From 5de5b536db035f998b196e2c3e5fba7590a435ea Mon Sep 17 00:00:00 2001
From: Bruno Rodrigues <bruno@brodrigues.co>
Date: Fri, 3 Jan 2025 20:03:31 +0100
Subject: [PATCH 01/31] function to parse REMOTES to a list

---
 R/fetchers.R | 28 +++++++++++++++++++++++++---
 1 file changed, 25 insertions(+), 3 deletions(-)

diff --git a/R/fetchers.R b/R/fetchers.R
index 3f87ea68..3612bed9 100644
--- a/R/fetchers.R
+++ b/R/fetchers.R
@@ -293,7 +293,29 @@ fetchzips <- function(archive_pkgs) {
 #' @noRd
 fetchpkgs <- function(git_pkgs, archive_pkgs) {
   paste(fetchgits(git_pkgs),
-    fetchzips(archive_pkgs),
-    collapse = "\n"
-  )
+        fetchzips(archive_pkgs),
+        collapse = "\n"
+        )
+}
+
+
+#' remotes2nix Generates a list to pass to rix(git_pkgs = ...) to generate a valid
+#' Nix expression from a REMOTES field in a DESCRIPTION file
+#' @param remotes String, output of read.dcf of the form
+#' "jimhester/highlite,\ngaborcsardi/gh,\nhadley/memoise"
+#' @return A list of lists to pass to rix(git_pkgs = ...)
+#' @noRd
+remotes2nix <- functions(remotes){
+  # Input looks like
+  # "jimhester/highlite,\ngaborcsardi/gh,\nhadley/memoise"
+  remotes <- gsub("\n", "", x = unlist(strsplit(remotes, ",")))
+
+  pkgs_names <- sub(".*?/", "", remotes)
+  urls <- paste0("https://github.com/", remotes)
+  commits <- rep("HEAD", length(remotes))
+
+  lapply(seq_along(pkgs_names), function(i) {
+    list("package_name" = pkgs_names[i], "repo_url" = urls[i], "commit" = commits[i])
+  })
+
 }

From 91338c3a27f291d38be7a7f049db473ee1328e1c Mon Sep 17 00:00:00 2001
From: Bruno Rodrigues <bruno@brodrigues.co>
Date: Fri, 3 Jan 2025 23:48:26 +0100
Subject: [PATCH 02/31] separating imports into CRAN imports and REMOTE
 imports; core functionality unaffected

---
 R/fetchers.R                                  | 54 ++++++++++++++-----
 R/nix_hash.R                                  | 10 ++--
 tests/testthat/_snaps/rix/one_git_default.nix | 28 +++++-----
 tests/testthat/test-get_sri_hash_deps.R       |  7 ++-
 tests/testthat/test-rix.R                     |  6 +--
 5 files changed, 69 insertions(+), 36 deletions(-)

diff --git a/R/fetchers.R b/R/fetchers.R
index 3612bed9..19d8a2c0 100644
--- a/R/fetchers.R
+++ b/R/fetchers.R
@@ -12,9 +12,13 @@ fetchgit <- function(git_pkg) {
 
   output <- get_sri_hash_deps(repo_url, commit)
   sri_hash <- output$sri_hash
-  imports <- output$deps
-  imports <- unlist(strsplit(imports, split = " "))
-  imports <- paste(c("", imports), collapse = "\n          ")
+  # If package has no remote dependencies
+  if(identical(output$deps$remotes, character(0))){
+    imports <- output$deps$imports
+    imports <- paste(c("", imports), collapse = "\n          ")
+  } else {
+    stop("not yet implemented!")
+  }
 
   sprintf(
     '
@@ -60,8 +64,7 @@ fetchzip <- function(archive_pkg, sri_hash = NULL) {
   if (is.null(sri_hash)) {
     output <- get_sri_hash_deps(repo_url, commit = NULL)
     sri_hash <- output$sri_hash
-    imports <- output$deps
-    imports <- unlist(strsplit(imports, split = " "))
+    imports <- output$deps$imports
     imports <- paste(c("", imports), collapse = "\n          ")
   } else {
     sri_hash <- sri_hash
@@ -105,7 +108,7 @@ remove_base <- function(list_imports) {
     list_imports
   )
 
-  paste(na.omit(imports_nobase), collapse = " ")
+  na.omit(imports_nobase)
 }
 
 
@@ -145,11 +148,25 @@ get_imports <- function(path) {
 
   columns_of_interest <- c("Depends", "Imports", "LinkingTo")
 
-  imports <- as.data.frame(read.dcf(desc_path))
+  imports_df <- as.data.frame(read.dcf(desc_path))
+
+  existing_columns <- intersect(columns_of_interest, colnames(imports_df))
 
-  existing_columns <- intersect(columns_of_interest, colnames(imports))
+  imports <- imports_df[, existing_columns, drop = FALSE]
 
