r-devel

r-devel@lists.fedoraproject.org

127 discussions

r bridge to mono
by D.Enrique ESCOBAR ESPINOZA 24 Apr '10

24 Apr '10

Hi, does any one know if there is a bridge to R from mono the multiplatform csharp interpreter? Thank you very much. -------------------------------------------------- Enrique ESCOBAR

2 1

R-repo
by Pierre-Yves Chibon 23 Apr '10

23 Apr '10

Dear all, There is a some group of people which is gathering at this moment to build a RPMs R-repository. This repository will be built using R2rpm which mean: - No -devel subpackage - Automated spec generation - Dependencies resolved based on the DESCRIPTION file We will make sure that the package that don't build have logs available. At the moment we are trying to put together all the infrastructure. We have started to build the first packages and are hoping to have the first generation of the repository in few days. For those of you who would be interested we have just set up a mailing list at: http://www.bioinformatics.org/mailman/listinfo/r-repo-dev Feel free to join the discussions to make of this project something useful for all. Regards, Pierre

1 0

R 2.11.0 in Fedora Updates Testing
by Tom Callaway 23 Apr '10

23 Apr '10

R 2.11.0 is built now for Fedora and EPEL. It is in "updates-testing". In accordance with the new policies on Fedora Updates, these new packages will not be pushed as official updates until they either receive positive testing from users, or sit in updates-testing for two weeks. You can help us test these packages, and move them forward. Here's how: 1. Go to the Fedora Updates web application (its real name is "Bodhi"): https://admin.fedoraproject.org/updates/ Once you're there, click the login blue box at the top left, and login with your Fedora Account. If you don't have a Fedora Account, you can skip this step. 2. Click on the link for the Fedora R test update that matches your release: Fedora 11: https://admin.fedoraproject.org/updates/rpy-2.0.8-2.fc11,R-2.11.0-1.fc11 Fedora 12: https://admin.fedoraproject.org/updates/rpy-2.0.8-2.fc12,R-2.11.0-1.fc12 EPEL-4 (RHEL-4): https://admin.fedoraproject.org/updates/R-2.11.0-1.el4 EPEL-5 (RHEL-5): https://admin.fedoraproject.org/updates/R-2.11.0-1.el5 3. Now, on your Fedora (or RHEL) system, run this command (as root, or with root privs) to install the test update: yum --enablerepo=updates-testing update R That should update R to the test update (if you don't want the full R suite, you can replace "R" in that string with "R-core"). 4. Test it! Make sure it does all the things you would expect it to. 5. Go back to the web page for the R update (step 2), and at the bottom, click "Add a comment >>" (If you didn't login, it will ask you for an email address and make you complete a captcha to make sure you are a unique individual.) In that text box which opens up, write a little bit about the testing you did and if it works okay for you or not. Then (this is the important part), click the "Works for me" or "Does not work" radio button below it, and click the Add Comment button. 6. That's it! If it worked, you've given that update a +1 karma vote. (If it didn't work, you've given it a -1 karma vote). Now, if three people give a +1, and the package update gets to +3, the Fedora Update system will automatically move the update from testing to a real update, and everyone will get it. Thanks in advance, ~spot, Fedora/EPEL R maintainer

1 0

R2rpm call for tester
by Pierre-Yves Chibon 06 Apr '10

06 Apr '10

Dear all, I have been working on R2spec fixing a couple of bugs here and there and switching to a template engine (jinja2) for the creation of the spec (based on the idea from Allen S. Rout). I have also spent some time today to get a first R2rpm script working. Of course it uses the class from R2spec, so I have put them together in one rpm. I would like to have some feedback before pushing these through the repo, so if you could quickly test them and give me feed back it would be really nice :) sources: https://fedorahosted.org/releases/r/2/r2spec/R2spec-3.0.0pre.tar.gz src.rpm: https://fedorahosted.org/releases/r/2/r2spec/R2spec-3.0.0-1.fc12.src.rpm rpm: https://fedorahosted.org/releases/r/2/r2spec/R2spec-3.0.0-1.fc12.noarch.rpm Have a nice sunday, Pierre

