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You now know how to declare and build reproducible development
environments using {rix} and Nix. This vignette will
explain how to install specific versions of CRAN packages and how to
install packages from GitHub.
It is important at this stage to understand that you should not call
install.packages() from a running Nix environment. If you
want to add packages while analyzing data, you need to add it the
default.nix expression and rebuild the environment. The
same goes for installing packages from Github; use the method described
in this vignette instead of using something like
remotes::install_github().
We recommend you create a script called create_env.R or
similar, and add the call to rix() there:
library(rix)
rix(r_ver = "4.4.0",
r_pkgs = c("dplyr", "ggplot2"),
system_pkgs = NULL,
git_pkgs = NULL,
ide = "code",
project_path = path_default_nix,
overwrite = TRUE,
print = TRUE)Then, add the packages you need to r_pkgs and run the
script again. Then, build the environment using nix-build
again, and drop into it using nix-shell. Calling
install.packages() is a bad idea for several reasons:
install.packages(), your environment would end up in a
state where the default.nix definition of the environment
and the actual environment don’t match anymore.install.packages() will likely simply not work,
and if it does, will cause issues. For example, if you call
install.packages("ggplot2") from one Nix shell, it will not
install {ggplot2} “inside” the Nix shell, but will install
it on your user’s system library of packages. This is because the Nix
shell cannot be changed at run-time, and so, R will instead install the
packages in the user’s library. This version of {ggplot2},
because it is in that system-wide library of packages, will be available
to any other Nix shell. If you call
install.packages("ggplot2") again from another Nix shell,
say 6 months later, this will replace the first version of
{ggplot2} with the latest version.Ideally, you should only manage R versions and R packages using Nix,
and uninstall any system-managed version of R and R packages. But if you
do wish to keep a system-managed version of R and R packages,
rix::rix() also runs rix::rix_init()
automatically which generates an .Rprofile file that avoids
any clashes between your global user library and Nix-managed libraries
of R packages.
It is possible to install an arbitrary version of a package that has been archived on CRAN:
path_default_nix <- tempdir()
rix(
r_ver = "4.2.1",
r_pkgs = c("dplyr@0.8.0", "janitor@1.0.0"),
system_pkgs = NULL,
git_pkgs = NULL,
ide = "other",
project_path = path_default_nix,
overwrite = TRUE
)#> # This file was generated by the {rix} R package v0.7.1 on 2024-07-01
#> # with following call:
#> # >rix(r_ver = "79b3d4bcae8c7007c9fd51c279a8a67acfa73a2a",
#> # > r_pkgs = c("dplyr@0.8.0",
#> # > "janitor@1.0.0"),
#> # > system_pkgs = NULL,
#> # > git_pkgs = NULL,
#> # > ide = "other",
#> # > project_path = path_default_nix,
#> # > overwrite = TRUE)
#> # It uses nixpkgs' revision 79b3d4bcae8c7007c9fd51c279a8a67acfa73a2a for reproducibility purposes
#> # which will install R version 4.2.1.
