- Transfer to r-opensci: fixed links

ropensci · Sep 12, 2024 · 00e6cd0 · 00e6cd0
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diff --git a/.github/workflows/make_inst_default.yaml b/.github/workflows/make_inst_default.yaml
@@ -30,7 +30,7 @@ jobs:
 
       - name: Generate .inst/extdata/default.nix
         run: |
-          nix-shell ./inst/extdata/default.nix --run "Rscript -e \"library(rix);rix('4.3.1', git_pkgs = list(package_name = 'rix', repo_url = 'https://github.com/b-rodrigues/rix/', commit = '${{ env.LATEST_COMMIT_HASH }}'), ide = 'other', project_path = 'inst/extdata', overwrite = TRUE)\""
+          nix-shell ./inst/extdata/default.nix --run "Rscript -e \"library(rix);rix('4.3.1', git_pkgs = list(package_name = 'rix', repo_url = 'https://github.com/ropensci/rix/', commit = '${{ env.LATEST_COMMIT_HASH }}'), ide = 'other', project_path = 'inst/extdata', overwrite = TRUE)\""
 
       - name: Check if PR exists
         id: check_pr

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -43,5 +43,5 @@ via [{fledge}](https://fledge.cynkra.com).
 ## Discussions
 
 For general discussion about the package, open a discussion on
-<https://github.com/b-rodrigues/rix/discussions>. To submit bug reports or
-request features, open an issue <https://github.com/b-rodrigues/rix/issues>.
+<https://github.com/ropensci/rix/discussions>. To submit bug reports or
+request features, open an issue <https://github.com/ropensci/rix/issues>.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -11,7 +11,7 @@ Description: Provides helper functions to create reproducible development
     environments using the Nix package manager.
 License: GPL (>= 3)
 URL: https://b-rodrigues.github.io/rix/
-BugReports: https://github.com/b-rodrigues/rix
+BugReports: https://github.com/ropensci/rix
 Depends:
     R (>= 2.10)
 Imports:

diff --git a/NEWS.md b/NEWS.md
@@ -68,7 +68,7 @@
 # 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](https://github.com/b-rodrigues/rix/pull/161)) and *RStudio server*
+- Added the possibility to use *radian* as the environment's console (courtesy of [kupac](https://github.com/ropensci/rix/pull/161)) and *RStudio server*
 - Added `ga_cachix()`, a function to create a GA workflow file that builds and pushes an environment to a Cachix cache
 
 
@@ -228,7 +228,7 @@
 ## Bug fixes
 
 - fix locale warnings when starting R in linux, which uses glibc (closes 
-  [#50](https://github.com/b-rodrigues/rix/issues/50)). Now, we use
+  [#50](https://github.com/ropensci/rix/issues/50)). Now, we use
   `glibcLocalesUtf8` from Nix for "x86_64-linux".
 
 
@@ -298,7 +298,7 @@
 
 - Patch `inst/exdata/default.nix` so that `LOCALE_ARCHIVE` shellHook that was set to 
   glibc locale does not fail on MacOS anymore 
-  ([#40](https://github.com/b-rodrigues/rix/issues/48); fixed with [37f7ab8](https://github.com/b-rodrigues/rix/commit/37f7ab84e5423721bdf05e41816dbc99353481e7)).
+  ([#40](https://github.com/ropensci/rix/issues/48); fixed with [37f7ab8](https://github.com/ropensci/rix/commit/37f7ab84e5423721bdf05e41816dbc99353481e7)).
 - `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.
@@ -308,15 +308,15 @@
 
 ## Bug fixes
 
-- `nix_build()` now correctly checks presence of `nix-build`. ([4be69b2](https://github.com/b-rodrigues/rix/commit/4be69b2c438276a1f636f3b407a124555bb12c9b))
+- `nix_build()` now correctly checks presence of `nix-build`. ([4be69b2](https://github.com/ropensci/rix/commit/4be69b2c438276a1f636f3b407a124555bb12c9b))
 
