NEWS.md

rix 0.14.2 (2025-01-01)

• rix(): it is now possible to generate expressions pointing to the development version of R and Bioconductor by using rix(r_ver = "r-devel") and rix(r_ver = "r-devel-bioc-devel).

rix 0.14.1 (2025-01-01)

• rix(): it is now possible to generate expressions pointing to the development version of Bioconductor by using rix(r_ver = "bioc-devel").

rix 0.14.0 (2024-12-31)

• This is a major release of {rix}:

  • We have forked the Nixpkgs Github repository to include more R packages in Nix, and have backported many fixes, which should improve the user experience on Apple Silicon devices.
  • We also set up a binary cache on Cachix (many thanks to Cachix for sponsoring the cache!) so now packages get pulled from the official binary cache, as well as from the rstats-on-nix cache. This greatly decreases build times.
  • rix() now includes a date argument, allowing users to build environments as of a date. Around 4 to 6 dates for each year that is supported are provided, starting from 2019. Check out available dates using the available_dates() function. Read the c - Using rix to build project specific environments vignette for more details. Should you want a specific date that is not available, feel free to open an issue requesting it.
  • rix() now only includes R versions 3.5.3 (released on March 2019) and up. Earlier versions were complicated to get working on macOS and we assume it is unlikely that many people would need earlier versions. Should that be the case however, feel free to open an issue requesting it.

  Many thanks to mihem for helping with testing this major release of {rix}!

rix 0.13.5 (2024-12-03)

• rix(): now correctly handles packages with several DESCRIPTION files, such as {basilisk}, thanks to mihem

rix 0.13.4 (2024-11-20)

• rix(): now correctly handles packages with no dependencies, thanks to jrosell

rix 0.13.3 (2024-11-20)

• rix(): Clearer error message when providing an R version that is too recent

rix 0.13.2 (2024-11-20)

• renv2nix(): switch from RemoteType to RemoteHost in renv.lock files to detect packages to be added from Github or Gitlab

rix 0.13.1 (2024-11-19)

• renv2nix(): added new argument, override_r_ver, to manually set R version in generated Nix expression. This deals with situations where an renv.lock lists a version of R that is not (yet) included in nixpkgs.

rix 0.13.0 (2024-11-18)

• renv2nix(): converts renv.lock file into a default.nix expression. For now, only the R version is matched, not package versions. Thanks to RichardJActon for implementing.

rix 0.12.4 (2024-09-27)

• rix_init(), rix(): previous attempt at fixing bug was only partially correct, it is now fixed. Several more tests were added to avoid this in the future.

rix 0.12.3 (2024-09-26)

Bug fixes

• rix_init(), rix(): fix bug in rix_init(), that led to empty .Rprofile files.

Chores

• Update inst/extdata/default.nix

rix 0.12.2 (2024-09-25)

Chores

• Update the url in the hex logo
• Update shipped inst/extdata/default.nix with this patch release of {rix}
• Remove duplicate NEWS entries in 0.12.1 released previously, which is the first CRAN release version.
• Added reference to Dolstra (2006) in the DESCRIPTION (forgotten in first CRAN release 0.12.1)

rix 0.12.1 (2024-09-25)

User-facing changes

• 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.

Chores

• Adhere to CRAN policies, resubmit with changes according to CRAN comments:
  • DESCRIPTION:
    • No package name in title field
    • Write 'Nix' in single quotes (software name)
    • Description text: Add more details about package functionality and implemented methods.
    • Added reference describing 'Nix'
  • All vignettes and tests now write to tempdir() instead of the user directory

rix 0.12.0 (2024-09-20)

Bug fixes

• Fix roxygen2 check note.

Chores

• Prepare for first CRAN submission! Polish the README.

rix 0.11.2 (2024-09-20)

Bug fixes

• fix R 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 0.11.1 (2024-09-20)

Bug fixes

• 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.

Development services

• 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.

Chores

• Update top-level default.nix for {rix} development environment.
• Remove pre-commit config because it does not play well with Nix (R-tooling/package inst based on {renv})
• Make R CMD check pass without NOTE because of file artefacts when running vignettes and doing tests (tests/testthat/test-rix.R)
• Polish lint and styling actions″LC_ALL = "en_US.UTF-8"

rix 0.11.0 (2024-09-12)

• Gitlab packages can now be installed as well

rix 0.10.0 (2024-09-12)

{rix} is now an rOpenSci package!

• Transfer to rOpenSci: updated more links
• Transfer to rOpenSci: added reviewers to DESCRIPTION
• Transfer to rOpenSci: update link in DESCRIPTION
• Transfer to rOpenSci: added link to CoC
• Transfer to rOpenSci: fixed links

rix 0.9.1 (2024-07-30)

• Fix directory creation in with_nix(), using recursive = TRUE in dir.create()

rix 0.9.0 (2024-07-22)

User-facing changes

• rix::rix(): It is not necessary anymore to provide the branch_name list element for R packages from GitHub in git_pkgs.

Bug fixes

• rix::rix():
  • error when 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.

Chores

• Github Actions: we now use rhub2 for checking the package
• rix::rix() docs: explain options(rix.sri_hash).
• Source code now follows tidyverse style guide thanks to {styler}
• Readme: added section explain comparing {rix} and Nix to other package managers

rix 0.8.0 (2024-07-02)

New features

• rix():
  • Added possibility to install local archives via local_r_pkgs argument.
  • Compute hash of git and CRAN archive packages locally if nix is installed. There also a new options(rix.sri_hash="API_server"), so that online hashing via http://git2nixsha.dev can be requested even when Nix is installed locally.