-  imports <- imports[, existing_columns, drop = FALSE]
+  existing_remotes <- intersect("Remotes", colnames(imports_df))
+
+  if(!identical(existing_remotes, character(0))){
+    remotes <- imports_df[, existing_remotes, drop = FALSE]
+
+    # remotes are of the form username/packagename so we need
+    # to only keep packagename
+    remotes <- gsub("\n", "", x = unlist(strsplit(remotes$Remotes, ",")))
+
+    remotes <- sub(".*?/", "", remotes)
+  } else {
+    remotes <- character(0)
+  }
 
   if (!is.null(imports) && length(imports) > 0) {
     output <- unname(trimws(unlist(strsplit(unlist(imports), split = ","))))
@@ -165,7 +182,18 @@ get_imports <- function(path) {
 
   output <- remove_base(unique(output))
 
-  gsub("\\.", "_", output)
+  output <- gsub("\\.", "_", output)
+
+  # Remote packages are included in imports, so we need
+  # remove remotes from imports
+  output_imports <- setdiff(output, remotes)
+  output_remotes <- remotes
+
+  list(
+    "package" = imports_df$Package,
+    "imports" = output_imports,
+    "remotes" = output_remotes
+    )
 }
 
 
@@ -305,7 +333,7 @@ fetchpkgs <- function(git_pkgs, archive_pkgs) {
 #' "jimhester/highlite,\ngaborcsardi/gh,\nhadley/memoise"
 #' @return A list of lists to pass to rix(git_pkgs = ...)
 #' @noRd
-remotes2nix <- functions(remotes){
+remotes2nix <- function(remotes){
   # Input looks like
   # "jimhester/highlite,\ngaborcsardi/gh,\nhadley/memoise"
   remotes <- gsub("\n", "", x = unlist(strsplit(remotes, ",")))
@@ -314,8 +342,10 @@ remotes2nix <- functions(remotes){
   urls <- paste0("https://github.com/", remotes)
   commits <- rep("HEAD", length(remotes))
 
-  lapply(seq_along(pkgs_names), function(i) {
+  pkgs <- lapply(seq_along(pkgs_names), function(i) {
     list("package_name" = pkgs_names[i], "repo_url" = urls[i], "commit" = commits[i])
   })
 
+  list("remote_name" = )
+
 }
diff --git a/R/nix_hash.R b/R/nix_hash.R
index 8fcac21b..b2292ce5 100644
--- a/R/nix_hash.R
+++ b/R/nix_hash.R
@@ -5,7 +5,7 @@
 #' @return list with following elements:
 #' - `sri_hash`: string with SRI hash of the NAR serialization of a Github repo
 #'      at a given deterministic git commit ID (SHA-1)
-#' - `deps`: string with R package dependencies separarated by space.
+#' - `deps`: list with three elements: 'package', its 'imports' and its 'remotes'
 #' @noRd
 nix_hash <- function(repo_url, commit) {
   if (grepl("(github)|(gitlab)", repo_url)) {
@@ -27,7 +27,7 @@ nix_hash <- function(repo_url, commit) {
 #' @return list with following elements:
 #' - `sri_hash`: string with SRI hash of the NAR serialization of a Github repo
 #'      at a given deterministic git commit ID (SHA-1)
-#' - `deps`: string with R package dependencies separarated by space.
+#' - `deps`: list with three elements: 'package', its 'imports' and its 'remotes'
 #' @noRd
 hash_url <- function(url) {
   tdir <- tempdir()
@@ -195,7 +195,7 @@ hash_cran <- function(repo_url) {
 #' @return list with following elements:
 #' - `sri_hash`: string with SRI hash of the NAR serialization of a Github repo
 #'      at a given deterministic git commit ID (SHA-1)
-#' - `deps`: string with R package dependencies separarated by space.
+#' - `deps`: list with three elements: 'package', its 'imports' and its 'remotes'
 #' @noRd
 hash_git <- function(repo_url, commit) {
   trailing_slash <- grepl("/$", repo_url)
@@ -226,7 +226,7 @@ hash_git <- function(repo_url, commit) {
 #' sake, NULL for archived CRAN packages.
 #' @return list with following elements:
 #' - `sri_hash`: string with SRI hash of the NAR serialization of a Github repo
-#' - `deps`: string with R package dependencies separarated by space.
+#' - `deps`: list with three elements: 'package', its 'imports' and its 'remotes'
 #' @noRd
 nix_hash_online <- function(repo_url, commit) {
   # handle to get error for status code 404
@@ -269,7 +269,7 @@ nix_hash_online <- function(repo_url, commit) {
 #' @return list with following elements:
 #' - `sri_hash`: string with SRI hash of the NAR serialization of a Github repo
 #'      at a given deterministic git commit ID (SHA-1)
-#' - `deps`: string with R package dependencies separarated by space.
+#' - `deps`: list with three elements: 'package', its 'imports' and its 'remotes'
 #' @noRd
 get_sri_hash_deps <- function(repo_url, commit) {
   # if no `options(rix.sri_hash=)` is set, default is `"check_nix"`
diff --git a/tests/testthat/_snaps/rix/one_git_default.nix b/tests/testthat/_snaps/rix/one_git_default.nix
index 46fc9698..eed8ead8 100644
--- a/tests/testthat/_snaps/rix/one_git_default.nix
+++ b/tests/testthat/_snaps/rix/one_git_default.nix
@@ -4,25 +4,23 @@ let
   