 
 # rix 0.1.0 (2023-08-11)
 
 ## New features
 
 - Added `nix_build()` helper that runs `nix-build` interactively from R. 
-  ([#22](https://github.com/b-rodrigues/rix/pull/22))
+  ([#22](https://github.com/ropensci/rix/pull/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

diff --git a/R/rix_helpers.R b/R/rix_helpers.R
@@ -37,7 +37,7 @@ let
 %s
 # It uses nixpkgs\' revision %s for reproducibility purposes
 # which will install R %s.
-# Report any issues to https://github.com/b-rodrigues/rix
+# Report any issues to https://github.com/ropensci/rix
 let
  pkgs = import (fetchTarball "%s") {};
 ',
@@ -57,7 +57,7 @@ let
 # edge packages and R.
 # Only use bleeding edge packages if absolutely needed!
 # Read more on https://b-rodrigues.github.io/rix/articles/z-bleeding_edge.html
-# Report any issues to https://github.com/b-rodrigues/rix
+# Report any issues to https://github.com/ropensci/rix
 let
  pkgs = import (fetchTarball "%s") {};
 ',

diff --git a/README.Rmd b/README.Rmd
@@ -19,7 +19,7 @@ output: github_document
   - [Recommended reading](#recommended-reading)
 
 <!-- badges: start -->
-[![R-hub v2](https://github.com/b-rodrigues/rix/actions/workflows/rhub.yaml/badge.svg)](https://github.com/b-rodrigues/rix/actions/workflows/rhub.yaml/badge.svg)
+[![R-hub v2](https://github.com/ropensci/rix/actions/workflows/rhub.yaml/badge.svg)](https://github.com/ropensci/rix/actions/workflows/rhub.yaml/badge.svg)
 [![runiverse-package rix](https://b-rodrigues.r-universe.dev/badges/rix?scale=1&color=pink&style=round)](https://b-rodrigues.r-universe.dev/rix)
 [![Docs](https://img.shields.io/badge/docs-release-blue.svg)](https://b-rodrigues.github.io/rix)
 [![Status at rOpenSci Software Peer Review](https://badges.ropensci.org/625_status.svg)](https://github.com/ropensci/software-review/issues/625)
@@ -212,7 +212,7 @@ can run a temporary R session with R using this command (it will build the same
 environment as the one above):
 
 ```
-nix-shell --expr "$(curl -sl https://raw.githubusercontent.com/b-rodrigues/rix/master/inst/extdata/default.nix)"
+nix-shell --expr "$(curl -sl https://raw.githubusercontent.com/ropensci/rix/master/inst/extdata/default.nix)"
 ```
 
 You can then create new development environment definitions, build them, and
@@ -233,7 +233,7 @@ clear.
 
 You can also try out Nix inside Docker. To know more, read 
 `vignette("z-advanced-topic-using-nix-inside-docker")`
-[link](https://github.com/b-rodrigues/rix/blob/HEAD/vignettes/z-advanced-topic-using-nix-inside-docker.Rmd).
+[link](https://github.com/ropensci/rix/blob/HEAD/vignettes/z-advanced-topic-using-nix-inside-docker.Rmd).
 
 ## How is Nix different from Docker+renv/{groundhog}/{rang}/(Ana/Mini)Conda/Guix? or Why Nix?
 

diff --git a/README.md b/README.md
@@ -21,7 +21,7 @@
 <!-- badges: start -->
 
 [![R-hub
-v2](https://github.com/b-rodrigues/rix/actions/workflows/rhub.yaml/badge.svg)](https://github.com/b-rodrigues/rix/actions/workflows/rhub.yaml/badge.svg)
+v2](https://github.com/ropensci/rix/actions/workflows/rhub.yaml/badge.svg)](https://github.com/ropensci/rix/actions/workflows/rhub.yaml/badge.svg)
 [![runiverse-package
 rix](https://b-rodrigues.r-universe.dev/badges/rix?scale=1&color=pink&style=round)](https://b-rodrigues.r-universe.dev/rix)
 [![Docs](https://img.shields.io/badge/docs-release-blue.svg)](https://b-rodrigues.github.io/rix)
@@ -221,7 +221,7 @@ If you don’t have R installed, but have the Nix package manager
 installed, you can run a temporary R session with R using this command
 (it will build the same environment as the one above):
 
-    nix-shell --expr "$(curl -sl https://raw.githubusercontent.com/b-rodrigues/rix/master/inst/extdata/default.nix)"
+    nix-shell --expr "$(curl -sl https://raw.githubusercontent.com/ropensci/rix/master/inst/extdata/default.nix)"
 
 You can then create new development environment definitions, build them,
 and start using them.
@@ -240,7 +240,7 @@ vignettes. Don’t hesitate to open an issue if something is not clear.
 
