rix_init(), rix(): fix bug in
rix_init(), that led to empty .Rprofile
files.inst/extdata/default.nixinst/extdata/default.nix with this patch
release of {rix}NEWS entries in 0.12.1 released
previously, which is the first CRAN release version.DESCRIPTION
(forgotten in first CRAN release 0.12.1)rix(): The is no default argument in
project_path anymore. Before, it defaulted to the current
directory, which violated CRAN policy to have any default path in
writing functions.DESCRIPTION:
tempdir() instead
of the user directoryR CMD check and R CMD build when
running them in a nix-shell --pure development environment
based on the default.nix of {rix} package root. Use
manually controlled Nix expression from r_ver = "latest"
pinned source.rix::rix(): Clean detrius files/folders in temporary
folders that are not needed. Also fixes failing vignette builds in
R CMD build (including helpers
rix::rix_init(), rix:::hash_url()) by properly
handling file connections, closing them on exit, and unlink temporary
file folders. (#308)nix_build(): Fix SIGINT termination (ctrl+c) for linux,
so that all the nix-build background processes are properly
stopped when the user interupts the build process.rix::rix(): when hashing Git provider packages (e.g.,
GitHub) remotely via the https://git2nixsha.dev API, https protocol is
now used (previously http). Hashing via this service is done when Nix is
not installed or when requested via option.default.nix for {rix} development
environment.pre-commit config because it does not play well
with Nix (R-tooling/package inst based on {renv})R CMD check pass without NOTE because
of file artefacts when running vignettes and doing tests
(tests/testthat/test-rix.R){rix} is now an rOpenSci package!
with_nix(), using
recursive = TRUE in dir.create()rix::rix(): It is not necessary anymore to provide the
branch_name list element for R packages from GitHub in
git_pkgs.rix::rix():
ide = "rstudio" and no additional R packages
are chosen. In the situation, the rStudioWrapper approach
does not work and the resulting Nix expression would not build. The
returned error states to either add rstudio to
system_pkgs, or add R packages in r_pkgs or
git_pkgs.rix::rix() docs: explain
options(rix.sri_hash).{styler}rix():
local_r_pkgs argument.options(rix.sri_hash="API_server"), so that online hashing
via http://git2nixsha.dev can be requested even when Nix is installed
locally.rix():
rix_init() to ensure runtime purity via
.Rprofile. This will exclude the system’s user library from
.libPaths(), so that the search path will only contain a
path each per package in the Nix store.message_type option to control signalling what is
done.nix_build(), with_nix(): stabilize API;
get rid of exec_mode in core functions. In most cases,
“non-blocking” system calls are being run for system commands like
nix-shell or nix-build.rix_init(), nix_build(), and
with_nix(): gain a message_type = "quiet",
which suppresses messages. Further, messaging is standardized via
internal helpers called.nix_file interface for
with_nix()default.nix files.ga_cachix(), a function to create a GA workflow
file that builds and pushes an environment to a Cachix cachewith_nix(): do not use --vanilla because
it does not respect custom code startup via .Rprofilenix_build() and with_nix(): improvements.
Remove nix-build artefact file by using
Sys.which() for checking availability.
with_nix(): clean all itermediary and output artefacts
(files) on exitrix() with shell_hook = NULL
default, Nix-R wrappers nix_build() and
with_nix(); update testfileswith_nix(): try sessionInfo(); fails under
R Nixpkgs on darwinR_LIBS_USER from .libPaths() in covr test
environmentnix_build() & with_nix(): fix
segmentation fault with adjusting LD_LIBRARY_PATH
temporarilynix_build(): consistently separate cmd and args for
nix-build system commandnix_build(): another guardrail for run-time purity of
Nixpkgs Rnix_file to specify specific
.nix filenix_shell() and with_nix() compatible
with RStudio on macOS, where the R session is not (yet) started from a
shell. Now /nix/var/nix/profiles/default/bin is added to
the PATH variable after nix_shell() or
with_nix() are called from an RStudio version of the system
(not as Nix package).rix::init() to initiate and maintain an isolated,
project-specific and pure R setup via NixglibcLocales patch -with_nix()
needs patch for R <= 4.2.0; glibcLocalesUtf8 ->
gibcLocaleswith_nix() to valuate function in R or shell
command via nix-shell environmenttar_nix_ga(), a function to run targets pipelines
on Github Actions using a Nix expressionwith_nix(): evaluate and return R functions or shell
commands in Nix env:
nix_file argument as alternative to
project_path. Specify *.nix fle defining the
Nix software environment in which you want to run
expr.macOS: made it compatible with system’s RStudio version
on macOS, where the R session can not (yet) be started from a shell when
launched from Dock. Now /nix/var/nix/profiles/default/bin
is added to the PATH variable while with_nix()
are called.nix_build() – invoke nix-build from R:
macOS: made it compatible with system’s RStudio version
on macOS, where the R session can not (yet) be started from a shell when
launched from Dock. Now /nix/var/nix/profiles/default/bin
is added to the PATH variable while with_nix()
are called.rix_init() – create an isolated, project-specific, and
runtime-pure R setup via Nix
nix_file argument to specify a specific
.nix filerix() – Generate a Nix expressions that build
reproducible development environments:
shell_hook = NULL becomes the new default; before it
was = "R --vanilla". The new default ensures that
with_nix() applied on a specific project_path
directory containing a custom .Rprofile file that was
generated with rix_init(), together with a
default.nix expression file, can read that profile file to
effectively enforce run-time pure R libraries (only from Nix
store).nix_build() – invoke nix-build from R:
nix-build binary. The internal helper now uses
Sys.which("nix-build") for checking availability on
PATH in the R session.R_LIBS_USER path from .libPaths().with_nix() – evaluate and return R functions or shell
commands in Nix env:
nix-shell) session environment when exiting.