   git_archive_pkgs = [
     (pkgs.rPackages.buildRPackage {
-      name = "lookup";
+      name = "housing";
       src = pkgs.fetchgit {
-        url = "https://github.com/jimhester/lookup/";
-        rev = "eba63db477dd2f20153b75e2949eb333a36cccfc";
-        sha256 = "sha256-arl7LVxL8xGUW3LhuDCSUjcfswX0rdofL/7v8Klw8FM=";
+        url = "https://github.com/rap4all/housing/";
+        rev = "1c860959310b80e67c41f7bbdc3e84cef00df18e";
+        sha256 = "sha256-s4KGtfKQ7hL0sfDhGb4BpBpspfefBN6hf+XlslqyEn4=";
       };
       propagatedBuildInputs = builtins.attrValues {
         inherit (pkgs.rPackages) 
-          gh
-          memoise
-          Rcpp
-          codetools
-          crayon
-          rex
-          highlite
-          jsonlite
-          rstudioapi
-          withr
-          httr;
+          dplyr
+          ggplot2
+          janitor
+          purrr
+          readxl
+          rlang
+          rvest
+          stringr
+          tidyr;
       };
     })
    ];
diff --git a/tests/testthat/test-get_sri_hash_deps.R b/tests/testthat/test-get_sri_hash_deps.R
index 07b9575e..a62299fc 100644
--- a/tests/testthat/test-get_sri_hash_deps.R
+++ b/tests/testthat/test-get_sri_hash_deps.R
@@ -6,7 +6,12 @@ testthat::test_that("get_sri_hash_deps returns correct sri hash and dependencies
     ),
     list(
       "sri_hash" = "sha256-s4KGtfKQ7hL0sfDhGb4BpBpspfefBN6hf+XlslqyEn4=",
-      "deps" = "dplyr ggplot2 janitor purrr readxl rlang rvest stringr tidyr"
+      "deps" = list(
+        "package" = "housing",
+        "imports" = c("dplyr", "ggplot2", "janitor", "purrr",
+                      "readxl", "rlang", "rvest", "stringr", "tidyr"),
+        "remotes" = character(0)
+      )
     )
   )
 })
diff --git a/tests/testthat/test-rix.R b/tests/testthat/test-rix.R
index d22d2d77..a7469e74 100644
--- a/tests/testthat/test-rix.R
+++ b/tests/testthat/test-rix.R
@@ -464,9 +464,9 @@ testthat::test_that("rix(), only one Github package", {
       r_pkgs = NULL,
       system_pkgs = NULL,
       git_pkgs = list(
-        package_name = "lookup",
-        repo_url = "https://github.com/jimhester/lookup/",
-        commit = "eba63db477dd2f20153b75e2949eb333a36cccfc"
+        package_name = "housing",
+        repo_url = "https://github.com/rap4all/housing/",
+        commit = "1c860959310b80e67c41f7bbdc3e84cef00df18e"
       ),
       ide = "other",
       project_path = path_default_nix,

From 1c728903d3e0b78e9951acb95441d484dae7b515 Mon Sep 17 00:00:00 2001
From: Bruno Rodrigues <bruno@brodrigues.co>
Date: Sat, 4 Jan 2025 00:25:21 +0100
Subject: [PATCH 03/31] fetchpkgs now returning full list of git deps

---
 R/fetchers.R                   | 11 +++++++----
 R/rix_helpers.R                |  3 +--
 tests/testthat/test-fetchers.R |  2 +-
 3 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/R/fetchers.R b/R/fetchers.R
index 19d8a2c0..a714b9d3 100644
--- a/R/fetchers.R
+++ b/R/fetchers.R
@@ -320,10 +320,13 @@ fetchzips <- function(archive_pkgs) {
 #' from the CRAN archives.
 #' @noRd
 fetchpkgs <- function(git_pkgs, archive_pkgs) {
-  paste(fetchgits(git_pkgs),
-        fetchzips(archive_pkgs),
-        collapse = "\n"
-        )
+  sprintf("
+  git_archive_pkgs = [%s  ];\n", 
+    paste(fetchgits(git_pkgs),
+          fetchzips(archive_pkgs),
+          collapse = "\n"
+          )
+  )
 }
 
 
diff --git a/R/rix_helpers.R b/R/rix_helpers.R
index 2c619887..cb674426 100644
--- a/R/rix_helpers.R
+++ b/R/rix_helpers.R
@@ -242,8 +242,7 @@ generate_git_archived_pkgs <- function(git_pkgs,
   if (flag_git_archive == "") {
     NULL
   } else {
-    sprintf("
-  git_archive_pkgs = [%s  ];\n", fetchpkgs(git_pkgs, archive_pkgs))
+    fetchpkgs(git_pkgs, archive_pkgs)
   }
 }
 