 You can also try out Nix inside Docker. To know more, read
 `vignette("z-advanced-topic-using-nix-inside-docker")`
-[link](https://github.com/b-rodrigues/rix/blob/HEAD/vignettes/z-advanced-topic-using-nix-inside-docker.Rmd).
+[link](https://github.com/ropensci/rix/blob/HEAD/vignettes/z-advanced-topic-using-nix-inside-docker.Rmd).
 
 ## How is Nix different from Docker+renv/{groundhog}/{rang}/(Ana/Mini)Conda/Guix? or Why Nix?
 

diff --git a/codemeta.json b/codemeta.json
@@ -4,8 +4,8 @@
   "identifier": "rix",
   "description": "Provides helper functions to create reproducible development environments using the Nix package manager.",
   "name": "rix: Rix: Reproducible Environments with Nix",
-  "codeRepository": "https://github.com/b-rodrigues/rix",
-  "issueTracker": "https://github.com/b-rodrigues/rix",
+  "codeRepository": "https://github.com/ropensci/rix",
+  "issueTracker": "https://github.com/ropensci/rix",
   "license": "https://spdx.org/licenses/GPL-3.0",
   "version": "0.5.1.9000",
   "programmingLanguage": {
@@ -141,7 +141,7 @@
   },
   "fileSize": "1016.338KB",
   "relatedLink": "https://b-rodrigues.github.io/rix/",
-  "releaseNotes": "https://github.com/b-rodrigues/rix/blob/master/NEWS.md",
-  "readme": "https://github.com/b-rodrigues/rix/blob/master/README.md",
-  "contIntegration": ["https://github.com/b-rodrigues/rix/actions/workflows/R-CMD-check.yaml", "https://github.com/b-rodrigues/rix/actions?query=workflow%3Apkgcheck"]
+  "releaseNotes": "https://github.com/ropensci/rix/blob/master/NEWS.md",
+  "readme": "https://github.com/ropensci/rix/blob/master/README.md",
+  "contIntegration": ["https://github.com/ropensci/rix/actions/workflows/R-CMD-check.yaml", "https://github.com/ropensci/rix/actions?query=workflow%3Apkgcheck"]
 }
diff --git a/default.nix b/default.nix
@@ -28,7 +28,7 @@
 # edge packages and R.
 # Only use bleeding edge packages if absolutely needed!
 # Read more on https://b-rodrigues.github.io/rix/articles/z-bleeding_edge.html
-# Report any issues to https://github.com/b-rodrigues/rix
+# Report any issues to https://github.com/ropensci/rix
 let
  pkgs = import (fetchTarball "https://github.com/rstats-on-nix/nixpkgs/archive/refs/heads/r-daily.tar.gz") {};
 

diff --git a/inst/extdata/default.nix b/inst/extdata/default.nix
@@ -2,22 +2,22 @@
 # with following call:
 # >rix(r_ver = "976fa3369d722e76f37c77493d99829540d43845",
 #  > git_pkgs = list(package_name = "rix",
-#  > repo_url = "https://github.com/b-rodrigues/rix/",
+#  > repo_url = "https://github.com/ropensci/rix/",
 #  > commit = "99d40737d09a407c2c935437cc5c3d89bdea326a"),
 #  > ide = "other",
 #  > project_path = "inst/extdata",
 #  > overwrite = TRUE)
 # It uses nixpkgs' revision 976fa3369d722e76f37c77493d99829540d43845 for reproducibility purposes
 # which will install R version 4.3.1.
-# Report any issues to https://github.com/b-rodrigues/rix
+# Report any issues to https://github.com/ropensci/rix
 let
  pkgs = import (fetchTarball "https://github.com/NixOS/nixpkgs/archive/976fa3369d722e76f37c77493d99829540d43845.tar.gz") {};
 
   git_archive_pkgs = [
     (pkgs.rPackages.buildRPackage {
       name = "rix";
       src = pkgs.fetchgit {
-        url = "https://github.com/b-rodrigues/rix/";
+        url = "https://github.com/ropensci/rix/";
         rev = "99d40737d09a407c2c935437cc5c3d89bdea326a";
         sha256 = "sha256-lrPgKOXfMvjvEso/8JZmVQ3Bd/FMjIVh7mMVsIMOs0k=";
       };

diff --git a/vignettes/b1-setting-up-and-using-rix-on-linux-and-windows.Rmd b/vignettes/b1-setting-up-and-using-rix-on-linux-and-windows.Rmd
@@ -139,7 +139,7 @@ following line in a terminal will drop you in an interactive R session that you
 can use to start generating expressions:
 
 ```
-nix-shell --expr "$(curl -sl https://raw.githubusercontent.com/b-rodrigues/rix/master/inst/extdata/default.nix)"
+nix-shell --expr "$(curl -sl https://raw.githubusercontent.com/ropensci/rix/master/inst/extdata/default.nix)"
 ```
 
