > libXmu-devel > libXt-devel > libjpeg-devel > libpng-devel > ncurses-devel > pkgconfig > readline-devel > tcl-devel > tetex-latex > texinfo > tk-devel These are very good points, thanks Enrico. What would people think about doing the suggested R/R-core/R-devel split instead? Users would still be able to get everything with yum install R, it would meet the guidelines, and minimal installs with R can simply have R-core. ~spot From pingou at pingoured.fr Thu Oct 23 14:46:09 2008 From: pingou at pingoured.fr (Pierre-Yves) Date: Thu, 23 Oct 2008 16:46:09 +0200 Subject: [Fedora-r-devel-list] Re: R-devel going away In-Reply-To: <1224772939.3601.54.camel@localhost.localdomain> References: <1224770108.3601.40.camel@localhost.localdomain> <87mygvcrd0.fsf@fc5.bigo.ensc.de> <1224772939.3601.54.camel@localhost.localdomain> Message-ID: <49008E31.7050204@pingoured.fr> Tom "spot" Callaway wrote: > These are very good points, thanks Enrico. What would people think about > doing the suggested R/R-core/R-devel split instead? Users would still be > able to get everything with yum install R, it would meet the guidelines, > and minimal installs with R can simply have R-core. Sounds like a good idea to me :) Pierre ~ pingou From pingou at pingoured.fr Thu Oct 23 14:46:09 2008 From: pingou at pingoured.fr (Pierre-Yves) Date: Thu, 23 Oct 2008 16:46:09 +0200 Subject: [Fedora-r-devel-list] Re: R-devel going away In-Reply-To: <1224772939.3601.54.camel@localhost.localdomain> References: <1224770108.3601.40.camel@localhost.localdomain> <87mygvcrd0.fsf@fc5.bigo.ensc.de> <1224772939.3601.54.camel@localhost.localdomain> Message-ID: <49008E31.7050204@pingoured.fr> Tom "spot" Callaway wrote: > These are very good points, thanks Enrico. What would people think about > doing the suggested R/R-core/R-devel split instead? Users would still be > able to get everything with yum install R, it would meet the guidelines, > and minimal installs with R can simply have R-core. Sounds like a good idea to me :) Pierre ~ pingou From jamatos at fc.up.pt Thu Oct 23 18:41:41 2008 From: jamatos at fc.up.pt (=?utf-8?q?Jos=C3=A9_Matos?=) Date: Thu, 23 Oct 2008 19:41:41 +0100 Subject: [Fedora-r-devel-list] Re: R-devel going away In-Reply-To: <1224786127.3898.97.camel@code.and.org> References: <1224770108.3601.40.camel@localhost.localdomain> <1224772939.3601.54.camel@localhost.localdomain> <1224786127.3898.97.camel@code.and.org> Message-ID: <200810231941.41824.jamatos@fc.up.pt> On Thursday 23 October 2008 19:22:07 James Antill wrote: > ?Well it kinda fits the "people expect foo-core + additions" _assuming_ > CRAN is a requirement, but really why don't we just package more of the > R modules so CRAN usage isn't a requirement? There are more than 1500 modules (the have been growing at an exponential rate in the last years). So while we would like to see more R packages in Fedora in are not even near to have a reasonable subset of R packaged. So for the moment CRAN is really a requirement to use R in Fedora. > -- > James Antill > Fedora -- Jos? Ab?lio From gnwiii at gmail.com Thu Oct 23 22:08:53 2008 From: gnwiii at gmail.com (George N. White III) Date: Thu, 23 Oct 2008 19:08:53 -0300 Subject: [Fedora-r-devel-list] Re: R-devel going away In-Reply-To: <200810231941.41824.jamatos@fc.up.pt> References: <1224770108.3601.40.camel@localhost.localdomain> <1224772939.3601.54.camel@localhost.localdomain> <1224786127.3898.97.camel@code.and.org> <200810231941.41824.jamatos@fc.up.pt> Message-ID: <22af238a0810231508j183fd334m6a1dc272e518f6b0@mail.gmail.com> On Thu, Oct 23, 2008 at 3:41 PM, Jos? Matos wrote: > On Thursday 23 October 2008 19:22:07 James Antill wrote: >> Well it kinda fits the "people expect foo-core + additions" _assuming_ >> CRAN is a requirement, but really why don't we just package more of the >> R modules so CRAN usage isn't a requirement? > > There are more than 1500 modules (the have been growing at an exponential rate > in the last years). So while we would like to see more R packages in Fedora in > are not even near to have a reasonable subset of R packaged. > > So for the moment CRAN is