diff --git a/tests/testthat/test-fetchers.R b/tests/testthat/test-fetchers.R
index ce1f6e68..2c6c2b72 100644
--- a/tests/testthat/test-fetchers.R
+++ b/tests/testthat/test-fetchers.R
@@ -119,6 +119,6 @@ testthat::test_that("Test fetchpkgs works", {
       ),
       archive_pkgs = c("AER@1.2-8", "dplyr@0.8.0")
     ),
-    "\n    (pkgs.rPackages.buildRPackage {\n      name = \"fusen\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/ThinkR-open/fusen\";\n        rev = \"d617172447d2947efb20ad6a4463742b8a5d79dc\";\n        sha256 = \"sha256-TOHA1ymLUSgZMYIA1a2yvuv0799svaDOl3zOhNRxcmw=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          attachment\n          cli\n          desc\n          devtools\n          glue\n          here\n          magrittr\n          parsermd\n          roxygen2\n          stringi\n          tibble\n          tidyr\n          usethis\n          yaml;\n      };\n    })\n\n\n    (pkgs.rPackages.buildRPackage {\n      name = \"housing\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/rap4all/housing/\";\n        rev = \"1c860959310b80e67c41f7bbdc3e84cef00df18e\";\n        sha256 = \"sha256-s4KGtfKQ7hL0sfDhGb4BpBpspfefBN6hf+XlslqyEn4=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          dplyr\n          ggplot2\n          janitor\n          purrr\n          readxl\n          rlang\n          rvest\n          stringr\n          tidyr;\n      };\n    })\n \n    (pkgs.rPackages.buildRPackage {\n      name = \"AER\";\n      src = pkgs.fetchzip {\n       url = \"https://cran.r-project.org/src/contrib/Archive/AER/AER_1.2-8.tar.gz\";\n       sha256 = \"sha256-OqxXcnUX/2C6wfD5fuNayc8OU+mstI3tt4eBVGQZ2S0=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          car\n          lmtest\n          sandwich\n          survival\n          zoo\n          Formula;\n      };\n    })\n\n\n    (pkgs.rPackages.buildRPackage {\n      name = \"dplyr\";\n      src = pkgs.fetchzip {\n       url = \"https://cran.r-project.org/src/contrib/Archive/dplyr/dplyr_0.8.0.tar.gz\";\n       sha256 = \"sha256-f30raalLd9KoZKZSxeTN71PG6BczXRIiP6g7EZeH09U=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          assertthat\n          glue\n          magrittr\n          pkgconfig\n          R6\n          Rcpp\n          rlang\n          tibble\n          tidyselect\n          BH\n          plogr;\n      };\n    })\n"
+"\n  git_archive_pkgs = [\n    (pkgs.rPackages.buildRPackage {\n      name = \"fusen\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/ThinkR-open/fusen\";\n        rev = \"d617172447d2947efb20ad6a4463742b8a5d79dc\";\n        sha256 = \"sha256-TOHA1ymLUSgZMYIA1a2yvuv0799svaDOl3zOhNRxcmw=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          attachment\n          cli\n          desc\n          devtools\n          glue\n          here\n          magrittr\n          parsermd\n          roxygen2\n          stringi\n          tibble\n          tidyr\n          usethis\n          yaml;\n      };\n    })\n\n\n    (pkgs.rPackages.buildRPackage {\n      name = \"housing\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/rap4all/housing/\";\n        rev = \"1c860959310b80e67c41f7bbdc3e84cef00df18e\";\n        sha256 = \"sha256-s4KGtfKQ7hL0sfDhGb4BpBpspfefBN6hf+XlslqyEn4=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          dplyr\n          ggplot2\n          janitor\n          purrr\n          readxl\n          rlang\n          rvest\n          stringr\n          tidyr;\n      };\n    })\n \n    (pkgs.rPackages.buildRPackage {\n      name = \"AER\";\n      src = pkgs.fetchzip {\n       url = \"https://cran.r-project.org/src/contrib/Archive/AER/AER_1.2-8.tar.gz\";\n       sha256 = \"sha256-OqxXcnUX/2C6wfD5fuNayc8OU+mstI3tt4eBVGQZ2S0=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          car\n          lmtest\n          sandwich\n          survival\n          zoo\n          Formula;\n      };\n    })\n\n\n    (pkgs.rPackages.buildRPackage {\n      name = \"dplyr\";\n      src = pkgs.fetchzip {\n       url = \"https://cran.r-project.org/src/contrib/Archive/dplyr/dplyr_0.8.0.tar.gz\";\n       sha256 = \"sha256-f30raalLd9KoZKZSxeTN71PG6BczXRIiP6g7EZeH09U=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          assertthat\n          glue\n          magrittr\n          pkgconfig\n          R6\n          Rcpp\n          rlang\n          tibble\n          tidyselect\n          BH\n          plogr;\n      };\n    })\n  ];\n"
   )
 })

From 486d7b97b86b8c4a11785aa23ad56d624e3cb190 Mon Sep 17 00:00:00 2001
From: Bruno Rodrigues <bruno@brodrigues.co>
Date: Sat, 4 Jan 2025 00:44:37 +0100
Subject: [PATCH 04/31] returning list for remote packages

---
 R/fetchers.R | 61 ++++++++++++++++++++--------------------------------
 1 file changed, 23 insertions(+), 38 deletions(-)

diff --git a/R/fetchers.R b/R/fetchers.R
index a714b9d3..600730da 100644
--- a/R/fetchers.R
+++ b/R/fetchers.R
@@ -16,12 +16,15 @@ fetchgit <- function(git_pkg) {
   if(identical(output$deps$remotes, character(0))){
     imports <- output$deps$imports
     imports <- paste(c("", imports), collapse = "\n          ")
+
   } else {
     stop("not yet implemented!")
+    # call fetchgit recursively on remotes?
+    # need to merge fetchgits and fetchgit?
   }
 
   sprintf(
-    '
+      '
     (pkgs.rPackages.buildRPackage {
       name = \"%s\";
       src = pkgs.fetchgit {
@@ -34,12 +37,14 @@ fetchgit <- function(git_pkg) {
       };
     })
 ',
-    package_name,
-    repo_url,
-    commit,
-    sri_hash,
-    imports
-  )
+package_name,
+repo_url,
+commit,
+sri_hash,
+imports
+)
+
+
 }
 
