apptainerize {rang}

Create an Apptainer/Singularity Definition File of The Resolved Result

Description

This function exports the result from resolve() to an Apptainer/Singularity definition file. For R version >= 3.1.0, the file is based on the versioned Rocker Docker image. For R version < 3.1.0, the Apptainer/Singularity definition is based on Debian and it compiles R from source.

Usage

apptainerize(
  rang,
  output_dir,
  materials_dir = NULL,
  post_installation_steps = NULL,
  image = c("r-ver", "rstudio", "tidyverse", "verse", "geospatial"),
  rang_as_comment = TRUE,
  cache = FALSE,
  verbose = TRUE,
  lib = NA,
  cran_mirror = "https://cran.r-project.org/",
  check_cran_mirror = TRUE,
  bioc_mirror = "https://bioconductor.org/packages/",
  no_rocker = FALSE,
  debian_version = c("lenny", "squeeze", "wheezy", "jessie", "stretch"),
  skip_r17 = TRUE,
  insert_readme = TRUE,
  copy_all = FALSE
)

apptainerize_rang(...)

apptainerise(...)

apptainerise_rang(...)

singularize(...)

singularize_rang(...)

singularise(...)

singularise_rang(...)

Arguments

rang

output from resolve()

output_dir

character, where to put the Apptainer/Singularity definition file and associated content

materials_dir

character, path to the directory containing additional resources (e.g. analysis scripts) to be copied into output_dir and in turn into the Apptainer/Singularity container

post_installation_steps

character, additional steps to be added before the in the end of ⁠%post⁠ section the Apptainer/Singularity definition file, see an example below

image

character, which versioned Rocker image to use. Can only be "r-ver", "rstudio", "tidyverse", "verse", "geospatial" This applies only to R version >= 3.1

rang_as_comment

logical, whether to write resolved result and the steps to reproduce the file to path as comment

cache

logical, whether to cache the packages now. Please note that the system requirements are not cached. For query with non-CRAN packages, this option is strongly recommended. For query with local packages, this must be TRUE regardless of R version. For R version < 3.1, this must be also TRUE if there is any non-CRAN packages.

verbose

logical, pass to install.packages(), the negated value is also passed as quiet to both install.packages() and download.file().

lib

character, pass to install.packages(). By default, it is NA (to install the packages to the default location)

cran_mirror

character, which CRAN mirror to use

check_cran_mirror

logical, whether to check the CRAN mirror

bioc_mirror

character, which Bioconductor mirror to use

no_rocker

logical, whether to skip using Rocker images even when an appropriate version is available. Please keep this as TRUE unless you know what you are doing

debian_version

when Rocker images are not used, which EOL version of Debian to use. Can only be "lenny", "etch", "squeeze", "wheezy", "jessie", "stretch". Please keep this as default "lenny" unless you know what you are doing

skip_r17

logical, whether to skip R 1.7.x. Currently, it is not possible to compile R 1.7.x (R 1.7.0 and R 1.7.1) with the method provided by rang. It affects snapshot_date from 2003-04-16 to 2003-10-07. When skip_r17 is TRUE and snapshot_date is within the aforementioned range, R 1.8.0 is used instead

insert_readme

logical, whether to insert a README file

copy_all

logical, whether to copy everything in the current directory into the container. If inst/rang is detected in output_dir, this is coerced to TRUE.

...

arguments to be passed to apptainerize

Details

The idea behind this is to determine the installation order of R packages locally. Then, the installation script can be deployed to another fresh R session to install R packages. dockerize() and apptainerize() are more reasonable ways because a fresh R session with all system requirements is provided. The current approach does not work in R < 2.1.0.

Value

output_dir, invisibly

References

Apptainer / Singularity

Kurtzer, G. M., Sochat, V., & Bauer, M. W. (2017) Singularity: Scientific containers for mobility of compute. PLOS ONE, 12(5):e0177459. doi:10.1371/journal.pone.0177459

The Rocker Project

Ripley, B. (2005) Packages and their Management in R 2.1.0. R News, 5(1):8–11.

See Also

resolve(), export_rang(), use_rang()

Examples

if (interactive()) {
    graph <- resolve(
        pkgs = c("openNLP", "LDAvis", "topicmodels", "quanteda"),
        snapshot_date = "2020-01-16"
    )
    apptainerize(graph, ".")
    ## An example of using post_installation_steps to install quarto
    install_quarto <- c("apt-get install -y curl git && \\
    curl -LO https://quarto.org/download/latest/quarto-linux-amd64.deb && \\
    dpkg -i quarto-linux-amd64.deb && \\
    quarto install tool tinytex")
    apptainerize(graph, ".", post_installation_steps = install_quarto)
}