Version 2 of the r image #167
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In case the package is ever sent down as a source package
Figure out the actual dependencies needed, rather than the -dev or -bin versions. This removes 130 uneeded packages, and saves 230mb of the image. The only testing done here is that the package imports cleanly, which definitly does fail if you remove the dependency entirely. It's possible that we have removed some optional dependencies that are not loaded on package import, but are are needed for certain. However, it is easy to add these back again if needed.
We only need a single cache for this, with subdirectories for each type. More readable and simplifies cache management.
AFAICT, this has no effect, for two reasons.
- ENV vars are only valid in the build stage that defined them, and we
defined them in the `base-r` stage. In the `r` stage it will run with
the default values, which should be empty anyway.
- You cannot save space by deleting things with docker. The objects
will still be in the previous layer. The only way to reduce space by
deleting file by removing them within the same RUN command that
created them, so they are never persisted to a layer.
In addition, because we use a persistant build cache, we don't want to
clear it at all! That would wipe the persistant cache out each build.
I manually checked that this made no different to the size, and it did
not, and I poked around to check:
```
> library("pak")
> cache_summary()
$cachepath
[1] "/root/.cache/R/pkgcache/pkg"
$files
[1] 0
$size
[1] 0
> cache_list()
> A data frame: 0 × 6
> ℹ 6 variables: fullpath <chr>, path <chr>, package <chr>, url <chr>,
> etag <chr>, sha256 <chr>
```
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Closes #51
Because pandoc is updated in v2 image.
Closes #74
The kableExtra package is included but we have chosen not to include phantomjs, which we think has gone unmaintained for a while.
Closes #75
As the v2 image installs binary R packages for Linux from the Posit Public Package Manager (formerly known as RStudio Package Manager).
Closes #88
Because survcomp is a Bioconductor package and we have currently chosen not to include Bioconductor packages.
Closes #101
As this is the next step for r-docker.
Closes #160
Adds sjPlot to v2 image.