Provision cluster library — hipercow

Provision a library. This runs a small task on the cluster to set up your packages. If you have changed your R version you will need to rerun this. See vignette("packages") for much more on this process.

Usage

hipercow_provision(
  method = NULL,
  ...,
  driver = NULL,
  environment = "default",
  check_running_tasks = TRUE,
  root = NULL
)

Arguments

method: The provisioning method to use, defaulting to NULL, which indicates we should try and detect the best provisioning mechanism for you; this should typically work well unless you are manually adding packages into your library (see Details). If given, must be one of auto, pkgdepends, script or renv; each of these are described in the Details and in vignette("packages").
...: Arguments passed through to conan. See Details.
driver: The name of the driver to use, or you can leave blank if only one is configured (this will be typical).
environment: The name of the environment to provision (see hipercow_environment_create for details).
check_running_tasks: Logical, indicating if we should check that no tasks are running before starting installation. Generally, installing packages while tasks are running is harmful as you may get unexpected results, a task may start while a package is in an inconsistent state, and on windows you may get a corrupted library if a package is upgraded while it is loaded. You can disable this check by passing FALSE. Not all drivers respond to this argument, but the windows driver does.
root: The hipercow root

Value

Nothing

Details

Our hope is that that most of the time you will not need to pass any options through ..., and that most of the time hipercow will do the right thing. Please let us know if that is not the case and you're having to routinely add arguments here.

Manually adding packages to an installation

One case where we do expect that you will pass options through to hipercow_provision is where you are manually adding packages to an existing library. The usage here will typically look like:

hipercow_provision("pkgdepends", refs = c("pkg1", "pkg2"))

where pkg1 and pkg2 are names of packages or pkgdepends references (e.g., username/repo for a GitHub package; see vignette("packages") for details).

Supported methods and options

There are four possible methods: pkgdepends, auto, script and renv.

The canonical source of documentation for all of these approaches is conan2::conan_configure.

`pkgdepends`

The simplest method to understand, and probably most similar to the approach in didehpc. This method installs packages from a list in pkgdepends.txt in your hipercow root, or via a vector of provided package references. Uses pkgdepends for the actual dependency resolution and installation.

Supported options (passed via ...)

refs: A character vector of package references to override pkgdepends.txt
policy: the policy argument to pkgdepends::new_pkg_installation_proposal (accepts lazy and upgrade)

`auto`

Uses pkgdepends internally but tries to do everything automatically based on your declared environments (see hipercow_environment_create and vignette("hipercow")) and the installation information recorded in the locally installed versions of the required packages.

This is experimental and we'd love to know how it works for you.

No options are supported, the idea is it's automatic :)

`script`

Runs a script (by default provision.R) on the cluster to install things however you want. Very flexible but you're on your own mostly. The intended use case of this option is where pkgdepends fails to resolve your dependencies properly and you need to install things manually. The remotes package will be pre-installed for you to use within your script.

Your script will run on a special build queue, which will run even when the cluster is very busy. However, this is restricted in other ways, allowing a maximum of 30 minutes and disallowing parallel running.

Supports one option:

script: The path for the script to run, defaulting to provision.R

`renv`

Uses renv to recreate your renv environment. You must be using renv locally for this to work, and at present your renv project root must be the same as your hipercow root.

No options are currently supported, but we may pass some renv options in the future; if you need more flexibility here please let us know.

Examples

cleanup <- hipercow_example_helper()
#> ℹ This example uses a special helper
writeLines(c("knitr", "data.table"), "pkgdepends.txt")
hipercow_provision()
#> ✔ Selected provisioning method 'pkgdepends'
#> /`-'\  _______  ___  ___ ____
#> \,T./ / __/ _ \/ _ \/ _ `/ _ \
#>   |   \__/\___/_//_/\_,_/_//_/
#>   |   ---- THE  LIBRARIAN ----
#> 
#> Bootstrapping from: /home/runner/work/_temp/Library
#> Installing into library: hipercow/lib
#> Using method pkgdepends
#> Running in path: /tmp/Rtmpw3JKrD/file16dc514fbc1b
#> Library paths:
#>   - /tmp/Rtmpw3JKrD/file16dc514fbc1b/hipercow/lib
#>   - /opt/R/4.4.1/lib/R/site-library
#>   - /opt/R/4.4.1/lib/R/library
#> id: 20241008152453
#> Logs from pkgdepends follow:
#> 
#> -------------------------------------------------------------------------------
#> 
#> 
#> ── repos 
#> • https://cloud.r-project.org
#> 
#> ── refs 
#> • knitr
#> • data.table
#> 
#> ✔ Updated metadata database: 4.45 MB in 9 files.
#> 
#> ℹ Updating metadata database
#> ✔ Updating metadata database ... done
#> 
#> + data.table   1.16.0 [bld][cmp][dl]
#> + evaluate     1.0.0  [bld][dl]
#> + highr        0.11   [bld][dl]
#> + knitr        1.48   [bld][dl]
#> + xfun         0.48   [bld][cmp][dl]
#> + yaml         2.3.10 [bld][cmp][dl]
#> ℹ Getting 6 pkgs with unknown sizes
#> ✔ Got highr 0.11 (source) (13.85 kB)
#> ✔ Got evaluate 1.0.0 (source) (34.81 kB)
#> ✔ Got yaml 2.3.10 (source) (94.56 kB)
#> ✔ Got xfun 0.48 (source) (164.96 kB)
#> ✔ Got knitr 1.48 (source) (583.01 kB)
#> ✔ Got data.table 1.16.0 (source) (5.30 MB)
#> ℹ Building evaluate 1.0.0
#> ℹ Building xfun 0.48
#> ℹ Building yaml 2.3.10
#> ℹ Building data.table 1.16.0
#> ✔ Built evaluate 1.0.0 (3.1s)
#> ✔ Installed evaluate 1.0.0  (36ms)
#> ✔ Built xfun 0.48 (5.2s)
#> ✔ Installed xfun 0.48  (1s)
#> ℹ Building highr 0.11
#> ✔ Built yaml 2.3.10 (6.3s)
#> ✔ Installed yaml 2.3.10  (32ms)
#> ✔ Built highr 0.11 (1.1s)
#> ✔ Installed highr 0.11  (1s)
#> ℹ Building knitr 1.48
#> ✔ Built knitr 1.48 (5s)
#> ✔ Installed knitr 1.48  (39ms)
#> ✔ Built data.table 1.16.0 (20.3s)
#> ✔ Installed data.table 1.16.0  (52ms)
#> ✔ Summary:   6 new  in 43.3s
#> 
#> -------------------------------------------------------------------------------
#> Writing library description to 'hipercow/lib/.conan/20241008152453'
#> Done!
hipercow_provision_list()
#> ℹ 1 conan installation recorded
#> • 1: 20241008152453 (moments ago) [0]

cleanup()
#> ℹ Cleaning up example