 
@@ -158,14 +163,19 @@ get_imports <- function(path) {
 
   if(!identical(existing_remotes, character(0))){
     remotes <- imports_df[, existing_remotes, drop = FALSE]
-
     # remotes are of the form username/packagename so we need
     # to only keep packagename
     remotes <- gsub("\n", "", x = unlist(strsplit(remotes$Remotes, ",")))
-
-    remotes <- sub(".*?/", "", remotes)
+    remotes_pkgs_names <- sub(".*?/", "", remotes)
+    urls <- paste0("https://github.com/", remotes)
+    commits <- rep("HEAD", length(remotes))
+    remote_pkgs <- lapply(seq_along(remotes_pkgs_names), function(i) {
+      list("package_name" = remotes_pkgs_names[i],
+           "repo_url" = urls[i],
+           "commit" = commits[i])
+    })
   } else {
-    remotes <- character(0)
+    remote_pkgs <- character(0)
   }
 
   if (!is.null(imports) && length(imports) > 0) {
@@ -186,13 +196,12 @@ get_imports <- function(path) {
 
   # Remote packages are included in imports, so we need
   # remove remotes from imports
-  output_imports <- setdiff(output, remotes)
-  output_remotes <- remotes
+  output_imports <- setdiff(output, remotes_pkgs_names)
 
   list(
     "package" = imports_df$Package,
     "imports" = output_imports,
-    "remotes" = output_remotes
+    "remotes" = remote_pkgs
     )
 }
 
@@ -328,27 +337,3 @@ fetchpkgs <- function(git_pkgs, archive_pkgs) {
           )
   )
 }
-
-
-#' remotes2nix Generates a list to pass to rix(git_pkgs = ...) to generate a valid
-#' Nix expression from a REMOTES field in a DESCRIPTION file
-#' @param remotes String, output of read.dcf of the form
-#' "jimhester/highlite,\ngaborcsardi/gh,\nhadley/memoise"
-#' @return A list of lists to pass to rix(git_pkgs = ...)
-#' @noRd
-remotes2nix <- function(remotes){
-  # Input looks like
-  # "jimhester/highlite,\ngaborcsardi/gh,\nhadley/memoise"
-  remotes <- gsub("\n", "", x = unlist(strsplit(remotes, ",")))
-
-  pkgs_names <- sub(".*?/", "", remotes)
-  urls <- paste0("https://github.com/", remotes)
-  commits <- rep("HEAD", length(remotes))
-
-  pkgs <- lapply(seq_along(pkgs_names), function(i) {
-    list("package_name" = pkgs_names[i], "repo_url" = urls[i], "commit" = commits[i])
-  })
-
-  list("remote_name" = )
-
-}

From 722619b671135a4e1f41f931c2d50341c89d350f Mon Sep 17 00:00:00 2001
From: Bruno Rodrigues <bruno@brodrigues.co>
Date: Sat, 4 Jan 2025 21:13:53 +0100
Subject: [PATCH 05/31] first prototype

---
 R/fetchers.R | 76 ++++++++++++++++++++++++++++++++++++++++------------
 1 file changed, 59 insertions(+), 17 deletions(-)

diff --git a/R/fetchers.R b/R/fetchers.R
index 600730da..f07c0219 100644
--- a/R/fetchers.R
+++ b/R/fetchers.R
@@ -13,19 +13,60 @@ fetchgit <- function(git_pkg) {
   output <- get_sri_hash_deps(repo_url, commit)
   sri_hash <- output$sri_hash
   # If package has no remote dependencies
-  if(identical(output$deps$remotes, character(0))){
-    imports <- output$deps$imports
-    imports <- paste(c("", imports), collapse = "\n          ")
 
+  imports <- output$deps$imports
+  imports <- paste(c("", imports), collapse = "\n          ")
+
+  remotes <- output$deps$remotes
+
+  main_package_expression <- generate_git_nix_expression(
+    package_name,
+    repo_url,
+    commit,
+    sri_hash,
+    imports,
+    remotes
+    )
+
+  if(is.null(remotes)){ # if no remote dependencies
+
+    output <- main_package_expression
+
+  } else { # if there are remote dependencies, start over
+    remote_packages_expressions <- fetchgits(remotes)
+
+    output <- paste0(remote_packages_expressions,
+                     main_package_expression,
+                     collapse = "\n")
+  }
+
+  output
+
+}
+
+
+generate_git_nix_expression <- function(
+                                        package_name,
+                                        repo_url,
+                                        commit,
+                                        sri_hash,
+                                        imports,
+                                        remote_deps = NULL
+                                        ){
+
+
+  # If there are remote dependencies, pass this string
+  flag_remote_deps <- if (is.null(remote_deps)) {
+    ""
   } else {
-    stop("not yet implemented!")
-    # call fetchgit recursively on remotes?
-    # need to merge fetchgits and fetchgit?
+    # Extract package names
+    remote_pkgs_names <- sapply(remote_deps, function(x)x$package_name)
+    paste0(" ++ [ ", paste0(remote_pkgs_names, collapse = " ")," ]")
   }
 