These file artefacts are now written in a subdirectory
with_nix under tempdir() of the current R
session and all files are deleted. Now, when an expr errors
in a Nix shell evaluation (i.e. custom R function), but had a previous
successful run with a different expr and/or R global
environment state with success and _out.Rds produced, the
current session fails to bring this output into the current R
session.project_path,
now attemps to record sessionInfo() with try.
We found failures of that command under older R versions on Nixpkgs for
macOS (i.e., aarch64-darwin).LD_LIBRARY_PATH.glibcLocalesUtf8 with
gibcLocales (imports all locales). This was necessary to
support Nixpkgs R versions <= 4.2.0, where
glibcLocalsUtf8 derivation was not yet available. We do not
sacrifice reproducibility but rather have larger total sizes of
derivations involved in the subshell (around 200MB extra).nix_build(): consistently separate cmd and
args for nix-build systemrix::init() to initialize and maintain an
isolated, project-specific, and pure R setup via Nix. It accomplishes
this by writing a custom .Rprofile that guarantees R
packages can only be attached from Nix paths, preventing unnoticed
loading from the system’s R user library (R_LIBS_USER and
ensuring runtime purity regarding packages and linked libraries).
Additionally, it appends /nix/var/nix/profiles/default/bin
to the PATH. Currently, this modification only takes effect
in the current R session and not in new R sessions for RStudio on MacOS.
This is because the default R session is not started from a shell. The
PATH will be modified by RStudio when starting the R
session, effectively after loading the local .Rprofile.
Future versions of RStudio will hopefully respect all environmental
variables from a shell environment.rix::rix(): patch for nixpkgs revisions corresponding
to R (r_ver) <= 4.2.0; nix-build failed
because attribute glibcLocalesUtf8 was not found. Fixed by
importing gibcLocales. Thanks @motorlearner for reporting.Added with_nix(), which can evaluate a function in R
or shell command via nix-shell environment, and return the
output into the current R session. This works for both evaluating R code
from a nix-R session within an other nix-R session, or also from a host
R session (i.e., on macOS or linux) within a specific nix-R session.
This feature is useful to test dependencies and specific setups of
software in controlled environments.
Added tar_nix_ga(), a function to run targets
pipelines on Github Actions using a Nix expression.
rix::rix(): fix missing pkgs.mkShell when
shell_hook = NULL. Both shell_hook = "" and
shell_hook = NULL are now producing valid nix
expressions.rix::rix() now defaults to "en_US.UTF-8"
for the relevant locale variables (LANG,
LC_ALL, LC_TIME, LC_MONETARY,
LC_PAPER, LC_MEASUREMENT) and sets these
environment variables in the Nix shell. These will be correctly
propagated into the Nix R session. Users can modify the locale setting
via
options(rix.nix_locale_variables = list(LANG = "de_CH.UTF-8", <...>),
e.g., but it needs to be an UTF-8 locale. This is because we only import
the glibcLocalesUtf8 subset, to not keep the size
reasonable.glibcLocalesUtf8 from Nix for
“x86_64-linux”.rix::rix(tex_pkgs = NULL)rix::rix() argument tex_pkgs.inst/extdata/default.nix so that it installs
{rix} v0.3.0.nix_build() now supports --max_jobs flag
of nix-build via
options(rix.nix_build_max_jobs = <integer>). Custom
settings of this option can be useful for leveraging full I/O latency or
efficient builds on shared memory multiprocessing systems.nix_build() in interactive use vignette
(#68).create_default_nix() so that
project_path is directory name.inst/extdata/default.nix to latest commit of
{rix} prior bumping.rix() to allow empty r_pkgs
(##67).rix() to do bug-free calling of
rix_build() within default nix shell.create_default_nix() to bootstrap
./inst/extdata/default.nixshell_hook arg for
rix::rix(), which will create a shellHook
entry in default.nix.inst/extdata/default.nix: use R --vanilla
in shellHook to not propagate user-specific .Renviron and
.Rprofile. Fixes #56inst/exdata/default.nix so that
LOCALE_ARCHIVE shellHook that was set to glibc locale does
not fail on MacOS anymore (#40; fixed with 37f7ab8).nix_build(): fix defensive check so the error message
is referring to project_path instead of
nix_file. The patch does not change correct behavior of
nix_build(), hence it is only of cosmetic nature.nix_build() now correctly checks presence of
nix-build. (4be69b2)nix_build() helper that runs
nix-build interactively from R. (#22)rix() now supports installing packages from GitHub and
the CRAN archives.rix() now supports using a nixpkgs
revision instead of an R version for reproducibilitydefault.nix files now also include the call
that was made to generate them as top-level comment.path argument of rix() changed to
project_path.