Category Archives: Updates

c2d4u and RRutter Ubuntu PPA Updates

On January 27, 2014 Raring Ringtail (13.04) reached end of life. I have been slowly removing the Raring repositories from the RRutter PPA, c2d4u PPA, and CRAN. I think I have most of that cleaned up, so there is no longer support for R in Raring from my sites.

In April, Trusty Tahr will be releases. This is Ubuntu 14.04 and a LTS. I have already added Trusty to the RRutter PPA and c2d4u PPA. Once Trusty is officially released, I will also make it available on CRAN. Initially, all the packages on c2d4u are copied from Precise. This saves building 2000+ packages on the PPA. New and updated packages will be built for Trusty and Precise, with the Saucy packages copied from Precise.

Since Ubuntu has moved to the shorter life span model for non-LTS releases, this will be my approach. Base R and the recommended packages (the RRutter PPA) will be built against each release, but on c2d4u I will only be building pacakges for the last two LTS releases. Any non-LTS releases on c2d4u will consists of packages copied from the a previous LTS. This may create some strange naming conventions for the packages on c2d4u, but most users will never notice. If something does not work, please let me know.

Finally, I have been playing around with the download stats available from PPA via the Launchpad API. As of noon on March 14 (Happy Pi Day!), here are the download numbers for the “r-base” (version 3.0.3) package:

  • Precise: 302
  • Saucy: 143
  • Lucid: 10
  • Quantal: 9
  • Trusty: 4

Backporting R 3.0.0 to Quantal, Precise, and Lucid

Today (May 4, 2013) I will begin the process of backporting R 3.0.0 to Quantal, Precise, and Lucid. This will include all the recommended packages and the packages for R found in the universe repository for Ubuntu. Things to keep in mind:

  • If you do not want to receive these upgrades and you use the CRAN repositories or my Launchpad PPA, please remove them from your apt/synaptic sources lists. This will keep you on your current versions.

  • You could pin the old versions (search google for “apt pinning”), but since updates will only be coming for R 3.0.0, it is easier to just remove the repositories.

  • This should be complete by Monday, but it may take longer depending on server load.

After the update process, base R and the recommended packages will be found on CRAN while all the other packages can be found at my PPA.

R 3.0.0 and Raring Ringtail (Ubuntu 13.04)

New .deb packages for R 3.0.0 on Raring Ringtail (13.04) are available on both CRAN and my Launchpad PPA. Some notes for this release.

  • The initial build for Raring Ringtail did not come with Tcl/Tk being supported. This issue has been addressed and the current release supports Tcl/Tk.

  • Due to a small configuration error on my server, the amd64 packages for Raring Ringtail did not sync to CRAN. This has been fixed and the 64-bit packages should be available soon on a CRAN mirror near you.

  • As has been previously discussed, R 3.0.0 requires that all packages be rebuilt against it. Therefore, all the r-cran-* packages found in the Ubuntu universe repository will not work with R 3.0.0. In an effort to rectify this, I have rebuilt a number of those packages against R 3.0.0 and they can be found at the RRutter PPA, but not CRAN. I am still having issues with a couple of packages, but I am working on those.

  • R 3.0.0 is still available for older Ubuntu releases on my RDev PPA. The plan is to upgrade Lucid, Precise, and Quantal this Friday evening (May 3rd, 2013) as well as many of the r-cran-* packages available in universe. If you do not want to upgrade to R 3.0.0, please remove the appropriate repository from you sources list.

Moving to R 3.0.0 on Ubuntu

As you may (or may not) be aware of, R 3.0.0 is scheduled to be released on April 3rd. Since this is a major release and there may be some growing pains (but I hope not) in the move 3.0.0, here is some information about how I will handle R 3.0.0 on CRAN and my PPAs for Ubuntu.

All packages must be rebuilt for R 3.0.0

Any installed packages you are currently using will have to be rebuilt using R 3.0.0. This could lead to some issues, especially is you are using the Ubuntu binaries on CRAN or my PPA. I will try to minimize these issues.

CRAN and RRutter PPA are now frozen to R 2.15.3 (with one exception)

Since many users would probably be alarmed to have production machines upgrade to R 3.0.0 without testing to see if any thing breaks, the packages on CRAN and the RRutter PPA will not be updated anymore. This means R is frozen with version 2.15.3 and the packages available will not be updated on CRAN or the RRutter PPA for now.