   sprintf(
-      '
-    (pkgs.rPackages.buildRPackage {
+    '
+    %s = (pkgs.rPackages.buildRPackage {
       name = \"%s\";
       src = pkgs.fetchgit {
         url = \"%s\";
@@ -34,17 +75,17 @@ fetchgit <- function(git_pkg) {
       };
       propagatedBuildInputs = builtins.attrValues {
         inherit (pkgs.rPackages) %s;
-      };
+      }%s;
     })
 ',
 package_name,
+package_name,
 repo_url,
 commit,
 sri_hash,
-imports
+imports,
+flag_remote_deps
 )
-
-
 }
 
 
@@ -166,16 +207,17 @@ get_imports <- function(path) {
     # remotes are of the form username/packagename so we need
     # to only keep packagename
     remotes <- gsub("\n", "", x = unlist(strsplit(remotes$Remotes, ",")))
-    remotes_pkgs_names <- sub(".*?/", "", remotes)
+    remote_pkgs_names <- sub(".*?/", "", remotes)
     urls <- paste0("https://github.com/", remotes)
     commits <- rep("HEAD", length(remotes))
-    remote_pkgs <- lapply(seq_along(remotes_pkgs_names), function(i) {
-      list("package_name" = remotes_pkgs_names[i],
+    remote_pkgs <- lapply(seq_along(remote_pkgs_names), function(i) {
+      list("package_name" = remote_pkgs_names[i],
            "repo_url" = urls[i],
            "commit" = commits[i])
     })
   } else {
-    remote_pkgs <- character(0)
+    remote_pkgs_names <- character(0)
+    remote_pkgs <- NULL
   }
 
   if (!is.null(imports) && length(imports) > 0) {
@@ -196,7 +238,7 @@ get_imports <- function(path) {
 
   # Remote packages are included in imports, so we need
   # remove remotes from imports
-  output_imports <- setdiff(output, remotes_pkgs_names)
+  output_imports <- setdiff(output, remote_pkgs_names)
 
   list(
     "package" = imports_df$Package,

From e28b0378057bda99edf26c01015babd092e92901 Mon Sep 17 00:00:00 2001
From: Bruno Rodrigues <bruno@brodrigues.co>
Date: Sat, 4 Jan 2025 22:09:16 +0100
Subject: [PATCH 06/31] handling of remote dependencies seems to work, need to
 check tests now

---
 R/fetchers.R | 13 +++++--------
 R/rix.R      |  8 +++++++-
 2 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/R/fetchers.R b/R/fetchers.R
index f07c0219..5ee23dbd 100644
--- a/R/fetchers.R
+++ b/R/fetchers.R
@@ -76,7 +76,7 @@ generate_git_nix_expression <- function(
       propagatedBuildInputs = builtins.attrValues {
         inherit (pkgs.rPackages) %s;
       }%s;
-    })
+    });
 ',
 package_name,
 package_name,
@@ -371,11 +371,8 @@ fetchzips <- function(archive_pkgs) {
 #' from the CRAN archives.
 #' @noRd
 fetchpkgs <- function(git_pkgs, archive_pkgs) {
-  sprintf("
-  git_archive_pkgs = [%s  ];\n", 
-    paste(fetchgits(git_pkgs),
-          fetchzips(archive_pkgs),
-          collapse = "\n"
-          )
-  )
+  paste(fetchgits(git_pkgs),
+        fetchzips(archive_pkgs),
+        collapse = "\n"
+        )
 }
diff --git a/R/rix.R b/R/rix.R
index 54d750ab..e8dcaaac 100644
--- a/R/rix.R
+++ b/R/rix.R
@@ -284,7 +284,13 @@ for more details."
   flag_git_archive <- if (
     !is.null(cran_pkgs$archive_pkgs) || !is.null(git_pkgs)
   ) {
-    "git_archive_pkgs"
+    # If git_pkgs is a list of lists, then sapply will succeed
+    # if not, then we can access "package_name" directly
+    git_pkgs_names <- tryCatch(
+      sapply(git_pkgs, function(x) x$package_name),
+      error = function(e) git_pkgs$package_name
+    )
+    paste0(cran_pkgs$archive_pkgs, git_pkgs_names, collapse = " ")
   } else {
     ""
   }

From 44cf22a694257f094858d2c66bb0767fe58c28e9 Mon Sep 17 00:00:00 2001
From: Bruno Rodrigues <bruno@brodrigues.co>
Date: Sat, 4 Jan 2025 22:24:05 +0100
Subject: [PATCH 07/31] correctly handling CRAN archive packages now again

