FAQ
General
Why is it called both CRANapt and r2u?
We started out with the hope to eventually provide CRAN binaries for multiple distributions (Debian, Ubuntu, ...), releases (testing/stable, LTS/current, ...), hardware platforms, and so on. But we had to start somewhere, so Ubuntu LTS for amd64 is the first instance. And as we are effectively only on Ubuntu, at least for now, the shorter 'r2u' crept up, and stuck.
How is it pronounced?
We think of the 'n' as silent so you can always say "oh I just crapted these packages onto my system".
A package reports it is uninstallable
Make sure you follow the 'Pinnning' section of the README.md and the setup
script.
Some (older) builds in the (main) Ubuntu distribution appear to sort higher
and would block an installation of the freshly made binary (under a
consistent naming scheme). The apt feature of 'pinning' is what we want
here to have an entire repository sort higher.
There can also be other issues related to CRAN allowing a hyphen in version (e.g. nlme is currently at 3.1-157. But Debian and Ubuntu use a hyphen to split off the build iteration count so version numbers are sometimes standardised to for example 3.1.157 switching the hyphen to a dot. Sadly that leads to different sorting. (See issue #7 for more on an issue that was caused by this.) In general we can not overcome this by pinning, and we continue to try to find a more comprehensive solution that is less invasive than changing many package version numbers.
What is the relationship with the c2d4u PPA ?
We are huge fans of the c2d4u repository and have used it for a decade or longer. It uses the proper build process, and sits on a very solid Launchpad infrastructure supported by Canonical. However, this also makes it a little less nimble and precludes for example use of external build resources. Overall it also still at a fraction of CRAN packages. So we created this repo as an experiment to see if we could scale a simple and direct approach, and in the hopes it can complement the c2d4u PPA and offer additional packages
As of 2024, that hope has come to fruition as c2d4u is now taken a well-deserved hiatus, and recommends switching to r2u instead.
Can I use (current) r2u with Debian?
In general, it is not a good idea to mix packages from Debian and Ubuntu in the same installation. The package management system works so well for either because it generally can rely on proper package versions, dependencies, and relationships between packages. Mixing, while it may work in small isolated cases, is really not suitable to such setups. So we recommend against using (the current r2u setup which is Ubuntu-only) on Debian. (This question was also asked in issue #8.)
Can I install Bioconductor packages from Ubuntu not in r2u
This used to be an issue in the earlier days. As of early 2024 and the BioConductor 3.18 release, we also ensure we had all packages covered by the (originall Debian and hence also in the) Ubuntu distribution. At that time, the distribution had around 170 packages whereas the set of packages covered by r2u increased to just over 400. With the combination of r2u generally having a newer version along with the recommended pinning you should always get the r2u version without issues.
As of late 2024, and BioConductor 3.20, we have well over 400 packages from BioConductor for the (currently three) LTS releases we support.
(And for historical context, back-then-when Ubuntu contained a number of
Debian packages r-bioc-*. However, as the distribution cutoff for the
'jammy' (22.04) cutoff was before Bioconductor 3.15 was released so these
packages had a dependency on the 'r-api-bioc-3.14' (virtual) package. To
satisfy this with our r2u packages, which were then based on the newer
Bioconductor 3.15 (and later upgraded to 3.16, 3.17, now 3.18), we added a
small virtual package
bioc-api-package that we
added to the repo. So after sudo apt install bioc-api-package installation
of the addional Bioconductor packages in jammy can proceed. For more details
see issue #11. Note that
none of what is described in this second paragraph to the question is needed
anymore given the changes described in the first. All good!)
Can I use it with other non-LTS Ubuntu releases?
Of course! You can always forward-upgrade. So for example the 22.04
("jammy") release works perfectly fine with 22.10 ("kinetic"). Just make sure
you keep the sources.list entry on the LTS release you have as we (just
like many other repositories) only provide LTS releases and no interim
releases.