2 20

Monthly update
by Pierre-Yves Chibon 01 Apr '10

01 Apr '10

As proposed there is the monthly reminder about the version of the packages in Fedora vs upstream. I did not clean the known false positive so far. spot -- R-nws is outdated, 2.0.0.3 vs 1.7.0.0 upstream denisarnaud -- R-msm is outdated, 0.9.5 vs 0.9.6 upstream orion -- R-car is outdated, 1.2 vs 1.2.16 upstream orion -- R-lmtest is outdated, 0.9 vs 0.9.26 upstream orion -- R-multcomp is outdated, 1.1 vs 1.1.6 upstream orion -- R-mvtnorm is outdated, 0.9 vs 0.9.9 upstream orion -- R-systemfit is outdated, 1.1 vs 1.1.4 upstream orion -- R-zoo is outdated, 1.6 vs 1.6.2 upstream jamatos -- R-mAr is outdated, 1.1.1 vs 1.1.2 upstream jamatos -- R-waveslim is outdated, 1.6.1 vs 1.6.3 upstream jamatos -- R-wavethresh is outdated, 2.2.11 vs 4.5 upstream nigelj -- R-RSQLite is outdated, 0.8.1 vs 0.8.4 upstream Total: 12 packages outdated/needing some work Regards, Pierre

1 0

R packages update
by Pierre-Yves Chibon 03 Mar '10

03 Mar '10

Dear all, I have been quickly playing with [1] to generate a kind of report on the package that would need work. There is the report: spot -- R-nws is outdated, 2.0.0.3 vs 1.7.0.0 upstream denisarnaud -- R-msm is outdated, 0.9.5 vs 0.9.6 upstream orion -- R-car is outdated, 1.2 vs 1.2.16 upstream orion -- R-lmtest is outdated, 0.9 vs 0.9.26 upstream orion -- R-multcomp is outdated, 1.1 vs 1.1.6 upstream orion -- R-mvtnorm is outdated, 0.9 vs 0.9.9 upstream orion -- R-systemfit is outdated, 1.1 vs 1.1.4 upstream orion -- R-zoo is outdated, 1.6 vs 1.6.2 upstream pingou -- R-Biostrings is outdated, 2.14.10 vs 2.14.12 upstream jamatos -- R-mAr is outdated, 1.1.1 vs 1.1.2 upstream jamatos -- R-waveslim is outdated, 1.6.1 vs 1.6.3 upstream nigelj -- R-RSQLite is outdated, 0.8.1 vs 0.8.3 upstream Total: 12 packages outdated/needing some work I believe all the packages of orion are false positive (it is the issue of the - in the version number). I believe R-nws is also wrong, but the page on the cran is not been updated since 1.7.0.0. We could imagine a monthly reminder if you are interested. Best regards, Pierre [1] http://rpms.famillecollet.com/rpmphp/rpm.php?type=R

3 2

Re: [Fedora-r-devel-list] [R-sig-Fedora] Improving RPM packaging for R; ideas gathered from the Debian folks
by Tom Callaway 15 Feb '10