---
 R/fetchers.R | 5 +++--
 R/rix.R      | 8 +++++++-
 2 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/R/fetchers.R b/R/fetchers.R
index 5ee23dbd..a89231d4 100644
--- a/R/fetchers.R
+++ b/R/fetchers.R
@@ -119,7 +119,7 @@ fetchzip <- function(archive_pkg, sri_hash = NULL) {
 
   sprintf(
     '
-    (pkgs.rPackages.buildRPackage {
+    %s = (pkgs.rPackages.buildRPackage {
       name = \"%s\";
       src = pkgs.fetchzip {
        url = \"%s\";
@@ -128,8 +128,9 @@ fetchzip <- function(archive_pkg, sri_hash = NULL) {
       propagatedBuildInputs = builtins.attrValues {
         inherit (pkgs.rPackages) %s;
       };
-    })
+    }),
 ',
+    package_name,
     package_name,
     repo_url,
     sri_hash,
diff --git a/R/rix.R b/R/rix.R
index e8dcaaac..2f240936 100644
--- a/R/rix.R
+++ b/R/rix.R
@@ -290,7 +290,13 @@ for more details."
       sapply(git_pkgs, function(x) x$package_name),
       error = function(e) git_pkgs$package_name
     )
-    paste0(cran_pkgs$archive_pkgs, git_pkgs_names, collapse = " ")
+    # CRAN archive pkgs are written as "AER@123"
+    # so we need to split at the '@' character and then
+    # walk through the list to grab the first element
+    # which will be the name of the package
+    pkgs <- strsplit(cran_pkgs$archive_pkg, split = "@")
+    pkgs_names <- sapply(pkgs, function(x)x[[1]])
+    paste0(c(pkgs_names, git_pkgs_names), collapse = " ")
   } else {
     ""
   }

From 92c2093c1f9efc6766783ca0922aab54d3b8d3ea Mon Sep 17 00:00:00 2001
From: b-rodrigues <b-rodrigues@users.noreply.github.com>
Date: Sat, 4 Jan 2025 21:29:45 +0000
Subject: [PATCH 08/31] Style via {styler}

---
 R/available_r.R                         |  6 ++-
 R/fetchers.R                            | 57 ++++++++++++-------------
 R/get_latest.R                          |  8 ++--
 R/rix.R                                 |  2 +-
 tests/testthat/test-fetchers.R          |  2 +-
 tests/testthat/test-get_sri_hash_deps.R |  6 ++-
 6 files changed, 42 insertions(+), 39 deletions(-)

diff --git a/R/available_r.R b/R/available_r.R
index fa955d4d..99a4e39b 100644
--- a/R/available_r.R
+++ b/R/available_r.R
@@ -21,8 +21,10 @@ available_df <- function() {
 #' available_r()
 available_r <- function() {
   r_versions <- unique(available_df()$`R.version`)
-  c("bleeding-edge", "frozen-edge", "r-devel", "bioc-devel",
-    "r-devel-bioc-devel", "latest-upstream", r_versions)
+  c(
+    "bleeding-edge", "frozen-edge", "r-devel", "bioc-devel",
+    "r-devel-bioc-devel", "latest-upstream", r_versions
+  )
 }
 
 #' List available dates.
diff --git a/R/fetchers.R b/R/fetchers.R
index a89231d4..fe4a7ed6 100644
--- a/R/fetchers.R
+++ b/R/fetchers.R
@@ -26,42 +26,37 @@ fetchgit <- function(git_pkg) {
     sri_hash,
     imports,
     remotes
-    )
+  )
 
-  if(is.null(remotes)){ # if no remote dependencies
+  if (is.null(remotes)) { # if no remote dependencies
 
     output <- main_package_expression
-
   } else { # if there are remote dependencies, start over
     remote_packages_expressions <- fetchgits(remotes)
 
     output <- paste0(remote_packages_expressions,
-                     main_package_expression,
-                     collapse = "\n")
+      main_package_expression,
+      collapse = "\n"
+    )
   }
 
   output
-
 }
 
 
-generate_git_nix_expression <- function(
-                                        package_name,
+generate_git_nix_expression <- function(package_name,
                                         repo_url,
                                         commit,
                                         sri_hash,
                                         imports,
-                                        remote_deps = NULL
-                                        ){
-
-
+                                        remote_deps = NULL) {
   # If there are remote dependencies, pass this string
   flag_remote_deps <- if (is.null(remote_deps)) {
     ""
   } else {
     # Extract package names
-    remote_pkgs_names <- sapply(remote_deps, function(x)x$package_name)
-    paste0(" ++ [ ", paste0(remote_pkgs_names, collapse = " ")," ]")
+    remote_pkgs_names <- sapply(remote_deps, function(x) x$package_name)
+    paste0(" ++ [ ", paste0(remote_pkgs_names, collapse = " "), " ]")
   }
 
   sprintf(
@@ -78,14 +73,14 @@ generate_git_nix_expression <- function(
       }%s;
     });
 ',
-package_name,
-package_name,
-repo_url,
-commit,
-sri_hash,
-imports,
-flag_remote_deps
-)
+    package_name,
+    package_name,
+    repo_url,
+    commit,
+    sri_hash,
+    imports,
+    flag_remote_deps
+  )
 }
 
 
@@ -203,7 +198,7 @@ get_imports <- function(path) {
 
   existing_remotes <- intersect("Remotes", colnames(imports_df))
 