#> # Report any issues to https://github.com/ropensci/rix
#> let
#> pkgs = import (fetchTarball "https://github.com/NixOS/nixpkgs/archive/79b3d4bcae8c7007c9fd51c279a8a67acfa73a2a.tar.gz") {};
#>
#> git_archive_pkgs = [
#> (pkgs.rPackages.buildRPackage {
#> name = "dplyr";
#> src = pkgs.fetchzip {
#> url = "https://cran.r-project.org/src/contrib/Archive/dplyr/dplyr_0.8.0.tar.gz";
#> sha256 = "sha256-f30raalLd9KoZKZSxeTN71PG6BczXRIiP6g7EZeH09U=";
#> };
#> propagatedBuildInputs = builtins.attrValues {
#> inherit (pkgs.rPackages)
#> assertthat
#> glue
#> magrittr
#> pkgconfig
#> R6
#> Rcpp
#> rlang
#> tibble
#> tidyselect
#> BH
#> plogr;
#> };
#> })
#>
#>
#> (pkgs.rPackages.buildRPackage {
#> name = "janitor";
#> src = pkgs.fetchzip {
#> url = "https://cran.r-project.org/src/contrib/Archive/janitor/janitor_1.0.0.tar.gz";
#> sha256 = "sha256-3NJomE/CNbOZ+ohuVZJWe2n1RVGUm8x8a0A0qzLmdN4=";
#> };
#> propagatedBuildInputs = builtins.attrValues {
#> inherit (pkgs.rPackages)
#> dplyr
#> tidyr
#> snakecase
#> magrittr
#> purrr
#> rlang;
#> };
#> })
#> ];
#>
#> system_packages = builtins.attrValues {
#> inherit (pkgs)
#> R
#> glibcLocales
#> nix;
#> };
#>
#> in
#>
#> pkgs.mkShell {
#> LOCALE_ARCHIVE = if pkgs.system == "x86_64-linux" then "${pkgs.glibcLocales}/lib/locale/locale-archive" else "";
#> LANG = "en_US.UTF-8";
#> LC_ALL = "en_US.UTF-8";
#> LC_TIME = "en_US.UTF-8";
#> LC_MONETARY = "en_US.UTF-8";
#> LC_PAPER = "en_US.UTF-8";
#> LC_MEASUREMENT = "en_US.UTF-8";
#>
#> buildInputs = [ git_archive_pkgs system_packages ];
#>
#> }The above expression will install R version 4.2.1, and
{dplyr} at version 0.8.0 and {janitor} at
version 1.0.0. This can be useful, especially for packages that have
been archived, but otherwise, this feature should ideally be used
sparingly. If you want to reconstruct an environment as it was around
2019, use the version of R that was current at that time. This will
ensure that every package that gets installed is at a version compatible
with that version of R, which might not be the case if you need to
install a very old version of one particular package.
It is also possible to install packages from Github:
path_default_nix <- tempdir()
rix(
r_ver = "4.2.1",
r_pkgs = c("dplyr", "janitor"),
git_pkgs = list(
list(
package_name = "housing",
repo_url = "https://github.com/rap4all/housing/",
commit = "1c860959310b80e67c41f7bbdc3e84cef00df18e"
),
list(
package_name = "fusen",
repo_url = "https://github.com/ThinkR-open/fusen",
commit = "d617172447d2947efb20ad6a4463742b8a5d79dc"
)
),
ide = "other",
project_path = path_default_nix,
overwrite = TRUE
)This will install two packages from Github: the
{housing} package and more specifically the code as it is
in the fusen branch; however the branch name is not
required, as the commit is enough to pin the exact version of the code
needed. The {fusen} package is also installed, as of commit
d617172447d.
It is also possible to install packages from a local
tar.gz file. For this, place the package in the same folder
where the default.nix will be generated, and write
something like this:
rix(
r_ver = "4.3.1",
local_r_pkgs = c("chronicler_0.2.1.tar.gz", "knitr_1.43.tar.gz"),
overwrite = TRUE
)This assumes that both chronicler_0.2.1.tar.gz and
knitr_1.43.tar.gz have been downloaded beforehand. If you
want to include a local package that you are developing, make sure to
first build it using devtools::build() to build the
.tar.gz archive, but if you can, consider uploading the
source code to your package on Github and installing it from Github
instead.
This example shows how to install packages from CRAN, from the CRAN archives and from GitHub:
path_default_nix <- tempdir()
rix(
r_ver = "4.2.1",
r_pkgs = c("dplyr", "janitor", "AER@1.2-8"),
git_pkgs = list(
list(
package_name = "housing",
repo_url = "https://github.com/rap4all/housing/",
commit = "1c860959310b80e67c41f7bbdc3e84cef00df18e"
),
list(
package_name = "fusen",
repo_url = "https://github.com/ThinkR-open/fusen",
commit = "d617172447d2947efb20ad6a4463742b8a5d79dc"
)
),
ide = "other",
project_path = path_default_nix,
overwrite = TRUE
)#> # This file was generated by the {rix} R package v0.7.1 on 2024-07-01
#> # with following call:
#> # >rix(r_ver = "79b3d4bcae8c7007c9fd51c279a8a67acfa73a2a",
#> # > r_pkgs = c("dplyr",
#> # > "janitor",
#> # > "AER@1.2-8"),
#> # > git_pkgs = list(list(package_name = "housing",
#> # > repo_url = "https://github.com/rap4all/housing/",
#> # > commit = "1c860959310b80e67c41f7bbdc3e84cef00df18e"),
#> # > list(package_name = "fusen",
#> # > repo_url = "https://github.com/ThinkR-open/fusen",
#> # > commit = "d617172447d2947efb20ad6a4463742b8a5d79dc")),
#> # > ide = "other",
#> # > project_path = path_default_nix,
#> # > overwrite = TRUE)
#> # It uses nixpkgs' revision 79b3d4bcae8c7007c9fd51c279a8a67acfa73a2a for reproducibility purposes
#> # which will install R version 4.2.1.