 This should immediately start an R session inside your terminal. You can now run
@@ -177,7 +177,7 @@ rix(
   r_pkgs = NULL,
   git_pkgs = list(
     package_name = "rix",
-    repo_url = "https://github.com/b-rodrigues/rix",
+    repo_url = "https://github.com/ropensci/rix",
     commit = "76d1bdd03d78589d399b4b9d473ecde616920a82"
   ),
   ide = "other",

diff --git a/vignettes/b2-setting-up-and-using-rix-on-macos.Rmd b/vignettes/b2-setting-up-and-using-rix-on-macos.Rmd
@@ -62,7 +62,7 @@ following line in a terminal will drop you in an interactive R session that you
 can use to start generating expressions:
 
 ```
-nix-shell --expr "$(curl -sl https://raw.githubusercontent.com/b-rodrigues/rix/master/inst/extdata/default.nix)"
+nix-shell --expr "$(curl -sl https://raw.githubusercontent.com/ropensci/rix/master/inst/extdata/default.nix)"
 ```
 
 This should immediately start an R session inside your terminal. You can now run

diff --git a/vignettes/c-using-rix-to-build-project-specific-environments.Rmd b/vignettes/c-using-rix-to-build-project-specific-environments.Rmd
@@ -76,7 +76,7 @@ rix(
 #> #  > print = TRUE)
 #> # It uses nixpkgs' revision 12a9c0004bc987afb1ff511ebb97b67497a68e22 for reproducibility purposes
 #> # which will install R version latest.
-#> # Report any issues to https://github.com/b-rodrigues/rix
+#> # Report any issues to https://github.com/ropensci/rix
 #> let
 #>  pkgs = import (fetchTarball "https://github.com/NixOS/nixpkgs/archive/12a9c0004bc987afb1ff511ebb97b67497a68e22.tar.gz") {};
 #>
@@ -175,7 +175,7 @@ The file looks like this:
 #> #  > 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/b-rodrigues/rix
+#> # Report any issues to https://github.com/ropensci/rix
 #> let
 #>  pkgs = import (fetchTarball "https://github.com/NixOS/nixpkgs/archive/79b3d4bcae8c7007c9fd51c279a8a67acfa73a2a.tar.gz") {};
 #>  

diff --git a/vignettes/d1-installing-r-packages-in-a-nix-environment.Rmd b/vignettes/d1-installing-r-packages-in-a-nix-environment.Rmd
@@ -105,7 +105,7 @@ rix(
 #> #  > 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/b-rodrigues/rix
+#> # Report any issues to https://github.com/ropensci/rix
 #> let
 #>  pkgs = import (fetchTarball "https://github.com/NixOS/nixpkgs/archive/79b3d4bcae8c7007c9fd51c279a8a67acfa73a2a.tar.gz") {};
 #>   
@@ -229,7 +229,7 @@ rix(
 #> #  > 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/b-rodrigues/rix
+#> # Report any issues to https://github.com/ropensci/rix
 #> let
 #>  pkgs = import (fetchTarball "https://github.com/NixOS/nixpkgs/archive/79b3d4bcae8c7007c9fd51c279a8a67acfa73a2a.tar.gz") {};
 #>
@@ -385,7 +385,7 @@ rix(
 #> #  > 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/b-rodrigues/rix
+#> # Report any issues to https://github.com/ropensci/rix
 #> let
 #>  pkgs = import (fetchTarball "https://github.com/NixOS/nixpkgs/archive/79b3d4bcae8c7007c9fd51c279a8a67acfa73a2a.tar.gz") {};
 #>  