User-facing changes

• rix():
  • Now runs 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.
  • New 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.

Chores

• Fine-tune formatting of *.nix files generated
• low-level requests with {curl} -> remove {httr} dependency
• ROpenSci review: complete documentation of internal functions
• remove nix_file interface for with_nix()
• document

rix 0.7.1 (2024-05-24)

• Better messages of comments on top of the generated default.nix files.

rix 0.7.0 (2024-05-21)

• Added the possibility to create "bleeding-edge" and "frozen-edge" environments
• Added the possibility to use radian as the environment's console (courtesy of kupac) and RStudio server
• Added ga_cachix(), a function to create a GA workflow file that builds and pushes an environment to a Cachix cache

rix 0.6.0.9000 (2024-05-05)

• with_nix(): do not use --vanilla because it does not respect custom code startup via .Rprofile
• nix_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 exit
• Patch rix() with shell_hook = NULL default, Nix-R wrappers nix_build() and with_nix(); update testfiles
• with_nix(): try sessionInfo(); fails under R Nixpkgs on darwin
• Do not remove R_LIBS_USER from .libPaths() in covr test environment
• nix_build() & with_nix(): fix segmentation fault with adjusting LD_LIBRARY_PATH temporarily
• nix_build(): consistently separate cmd and args for nix-build system command
• nix_build(): another guardrail for run-time purity of Nixpkgs R
• implement nix_file to specify specific .nix file
• Make nix_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).
• Add rix::init() to initiate and maintain an isolated, project-specific and pure R setup via Nix
• update with glibcLocales patch -with_nix() needs patch for R <= 4.2.0; glibcLocalesUtf8 -> gibcLocales
• Implement with_nix() to valuate function in R or shell command via nix-shell environment
• Added tar_nix_ga(), a function to run targets pipelines on Github Actions using a Nix expression

rix 0.6.0 (2024-02-02)

New features

• with_nix(): evaluate and return R functions or shell commands in Nix env:

  • added 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

  • added nix_file argument to specify a specific .nix file

User facing changes

• rix() -- 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).

Bug fixes

• nix_build() -- invoke nix-build from R:

  • avoided empty file artefact when checking for presence of nix-build binary. The internal helper now uses Sys.which("nix-build") for checking availability on PATH in the R session.
  • added another guardrail for run-time purity of Nixpkgs R by removing the R_LIBS_USER path from .libPaths().

• with_nix() -- evaluate and return R functions or shell commands in Nix env:

  • Now cleans all itermediary and output artefacts (files) written in Nix shell (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.
  • The code run the Nix-R session defined by 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).
  • Fix segmentation faults in tests by temporarily setting LD_LIBRARY_PATH.
  • Patched the import of 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).

Quality and unit testing

• added test suite of 17 unit tests using {testthat}
• Add GitHub actions runners on the repository that use system's R or Nix R environments configured with Nix.

Internal refactoring

• nix_build(): consistently separate cmd and args for nix-build system

rix 0.5.1.9000 (2024-01-17)

• Added rix::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 0.5.1 (2024-01-16)

Bug fixes

• 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.

rix 0.5.0 (2024-01-07)

Features

• 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 0.4.1 (2023-10-06)

Bug fixes

• rix::rix(): fix missing pkgs.mkShell when shell_hook = NULL. Both shell_hook = "" and shell_hook = NULL are now producing valid nix expressions.

rix 0.4.0 (2023-09-26)

Features

• 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.

Bug fixes

• fix locale warnings when starting R in linux, which uses glibc (closes #50). Now, we use glibcLocalesUtf8 from Nix for "x86_64-linux".

rix 0.3.1 (2023-09-11)

Chore

• Remove boilerplate code for rix::rix(tex_pkgs = NULL)

rix 0.3.0 (2023-09-10)

• Added support for installing TeX Live packages via new rix::rix() argument tex_pkgs.

Chore

• update inst/extdata/default.nix so that it installs {rix} v0.3.0.

rix 0.2.1.9002 (2023-09-02)

• 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.

rix 0.2.1.9001 (2023-08-29)

• Include nix_build() in interactive use vignette (#68).

rix 0.2.1.9000 (2023-08-29)

Chore

• Fix internal create_default_nix() so that project_path is directory name.
• Updated inst/extdata/default.nix to latest commit of {rix} prior bumping.

rix 0.2.1 (2023-08-26)

Bug fixes

• Patch rix() to allow empty r_pkgs (##67).
• Patch rix() to do bug-free calling of rix_build() within default nix shell.

Chore

• New internal helper create_default_nix() to bootstrap ./inst/extdata/default.nix

rix 0.2.0 (2023-08-25)

New features

• Updated Nix historical revision data to include R version 4.3.1.
• Provision a new shell_hook arg for rix::rix(), which will create a shellHook entry in default.nix.

Bug fixes

• inst/extdata/default.nix: use R --vanilla in shellHook to not propagate user-specific .Renviron and .Rprofile. Fixes #56

rix 0.1.2 (2023-08-14)

Bug fixes

• Patch inst/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.

rix 0.1.1 (2023-08-11)

Bug fixes

• nix_build() now correctly checks presence of nix-build. (4be69b2)

rix 0.1.0 (2023-08-11)

New features

• Added 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 reproducibility
• Generated default.nix files now also include the call that was made to generate them as top-level comment.

Changes

• The path argument of rix() changed to project_path.

rix 0.0.9999

• Basic functionality added.