At some point, likely around May 1st, I will move CRAN and the RRutter PPA to version 3.0.0. This should give users plenty of time to remove those repositories from apt so the upgrades do not occur. I will warn everyone when I am about to do this.

The one exception to this rule will be the forth coming Ubuntu 13.04 (Raring Ringtail). When I add this release to CRAN and the PPA, I will be using R 3.0.0 and packages built against 3.0.0.

R 3.0.0 and recommended packages will be available on RDev PPA

If you do want to upgrade R to 3.0.0, you can use my RDdev PPA. This will have the latest version of R and the recommended packages built against it. Instructions on how to install the PPA are available at the RDdev PPA webpage. As of right now, only 12.10 (quantal) builds are available, but others will be added when bugs are worked out. Please, do not have the RDev PPA and (CRAN or RRutter PPA) enabled at the same time, as that could cause issues.

What about c2d4u?

Excellent question.

Stopping support for Hardy and Oneiric

Both Hardy (8.04) and Oneiric (11.10) are ending support in April 2013. Therefore, I will not be updating any version of R for these releases. I, for one, am happy to finally be able to rid myself of the albatross (or should I say heron) that is Hardy. I will not delete these files for a while, but there will be no further updates. Support for Lucid (10.04) will continue until April 2015 or until something becomes very broken.

Are you sure you don’t have anything to say about c2d4u?

c2d4u is an ambitious project that houses over 1000 packages for R as Ubuntu binaries that can be installed via apt or synaptic. You should really check it out. It has great packages like RCpp and ggplot2, among others.

My first priority will be is to build all the packages for Ubuntu 13.04 (Raring Ringtail) using R 3.0.0. After that is complete, I will start rebuilding the packages for 12.04 (Precise), the latest LTS, against 3.0.0. If I still have any patience left, I will convert the 12.10 (Quantal) packages over.

If you have any questions, please email me. My contact information can be found above.

R 2.15.3 .deb packages now available for Ubuntu

The latest version of R (2.15.3) is now available for Ubuntu. You can find the packages on CRAN or via my Launchpad PPA.

Just before the release of 2.15.3, a patch for “r-base” was released dealing with MD5 sums in the package the caused some problems on Quantal, but those have been resolved.

Also, a change in the version of “libtiff-dev” dependency caused some delays in the versions of “r-base” for Ubuntu releases prior to Quantal from building. Those issues have been resolved as well and the 2.15.3 is or will soon be available on the CRAN mirrors.

If there are any issues, please feel free to contact me.

rjags Updated and Numbering Corrected

On September 18th, Martyn Plummer updated rjags. Normally, this wouldn’t be a big deal, but a question came across the R-sig-debian mailing list about the package at the same time, and I noticed that my Ubuntu 12.04 (precise) machine was using version 3.3 from the Ubuntu universe repository and not the 3.5 version that is available at the RRutter or c2d4u PPAs.

Turns out the version numbering system used by Martyn is not compatible with the Ubuntu numbering system used for the package in the universe repository. The universe package is numbered “3.3” while Matryn’s numbering format uses all dashes, “3-5”. The debian version of the package has not been updated since 3.3, so the source package used to create my update was genereated via the cran2deb4ubuntu project and kept Martyn’s “-” version numbering.

Even though rjags 3-5 was available in the PPA, rjags 3.3 was considered a more recent version by Ubuntu and the package was never upgraded. It is possible to use apt pinning or synaptic to force the “newer” version, but I have correct the numbering issue and the newest version of r-cran-jags is numbered “3.7” and will update automatically.

Not sure if any other packages on c2d4u have similar issues. If anybody spots one, please let me know.

R 2.15.1 Available

Ubuntu packages for the latest release of R are now available on CRAN and RutteR PPA. If you have either repository installed, Ubuntu should have updated R automatically. If you do not have either repository isnallted, see the Installing R tab above.

The announcment from the R Core Team about 2.15.1 can be found here.

For Ubuntu (and Debian) users, the following has also been added:

  • src/X11/*: Applied revised patch by Philip Johnson to to set the X11 icon and window class for improved desktop experience; patch source and support files are in debian/icon-class-patch/.
  • debian/rules: Install icon png file and desktop file from Philip too
  • debian/r-base-core.dirs: Add two directories for icon and desktop

In short, this means when you create windows from within R, the R logo will appear in the window title bar (if your desktop has that feature enabled) and in any application that manages your windows.