really a requirement to use R in Fedora. There have always been conflicts between the CRAN package system and Fedora or other linux packaging Guidelines. Users can install CRAN packages without root privileges, but then the search function won't know about the user's packages, and packages that rely on other library (gsl, hdf5, etc) still need -dev RPM's. Linux distros should not be trying to enforce guidelines for mainstream packages with their own robust package management and archive networks. Instead, they should look for ways to improve support for users who rely on those 3rd party systems. For example: R-base: basic runtime without dev dependencies, for sites that provide binary CRAN packages (e.g., on a shared directory) so users don't need to do compiles. R-core: R-base + -dev dependencies for those who want to install source packages from CRAN (e.g., most individual R users) R-X-sup(plement): -dev dependencies needed to build package X (e.g., R-hdf5-sup requires hdf5-dev for the hdf5 package from CRAN, gsl-dev for gsl, etc.). These aren't strictly necessary, but would serve to link package versions on CRAN with the versions of the support libs in Fed, something that can take some effort (e.g., peeking in the sources) to determine. For sites where users need to ask admins to install libraries, this simplifies the problem of telling the admin which libs to install. In the long run, linux distros should look at devising ways to capture information from these 3rd party package managers to help resolve dependencies automatically. -- George N. White III Head of St. Margarets Bay, Nova Scotia From jamatos at fc.up.pt Fri Oct 24 06:52:17 2008 From: jamatos at fc.up.pt (=?iso-8859-1?q?Jos=E9_Matos?=) Date: Fri, 24 Oct 2008 07:52:17 +0100 Subject: [Fedora-r-devel-list] Re: R-devel going away In-Reply-To: <22af238a0810231508j183fd334m6a1dc272e518f6b0@mail.gmail.com> References: <1224770108.3601.40.camel@localhost.localdomain> <200810231941.41824.jamatos@fc.up.pt> <22af238a0810231508j183fd334m6a1dc272e518f6b0@mail.gmail.com> Message-ID: <200810240752.18594.jamatos@fc.up.pt> On Thursday 23 October 2008 23:08:53 George N. White III wrote: > > There have always been conflicts between the CRAN package system and > Fedora or other linux packaging Guidelines. Users can install CRAN > packages without root privileges, but then the search function won't know > about the user's packages, and packages that rely on other library (gsl, > hdf5, etc) still need -dev RPM's. Linux distros should not be trying to > enforce guidelines > for mainstream packages with their own robust package management and > archive networks. Playing devil's advocate I should remark that first each language is building its own repository and packaging system in a sense we have lots of equivalents of (yum+rpm) for each language (perl, php, python, R, tex, ...). On the other hand for the system to be really useful it must use the least possible denominator (read the dumbest wins- pun intended ;-) ). > Instead, they should look for ways to improve support > for users who rely on those 3rd party systems. For example: > > R-base: basic runtime without dev dependencies, for sites that provide > binary CRAN packages (e.g., on a shared directory) so users don't need to > do compiles. > > R-core: R-base + -dev dependencies for those who want to install source > packages from CRAN (e.g., most individual R users) > > R-X-sup(plement): -dev dependencies needed to build package X (e.g., > R-hdf5-sup requires hdf5-dev for the hdf5 package from CRAN, gsl-dev > for gsl, etc.). These aren't strictly necessary, but would serve to > link package versions on CRAN with the versions of the support libs in > Fed, > something that can take some effort (e.g., peeking in the sources) to > determine. For sites > where users need to ask admins to install libraries, this simplifies > the problem of telling the admin which libs to install. I am not sure if this is right path or the right balance. Another possible choice is to expand R2spec in scope and not only create rpm spec files but to discover the