matches expectations in the directive sequences
not strictly required after preassemble because we have no root steps between preassemble and assemble,
so we could remove the `last_user = "root"` there instead
includes regression test
ggplot2 is a big library with a bunch of dependencies,
making our already slow R tests even slower. This PR
switches them to using the tinytest library, which has
no dependencies and is much smaller.
r-recommended is a collection of common CRAN packages,
which cause conflicts when trying to install older R.
These same packages can be regular dependencies retrieved from CRAN.
PPA is a specific kind of apt repository, hosted on
launchpad.net. We use https://cran.r-project.org/bin/linux/ubuntu/,
which is just a regular apt repository. The PPA terminology
always confused me, so this just clears that up
- MRAN doesn't seem to have R 4.1 specific snapshots, so let's
default to RSPM for anything 4.1+.
- Otherwise, snapshot dates in 2022 will result in using rspm
We were doing this from an old MRAN snapshot. I moved the pin
a little ahead, so IRKernel can also be installed from CRAN
instead of from GitHub. R <= 4.0 gets the old version, and anything
newer gets a more recent version of devtools. This gives us
fast installs for IRkernel with binary packages.
Also add a R 4.0 and R 4.1 test
packagemanager.rstudio.com is a CRAN mirror provided
by rstudio, with *binary packages* prebuilt for many Linux
Distributions! https://www.rstudio.com/blog/announcing-public-package-manager/
has more excellent detail. It cuts down install times for R packages
by almost 90% in some cases!
Like MRAN (which we use now), they also provide a daily snapshot
of CRAN at that date
(https://docs.rstudio.com/rspm/news/#rstudio-package-manager-2021090).
The URL for CRAN for a particular date can be fetched via an API
call. We call that API, and if there is no snapshot for that date
(anything before Oct 2017), we fall back on to MRAN. Adds a test
to test this fallback.
One possible issue about changing existing binder repos to use binary
builds rather than source builds is that the binary builds sometimes
require you have an apt package installed, and will fail if it is
not. We had to install the zmq library apt package for example -
source installs compile zmq from source, which is where the speedup
comes from. But unlike python wheels or conda packages, these binary
builds are not self-contained - they are linked to apt packages from
the specific distros. So some repos that worked before might fail now.
We can choose a more recent cut-off date to prevent this from happening.
- make sure to set PYTHONUNBUFFERED
- implement tee with subprocess readlines
- forward all relevant signals from entrypoint to 'true' command
- add monitor process to ensure child shuts down if parent does (maybe not useful in docker?)
This content provider allows to retrieve the content from a
Software Heritage (SWH) persistent identifier (SWHID).
Typical usage:
repo2docker swh:1:rev:94dca98c006b80309704c717b5d83dff3c1fa3a0
It uses the SWH public vault API to retrieve the content of the given
directory.
Most of the times, this will not need an authentication
token to bypass the rate-limiting of the SWH API.
Without authentication, one should be allowed to retrieve one
directory content per minute.
If this is not enought, then the user must use authenticated calls to
the SWH API.
For this, a new `swh_token` config item has been added to the Repo2Docker
application class.
To use authentication:
repo2docker --config cfg.json swh:1:rev:94dca98c006b80309704c717b5d83dff3c1fa3a0
with the swh_token config option being defined in the cfg.json config file.
The version bump #915 broke the Nix buildpack in case one does a build.
Nix 2.3 enables sandboxing by default. Building inside a Docker
container, while Nix is having sandboxing enabled is not possible. Thus,
sandbox = false should be set in /etc/nix/nix.conf.
Changes in stencila mean it doesn't work anymore and it's not feasible to update nbstencilaproxy
Instead, show only a warning about removed support for stencila
Simon Li