15 Feb '10

On 02/03/2010 09:12 PM, Paul Johnson wrote: > One of the really handy R packaging ideas they have > is to customize R environment so that there are several directories in > the package path. > > It adjusts the etc/Renviron file so that it has: > > R_LIBS_USER=${R_LIBS_USER-'~/R/i486-pc-linux-gnu-library/2.10'} > R_LIBS_SITE=${R_LIBS_SITE-'/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library'} > > That would be pretty easy to add into the R packaging for RPM systems. > > The benefit is as follows. > > If an unprivileged user tries to install an R package, there's no > error, but rather it installs the rpm under $HOME/R/i386. Well, I don't think a standard setup will permit an unprivileged user to install rpm packages, but this should work when building things from CRAN, I suppose. My only concerns are: 1) Users shouldn't be assuming that /usr/local/lib/R exists. Fedora packages can't create that directory, and we don't really want the first user to hit that directory to create it with their own ownership privs. 2) Right now, we have two locations for R packages from Fedora: %{_libdir}/R/library/* and %{_datadir}/R/library/* (arch vs noarch). I'm not sure it is worth making another set of separate directories. Or to sum it up, I think the R_LIBS_USER setting makes some sense, but I'm not sure the additional complexity of R_LIBS_SITE adds any value. Also, I'm not sure why there is so much hierarchy in the proposed setting for R_LIBS_USER. The R version, perhaps is understandable, but the target architecture? > "Over there" in r-sig-deb, I learned that Dirk Eddelbuettel and > Charles Blundell developed a thing called "cran2deb". > > http://www.mail-archive.com/debian-science@lists.debian.org/msg03306.html > > That has debian packages of almost every R package you can get on CRAN. I'm not personally a fan of autogenerated packages. If people are interested in a CRAN package, we can get it added to Fedora and properly maintained. The number of times that RScaLAPACK has broken has convinced me of the value of having someone responsible for keeping these bits alive. :) With that said, various folks have made some good tools for making quick and easy R module RPM packages, and those are an excellent first step for getting those packages into Fedora. ~spot

2 1

Re: [Fedora-r-devel-list] [R-sig-Fedora] Improving RPM packaging for R; ideas gathered from the Debian folks
by Tom Callaway 08 Feb '10

08 Feb '10

On 02/08/2010 04:07 PM, Peter Dalgaard wrote: > Think networked drives. Is the users home dir mounted on Linux, Solaris, > Mac, or maybe a P: drive on Windows? Well, having also been there, I think that sort of environment involves customization beyond that provided by the distribution. Or, to put it succinctly, we should not target madness by default. :) ~spot

1 0

Building RPMs from CRAN...
by Allen S. Rout 13 Jan '10

13 Jan '10

Pierre-Yves <pingou(a)pingoured.fr> writes on R-devel: > One of them is R2spec [1], which I have worked on. I would also > point you to a 'fork' of R2spec [2] which aims at building RPM more > than spec (reason why they did not merge). R2spec aims a helping to > generate spec files as close as possible to the final one for > inclusion in official Fedora/EPEL repositories. Allen S. Rout have > made a nice job converting R2spec to generate RPM directly, solving > some of the circular dependences issues. I appreciate your kind mention of my effort, Pierre-Yves. Thank you! I am dissapointed that you don't see a merge in the future. I would like to change that if I can. What would you like me to change? It is my hope that the R2spec code will make it possible, eventually, to build and maintain _all_ the CRAN packages as RPMs, without the extensive by-hand treatment they now get. I understand that, if this is to happen, more folks than just me need to be happy with the code. :) - Allen S. Rout

2 2

R 2.10.0 updates
by Tom Callaway 22 Nov '09

22 Nov '09

Sorry that this one didn't make it in time to be tagged for Fedora 12, but it will be available as a 0day update. Fedora 10: https://admin.fedoraproject.org/updates/rpy-1.0.3-13.fc10,R-2.10.0-1.fc10 Fedora 11: https://admin.fedoraproject.org/updates/rpy-2.0.6-7.fc11,R-2.10.0-1.fc11 Fedora 12: https://admin.fedoraproject.org/updates/rpy-2.0.6-7.fc12,R-2.10.0-1.fc12 EL-4: https://admin.fedoraproject.org/updates/R-2.10.0-1.el4 EL-5: https://admin.fedoraproject.org/updates/R-2.10.0-1.el5 Remember that EL-4 and EL-5 updates for R have to sit in updates-testing for 3 weeks, unless they receive 3 "positive" karma votes. If you use these packages and you want them to hit the updates repository sooner, please test them and give feedback at the above links. Thanks, ~spot

3 5

← Newer
1
2
3
4
5
6
7
...
13
Older →

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

r-devel