different dependencies and how they are solved inside. There is no reason that we can not rebuild the whole CRAN (or almost all of it) automatically. > In the long run, linux distros should look at devising ways to capture > information from these > 3rd party package managers to help resolve dependencies automatically. As everything with free software the survival of the fittest means that this will only happen if there are people interested in spending resources to make this possible. -- Jos? Ab?lio From pingou at pingoured.fr Fri Oct 24 07:43:19 2008 From: pingou at pingoured.fr (Pierre-Yves) Date: Fri, 24 Oct 2008 09:43:19 +0200 Subject: [Fedora-r-devel-list] Re: R-devel going away In-Reply-To: <200810240752.18594.jamatos@fc.up.pt> References: <1224770108.3601.40.camel@localhost.localdomain> <200810231941.41824.jamatos@fc.up.pt> <22af238a0810231508j183fd334m6a1dc272e518f6b0@mail.gmail.com> <200810240752.18594.jamatos@fc.up.pt> Message-ID: <49017C97.6040808@pingoured.fr> Jos? Matos wrote: > On Thursday 23 October 2008 23:08:53 George N. White III wrote: >> There have always been conflicts between the CRAN package system and >> Fedora or other linux packaging Guidelines. Users can install CRAN >> packages without root privileges, but then the search function won't know >> about the user's packages, and packages that rely on other library (gsl, >> hdf5, etc) still need -dev RPM's. Linux distros should not be trying to >> enforce guidelines >> for mainstream packages with their own robust package management and >> archive networks. > > Playing devil's advocate I should remark that first each language is building > its own repository and packaging system in a sense we have lots of equivalents > of (yum+rpm) for each language (perl, php, python, R, tex, ...). > > On the other hand for the system to be really useful it must use the least > possible denominator (read the dumbest wins- pun intended ;-) ). > >> Instead, they should look for ways to improve support >> for users who rely on those 3rd party systems. For example: >> >> R-base: basic runtime without dev dependencies, for sites that provide >> binary CRAN packages (e.g., on a shared directory) so users don't need to >> do compiles. >> >> R-core: R-base + -dev dependencies for those who want to install source >> packages from CRAN (e.g., most individual R users) >> >> R-X-sup(plement): -dev dependencies needed to build package X (e.g., >> R-hdf5-sup requires hdf5-dev for the hdf5 package from CRAN, gsl-dev >> for gsl, etc.). These aren't strictly necessary, but would serve to >> link package versions on CRAN with the versions of the support libs in >> Fed, >> something that can take some effort (e.g., peeking in the sources) to >> determine. For sites >> where users need to ask admins to install libraries, this simplifies >> the problem of telling the admin which libs to install. > > I am not sure if this is right path or the right balance. > > Another possible choice is to expand R2spec in scope and not only create rpm > spec files but to discover the different dependencies and how they are solved > inside. > > There is no reason that we can not rebuild the whole CRAN (or almost all of > it) automatically. R2spec [1] can handles the generation of spec for R-libraries pretty easily, but the spec always needs some revision behind. However, I had started some time ago a small script to update the spec file when there is a new release of an already package R-library. This might be something that I should develop maybe a bit more now (especially since Bioconductor 2.3 has been released with R 2.8.0) Should that be included in R2spec or in a separate tool ? > >> In the long run, linux distros should look at devising ways to capture >> information from these >> 3rd party package managers to help resolve dependencies automatically. > > As everything with free software the survival of the fittest means that this > will only happen if there are people interested in spending resources to make > this possible. -- For those who do not know it R2spec https://fedorahosted.org/r2spec Present in Fedora 8,9 