#> # Report any issues to https://github.com/ropensci/rix
#> let
#> pkgs = import (fetchTarball "https://github.com/NixOS/nixpkgs/archive/79b3d4bcae8c7007c9fd51c279a8a67acfa73a2a.tar.gz") {};
#>
#> rpkgs = builtins.attrValues {
#> inherit (pkgs.rPackages)
#> dplyr
#> janitor;
#> };
#>
#> git_archive_pkgs = [
#> (pkgs.rPackages.buildRPackage {
#> name = "housing";
#> src = pkgs.fetchgit {
#> url = "https://github.com/rap4all/housing/";
#> rev = "1c860959310b80e67c41f7bbdc3e84cef00df18e";
#> sha256 = "sha256-s4KGtfKQ7hL0sfDhGb4BpBpspfefBN6hf+XlslqyEn4=";
#> };
#> propagatedBuildInputs = builtins.attrValues {
#> inherit (pkgs.rPackages)
#> dplyr
#> ggplot2
#> janitor
#> purrr
#> readxl
#> rlang
#> rvest
#> stringr
#> tidyr;
#> };
#> })
#>
#>
#> (pkgs.rPackages.buildRPackage {
#> name = "fusen";
#> src = pkgs.fetchgit {
#> url = "https://github.com/ThinkR-open/fusen";
#> rev = "d617172447d2947efb20ad6a4463742b8a5d79dc";
#> sha256 = "sha256-TOHA1ymLUSgZMYIA1a2yvuv0799svaDOl3zOhNRxcmw=";
#> };
#> propagatedBuildInputs = builtins.attrValues {
#> inherit (pkgs.rPackages)
#> attachment
#> cli
#> desc
#> devtools
#> glue
#> here
#> magrittr
#> parsermd
#> roxygen2
#> stringi
#> tibble
#> tidyr
#> usethis
#> yaml;
#> };
#> })
#>
#> (pkgs.rPackages.buildRPackage {
#> name = "AER";
#> src = pkgs.fetchzip {
#> url = "https://cran.r-project.org/src/contrib/Archive/AER/AER_1.2-8.tar.gz";
#> sha256 = "sha256-OqxXcnUX/2C6wfD5fuNayc8OU+mstI3tt4eBVGQZ2S0=";
#> };
#> propagatedBuildInputs = builtins.attrValues {
#> inherit (pkgs.rPackages)
#> car
#> lmtest
#> sandwich
#> survival
#> zoo
#> Formula;
#> };
#> })
#> ];
#>
#> system_packages = builtins.attrValues {
#> inherit (pkgs)
#> R
#> glibcLocales
#> nix;
#> };
#>
#> in
#>
#> pkgs.mkShell {
#> LOCALE_ARCHIVE = if pkgs.system == "x86_64-linux" then "${pkgs.glibcLocales}/lib/locale/locale-archive" else "";
#> LANG = "en_US.UTF-8";
#> LC_ALL = "en_US.UTF-8";
#> LC_TIME = "en_US.UTF-8";
#> LC_MONETARY = "en_US.UTF-8";
#> LC_PAPER = "en_US.UTF-8";
#> LC_MEASUREMENT = "en_US.UTF-8";
#>
#> buildInputs = [ git_archive_pkgs rpkgs system_packages ];
#>
#> }The next vignette,
vignette("d2-installing-system-tools-and-texlive-packages-in-a-nix-environment"),
explains how you can install tools such as text editors, git, Quarto,
TexLive packages, and any other tool available through
nixpkgs for your development environments.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.