When running 22.10 / 23.04 / 23.10 / 24.10 on a laptop with r2u, we are aware of one
binary for the av which ends up
with a library dependency no longer satisified by the distribution. So we
built ourselves an ad-hoc new binary of r-cran-av for the distro we ran. We
will keep an eye on this to see if it affects other packages. If you find
one, please file an issue. We think we can address this with a supplementary
repo on an 'as-needed' basis.
Why does it have more packages than CRAN ?
We (at least currently) do not purge packages from r2u that have been archived at CRAN. Hence the set of packages at r2u grows faster and further leading to a (as of fall 2023) ten percent difference relative to CRAN.
What about other architectures besides x86_64 ?
Excellent question. CRAN builds for at least three different OSs, Debian binaries are provided on maybe 15 hardware platforms so 'how hard can it be?' you may ask (and some have in issues #40 and #55).
Sadly, quite hard. This is essentially somewhere between the third or fourth time I tried to build
something like this (some history is in this paper), and it only
got as (amazingly !) far as it is has gotten because I could build on existing binaries. None of
that rich infrastructure exists for other hardware platforms, and recall that all this also works by
plugging into and relying on apt so it would have to be a Debian (or Ubuntu) platform.
But hey if you read this and happen to be, say, a product manager at a large cloud provider, get in
touch. I have the infrastructure here, and nearly three decades of experience creating .deb
packages. This can be done and on some platforms (maybe graviton ?) it would make some quite a ton
of sense. But until then we remain in a x86_64 world.
Why can I not uninstall packages with remove.packages() ?
This issue is known and documented, for example under known issues in the main GitHub
README shadowed in the main
page of the documentation. The bspm package
traces install.packages() to facilitate installation; removal is a little more complicated as
discussed in this issue at the bspm repo. However,
bspm provides a function bspm::remove_sys() to remove a package installed via r2u as a system
package.
Can I install and use older versions by choice ?
Of course! One key aspect of using R on Debian / Ubuntu is that the order the library path
directories (shown by calling .libPaths()) such that the system libraries come last. This means
that you can always call bspm::disable(); install.packages("some_package") to install
some_package into either your personal repository within $HOME or into
/usr/local/lib/R/site-packages/. Just make sure to disable bspm to be able to install
'normally' from source.
See issue #75 where this is discussed a little too and an example is provided.
Should I install bspm?
We find it helpful. It allows you to use install.packages() in R, or script
install.r, and refer to CRAN and BioConductor packages by their names
which is more natural. bspm will call apt for you. Hence our default
Docker image has bspm installed and enabled by default.
(Also see below though for docker build and bspm.)
bspm is a little noisy
You can wrap suppressMessages() around bspm::enable(). We now do so in
the Docker image.
With the 22.04 "jammy" container I get 'Cannot connect' errors
We found that adding --security-opt seccomp=unconfined to the docker
invocation silenced those on AWS hosts and possibly other systems.
This may be related to Ubuntu hosts only.
A side-effect of this required security policy statement for bspm is that
bspm is not available when building containers off r2u.
It appears that Docker rules this out during builds.
The only remedy is to use bspm::disable() and to rely on just apt to
install the r2u packages in derived containers.
Can one use r2u with Singularity containers?
Yes, as discussed in this GitHub issue.
The key is that Singularity does not allow root access, yet we need to install packages
via bspm. The best answer is this to start from the base container, add packages as needed to
create a new Docker container -- and transfer / transform that container for Singularity use.
The running example in that issue is installing Seurat
and moderately complex and extended dependencies. Thanks to how r2u is set up a simpler Dockerfile
such as
FROM rocker/r2u:22.04
RUN install.r Seurat
which by using install.r (from littler along with
bspm turns this into a call to apt. Call as, say, docker build -t r2u_seurat:22.04 .
and enjoy the resulting container r2u_seurat:22.04 (or give it any other suitable name) and build
a suitable .sif from it as discussed in the issue.
How can one know when it was updated
We follow P3M/PPM/RSPM builds so their update tracker there can be helpful. We currently have no 'lastBuilt' tag on the website but could add one if that helped.