and rawhide (10) and in EPEL 4 and 5. -- Regards, Pierre From gnwiii at gmail.com Fri Oct 24 10:13:35 2008 From: gnwiii at gmail.com (George N. White III) Date: Fri, 24 Oct 2008 07:13:35 -0300 Subject: [Fedora-r-devel-list] Re: R-devel going away In-Reply-To: <200810240752.18594.jamatos@fc.up.pt> References: <1224770108.3601.40.camel@localhost.localdomain> <200810231941.41824.jamatos@fc.up.pt> <22af238a0810231508j183fd334m6a1dc272e518f6b0@mail.gmail.com> <200810240752.18594.jamatos@fc.up.pt> Message-ID: <22af238a0810240313t6c9aa737y98ceea53c2ef0118@mail.gmail.com> On Fri, Oct 24, 2008 at 3:52 AM, Jos? Matos wrote: > On Thursday 23 October 2008 23:08:53 George N. White III wrote: >> >> There have always been conflicts between the CRAN package system and >> Fedora or other linux packaging Guidelines. Users can install CRAN >> packages without root privileges, but then the search function won't know >> about the user's packages, and packages that rely on other library (gsl, >> hdf5, etc) still need -dev RPM's. Linux distros should not be trying to >> enforce guidelines >> for mainstream packages with their own robust package management and >> archive networks. > > Playing devil's advocate I should remark that first each language is building > its own repository and packaging system in a sense we have lots of equivalents > of (yum+rpm) for each language (perl, php, python, R, tex, ...). > > On the other hand for the system to be really useful it must use the least > possible denominator (read the dumbest wins- pun intended ;-) ). It is really a question of the minimal effort needed to learn how to install the desired package. People will try to to use a tool they already know, then use the simplest tool. There is an advantage to being able to use the same tools on more than one platform. R and TeX are a bit different in that many users rely on them throughout their careers, using multiple platforms or working with colleagues who use different platforms. A colleague using Windows says: "you should do (in R): install.packages('hdf5')". When that fails, that colleague is unlikely to know how to solve the problem. There is another elephant in this room: security policies are being revised to require that end-user apps be installed and managed with user privileges. In practice, large organizations are moving to a model where "root" must have training/certification, with chargebacks when users need rpm package installs. At such sites, users are going back to the pre-package days where apps are installed from sources, or adopting a system like openpkg that uses RPM packages but can (if used to manage only applications) be used without root privs. Sooner or later, linux distros will have to deal with this. -- George N. White III Head of St. Margarets Bay, Nova Scotia From pingou at pingoured.fr Mon Oct 27 19:57:46 2008 From: pingou at pingoured.fr (Pierre-Yves) Date: Mon, 27 Oct 2008 20:57:46 +0100 Subject: [Fedora-r-devel-list] Re: Heads-up - Bioconductor - Requires R >= 2.x.y In-Reply-To: <49061CCD.6060404@yahoo.fr> References: <49061CCD.6060404@yahoo.fr> Message-ID: <49061D3A.8030300@pingoured.fr> Dear all, I am currently updating the libraries from bioconductor to the version 2.3 of bioconductor made for R 2.8.0. I am adding to all these package a global variable Rversion which is then used in the Requires and BuilRequires sections. This means that those packages will not be available for previous version of R. I am planning to generalize this and to add this in R2spec. Regards, Pierre From jamatos at fc.up.pt Tue Oct 28 13:33:22 2008 From: jamatos at fc.up.pt (=?iso-8859-1?q?Jos=E9_Matos?=) Date: Tue, 28 Oct 2008 13:33:22 +0000 Subject: [Fedora-r-devel-list] Re: R-devel going away In-Reply-To: <49017C97.6040808@pingoured.fr> References: <1224770108.3601.40.camel@localhost.localdomain> <200810240752.18594.jamatos@fc.up.pt> <49017C97.6040808@pingoured.fr> Message-ID: <200810281333.22426.jamatos@fc.up.pt> On Friday 24 October 2008 08:43:19 Pierre-Yves wrote: > Should that be included in R2spec or in a separate tool ? The former IMHO. -- Jos? Ab?lio