Replacing apt-key on Ubuntu CRAN If you have used apt-key on Ubuntu (or Debian) recently, you may mave noticed a message along the lines of Warning: apt-key is deprecated. Manage keyring files in trusted.gpg.d instead (see apt-key(8)). The final Ubuntu release with apt-key will be Ubuntu 22.04.
As the warning suggests, keyring files should be located in the /etc/apt/trusted.gpg.d/ directory. The first step is to download my .asc key file, which is an armored, ASCII version of my public key file.
Ubuntu binaries for R 4.0, the newest release, are now available in the usual locations, with some caveats. As with previous transitions to major releases, 4.0 binaries are have their own PPA or in their own directory on CRAN.
Launchpad PPA If you like to use Launchpad PPAs, the R 4.0 binaries can be found at RRutter 4.0. The recommended packages built against 4.0 can also be found here.
R packages for Cosmic Cuttlefish (18.10) have been added to the RRutter3.5 PPA and therefore have been mirrored to CRAN. These are the base packages for R, plus the recommended packages as well as a couple of others (jags, ess, rpy2, and littler). Most of these are already available in the standard 18.10 repositories, but as packages are updated, I will update them for CRAN.
Since the lifespan of Cosmic Cuttlefish is so short (support ends July 2019), I will not be creating a version of c2d4u for Cosmic.
86 new or updated packages added to c2d4u this weekend. The new CRAN Task View Missing Data, which was added last month.
A number of packages require R 3.5, so the number of packages updated on the R 3.5 version of c2d4u is less. Also, the rstan package, and anything related are not available for Trusty. This is due to the need of the C++14 standard for rstan. If there are any suggestions on how to get this to build on Launchpad, let me know.
64 new or updated packages on c2d4u were uploaded on August 25th. Packages are listed below.
Currently on the version 3.5 c2d4u PPA, there are 4059 packages for Bionic, 3674 for Xenial, and 3673 for Trusty. As always, if something fails to install or does not play well with other packages, please let me know.
PPA for packages built against R 3.4.*: c2d4u
PPA for packages built against R 3.
Thanks to a couple of users of the Ubuntu page on the CRAN, I was recently alerted to a duplicate key on the keyserver.ubuntu.com website. If you search for my key using the short ID string, you will find two keys listed.
One of the keys is mine, uid “Michael Rutter”. The other key, even though the date suggests otherwise, appears to be new. The uid is “Totally Legit Signing Key”.
On c2d4u, 58 packages were updated or added on August 18th. The list is below. As with many recent updates, a couple of packages require R 3.5. These packages are not being updated on the 3.4 c2d4u. I also updated ess on CRAN to the most recent version, which does not install. Dirk Eddelbuettel is uploading a new version that will hopefully fix things.
PPA for packages built against R 3.
Weekly c2d4u update. 66 packages either updated or new. One more package, lfe, requiring R 3.5, therefore not available on c2d4u for R 3.4. Don’t forget to install an additional PPA in order to support the spatial packages: ubuntugis-stable.
PPA for packages built against R 3.4.*: c2d4u
PPA for packages built against R 3.5.*: c2d4u3.5
package r_version BDgraph 2.51 CodeDepends 0.6.0 CopulaREMADA 1.
Weekly c2d4u update. 101 packages either updated or new. The transition to R 3.5 is starting to be seen on CRAN, as some packages are now requiring the latest version. Of the packages listed below, piecewisesem and dae are not available on c2d4u, which is based on R 3.4. At some point, updates to that version of c2d4u will stop if too many pacakges are R 3.5 dependent.
PPA for packages built against R 3.
Overview R 3.5.0 was released a few weeks ago. As it changes some (important) internals, packages installed with a previous version of R have to be rebuilt. This was known and expected, and we took several measured steps to get R binaries to everybody without breakage.
The question of but how do I upgrade without breaking my system was asked a few times, e.g., on the r-sig-debian list as well as in this StackOverflow question.
Weekly c2d4u update. 81 packages either updated or new. Package of note this week is sp, a workhorse package for spatial data in R. The issue for Ubuntu is that the binary package has an epoch number of 1 (1:1:1.3-1 to be exact). These epoch numbers are often used in Debian/Ubuntu when the version numbering scheme changes, and the new version is lower than the old version. By adding the “1:”, Ubuntu can deal with the change in numbering correctly.
Small weekly update to c2d4u. 21 packages in total either updated or new.
PPA for pacakges built against R 3.4.*: c2d4u
PPA for pacakges built against R 3.5.*: c2d4u3.5
package r_version BART 1.7 BAS 1.5.1 BoSSA 3.3 CompRandFld 1.0.3-5 Compositional 3.1 DepthProc 2.0.3 FixedPoint 0.5 GDINA 2.1.15 HH 3.1-35 MOCCA 1.3 OBsMD 3.0 PBSmapping 2.
When R 3.5 was released, the good folks at the Bioconductor project also released a new version, 3.7. Since I was rebuilding for R 3.5, I didn’t immediately include the updates to Bioconductor in my builds. I have now taken the time to include the update, so there are an additional 83 updated/new packages on c2d4u. (3.4 or 3.5 versions)
My PPAs do not provide all the Bioconductor packages. Some are included in a CRAN Task View, therefore they are included in c2d4u.
On the c2d4u PPAs, my goal is to update and add new packages (from CRAN Task Views) on a weekly basis, usually on the weekend. While I was building c2d4u3.5, I put this on hold, as I didn’t want to build new (to the PPA) packages at the same time as checking old ones.
For this update, 230 R packages were either updated or added as new. At this time, I don’t provide information that distinguishes between updated or new, but that feature may be added in the future.
After building 10,742 packages on Launchpad, I would like announce that cran2deb4ubuntu3.5 (c2d4u3.5 for short) is now available for testing and maybe even actually use. It wasn’t difficult to find if you know your way around launchpad, but you can find the PPA here: https://launchpad.net/~marutter/+archive/ubuntu/c2d4u3.5
Many things to consider before you add this PPA to your Ubuntu machine.
The PPA supplies binaries for Trusty (14.04), Xenial (16.04), and Bionic (18.
One of the advantages of using Launchpad’s PPA system is that it allows you to easily use the work of others backporting packages to older releases.
For example, the package jgr has a build requirement of libjq. jq is a command-line JSON processor, and the jqr package is required by a small number of other R packages, either directly or indirectly. The Ubuntu packages libjq-dev is available in Bionic, but not be default in Trusty or Xenial.
One of the research projects I have been working on for many years is a model that predicts E. coli levels at Presque Isle State Park beaches in Erie, PA. Presque Isle State Park brings in approximately 4.5 million visitors a year, and thanks to the Pennsylvania State Park system, is 100% free to use. A variety of different tools are used to protect swimmers from harmful bacteria, including my random forest model RoboHarry, named after the former lead ranger at the park.
I am slowly rebuilding the set of packages in c2d4u for use with R 3.5.0. Since packages built under version 3.4.* are not compatible with 3.5.0, they all need to be rebuilt. This includes the packages that came with the new Ubuntu Bionic (18.04) release. It is taking some time.
One of the challenges with using Launchpad is that once a package is built, it needs to be published. This takes some time (around 20 minutes).