diff --git a/vignettes/d2-installing-system-tools-and-texlive-packages-in-a-nix-environment.Rmd b/vignettes/d2-installing-system-tools-and-texlive-packages-in-a-nix-environment.Rmd
@@ -76,7 +76,7 @@ rix(
 #> #  > overwrite = TRUE)
 #> # It uses nixpkgs' revision 12a9c0004bc987afb1ff511ebb97b67497a68e22 for reproducibility purposes
 #> # which will install R version latest.
-#> # Report any issues to https://github.com/b-rodrigues/rix
+#> # Report any issues to https://github.com/ropensci/rix
 #> let
 #>  pkgs = import (fetchTarball "https://github.com/NixOS/nixpkgs/archive/12a9c0004bc987afb1ff511ebb97b67497a68e22.tar.gz") {};
 #>
@@ -114,7 +114,7 @@ You can look for all the available software
 [here](https://search.nixos.org/packages?channel=unstable&from=0&size=50&sort=relevance&type=packages&query=).
 Simply look for the right package name, and add it to the `system_pkgs` argument
 of `rix()`. If you have trouble finding something, don’t hesitate to 
-[open an issue ](https://github.com/b-rodrigues/rix/issues) and ask for support!
+[open an issue ](https://github.com/ropensci/rix/issues) and ask for support!
 
 ## Installing TexLive packages
 
@@ -149,7 +149,7 @@ rix(
 #> #  > print = TRUE)
 #> # It uses nixpkgs' revision 12a9c0004bc987afb1ff511ebb97b67497a68e22 for reproducibility purposes
 #> # which will install R version latest.
-#> # Report any issues to https://github.com/b-rodrigues/rix
+#> # Report any issues to https://github.com/ropensci/rix
 #> let
 #>  pkgs = import (fetchTarball "https://github.com/NixOS/nixpkgs/archive/12a9c0004bc987afb1ff511ebb97b67497a68e22.tar.gz") {};
 #>

diff --git a/vignettes/e-interactive-use.Rmd b/vignettes/e-interactive-use.Rmd
@@ -145,7 +145,7 @@ expressions. In this case you might consider installing Nix first, and then run
 the following command inside your terminal to get dropped into a temporary Nix
 shell, which you can then use to generate new `default.nix` files:
 
-    nix-shell --expr "$(curl -sl https://raw.githubusercontent.com/b-rodrigues/rix/master/inst/extdata/default.nix)"
+    nix-shell --expr "$(curl -sl https://raw.githubusercontent.com/ropensci/rix/master/inst/extdata/default.nix)"
 
 Running the command above will download R and `{rix}` and then start an R
 session inside your terminal. You can now run something like this:

diff --git a/vignettes/z-advanced-topic-handling-packages-with-remote-dependencies.Rmd b/vignettes/z-advanced-topic-handling-packages-with-remote-dependencies.Rmd
@@ -195,6 +195,6 @@ reasons:
 
 Because of these reasons, we believe that it is safer for users that really need
 to use such packages to manually edit their Nix expressions. Don't hesitate to
-[open an issue](https://github.com/b-rodrigues/rix/issues) if you require
+[open an issue](https://github.com/ropensci/rix/issues) if you require
 assistance.
 
diff --git a/vignettes/z-advanced-topic-using-nix-inside-docker.Rmd b/vignettes/z-advanced-topic-using-nix-inside-docker.Rmd
@@ -40,7 +40,7 @@ RUN apt install curl -y
 # We don't have R nor {rix} in this image, so we can bootstrap it by downloading
 # the default.nix file that comes with {rix}. You can also download it beforehand
 # and then copy it to the Docker image
-RUN curl -O https://raw.githubusercontent.com/b-rodrigues/rix/master/inst/extdata/default.nix
+RUN curl -O https://raw.githubusercontent.com/ropensci/rix/master/inst/extdata/default.nix
 
 # Copy a script to generate the environment of interest using {rix}
 COPY generate_env.R .
@@ -106,7 +106,7 @@ RUN apt update -y
 RUN apt install curl -y
 
 # Get a default.nix with R and rix
-RUN curl -O https://raw.githubusercontent.com/b-rodrigues/rix/master/inst/extdata/default.nix
+RUN curl -O https://raw.githubusercontent.com/ropensci/rix/master/inst/extdata/default.nix
 
 # Copy a script to generate the environment of interest using rix
 COPY generate_env.R .

diff --git a/vignettes/z-binary_cache.Rmd b/vignettes/z-binary_cache.Rmd
@@ -134,5 +134,5 @@ NixOS's public cache, our `rstats-on-nix` cache, and your own, so your cache
 will only end up holding the binaries not found in the other two caches!
 
 Take a look at
-[this package’s](https://github.com/b-rodrigues/rix/blob/master/.github/workflows/cachix_dev_env.yml)
+[this package’s](https://github.com/ropensci/rix/blob/master/.github/workflows/cachix_dev_env.yml)
 repository for an example of how this is done in practice.