-  if(!identical(existing_remotes, character(0))){
+  if (!identical(existing_remotes, character(0))) {
     remotes <- imports_df[, existing_remotes, drop = FALSE]
     # remotes are of the form username/packagename so we need
     # to only keep packagename
@@ -212,9 +207,11 @@ get_imports <- function(path) {
     urls <- paste0("https://github.com/", remotes)
     commits <- rep("HEAD", length(remotes))
     remote_pkgs <- lapply(seq_along(remote_pkgs_names), function(i) {
-      list("package_name" = remote_pkgs_names[i],
-           "repo_url" = urls[i],
-           "commit" = commits[i])
+      list(
+        "package_name" = remote_pkgs_names[i],
+        "repo_url" = urls[i],
+        "commit" = commits[i]
+      )
     })
   } else {
     remote_pkgs_names <- character(0)
@@ -245,7 +242,7 @@ get_imports <- function(path) {
     "package" = imports_df$Package,
     "imports" = output_imports,
     "remotes" = remote_pkgs
-    )
+  )
 }
 
 
@@ -373,7 +370,7 @@ fetchzips <- function(archive_pkgs) {
 #' @noRd
 fetchpkgs <- function(git_pkgs, archive_pkgs) {
   paste(fetchgits(git_pkgs),
-        fetchzips(archive_pkgs),
-        collapse = "\n"
-        )
+    fetchzips(archive_pkgs),
+    collapse = "\n"
+  )
 }
diff --git a/R/get_latest.R b/R/get_latest.R
index ffce87a2..8b3f0e8e 100644
--- a/R/get_latest.R
+++ b/R/get_latest.R
@@ -36,9 +36,11 @@ get_latest <- function(r_version) {
       "'bleeding-edge' and 'frozen-edge'."
     )
   } else if (
-           !(r_version %in% c("r-devel-bioc-devel", "r-devel", "bioc-devel",
-                              "bleeding-edge", "frozen-edge", available_r()))
-         ) {
+    !(r_version %in% c(
+      "r-devel-bioc-devel", "r-devel", "bioc-devel",
+      "bleeding-edge", "frozen-edge", available_r()
+    ))
+  ) {
     stop(
       "The provided R version is too recent,\nand not yet included in `nixpkgs`.\n",
       "You can list available versions using `available_r()`.\n",
diff --git a/R/rix.R b/R/rix.R
index 2f240936..64574f10 100644
--- a/R/rix.R
+++ b/R/rix.R
@@ -295,7 +295,7 @@ for more details."
     # walk through the list to grab the first element
     # which will be the name of the package
     pkgs <- strsplit(cran_pkgs$archive_pkg, split = "@")
-    pkgs_names <- sapply(pkgs, function(x)x[[1]])
+    pkgs_names <- sapply(pkgs, function(x) x[[1]])
     paste0(c(pkgs_names, git_pkgs_names), collapse = " ")
   } else {
     ""
diff --git a/tests/testthat/test-fetchers.R b/tests/testthat/test-fetchers.R
index 2c6c2b72..27873cb4 100644
--- a/tests/testthat/test-fetchers.R
+++ b/tests/testthat/test-fetchers.R
@@ -119,6 +119,6 @@ testthat::test_that("Test fetchpkgs works", {
       ),
       archive_pkgs = c("AER@1.2-8", "dplyr@0.8.0")
     ),
-"\n  git_archive_pkgs = [\n    (pkgs.rPackages.buildRPackage {\n      name = \"fusen\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/ThinkR-open/fusen\";\n        rev = \"d617172447d2947efb20ad6a4463742b8a5d79dc\";\n        sha256 = \"sha256-TOHA1ymLUSgZMYIA1a2yvuv0799svaDOl3zOhNRxcmw=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          attachment\n          cli\n          desc\n          devtools\n          glue\n          here\n          magrittr\n          parsermd\n          roxygen2\n          stringi\n          tibble\n          tidyr\n          usethis\n          yaml;\n      };\n    })\n\n\n    (pkgs.rPackages.buildRPackage {\n      name = \"housing\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/rap4all/housing/\";\n        rev = \"1c860959310b80e67c41f7bbdc3e84cef00df18e\";\n        sha256 = \"sha256-s4KGtfKQ7hL0sfDhGb4BpBpspfefBN6hf+XlslqyEn4=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          dplyr\n          ggplot2\n          janitor\n          purrr\n          readxl\n          rlang\n          rvest\n          stringr\n          tidyr;\n      };\n    })\n \n    (pkgs.rPackages.buildRPackage {\n      name = \"AER\";\n      src = pkgs.fetchzip {\n       url = \"https://cran.r-project.org/src/contrib/Archive/AER/AER_1.2-8.tar.gz\";\n       sha256 = \"sha256-OqxXcnUX/2C6wfD5fuNayc8OU+mstI3tt4eBVGQZ2S0=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          car\n          lmtest\n          sandwich\n          survival\n          zoo\n          Formula;\n      };\n    })\n\n\n    (pkgs.rPackages.buildRPackage {\n      name = \"dplyr\";\n      src = pkgs.fetchzip {\n       url = \"https://cran.r-project.org/src/contrib/Archive/dplyr/dplyr_0.8.0.tar.gz\";\n       sha256 = \"sha256-f30raalLd9KoZKZSxeTN71PG6BczXRIiP6g7EZeH09U=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          assertthat\n          glue\n          magrittr\n          pkgconfig\n          R6\n          Rcpp\n          rlang\n          tibble\n          tidyselect\n          BH\n          plogr;\n      };\n    })\n  ];\n"
+    "\n  git_archive_pkgs = [\n    (pkgs.rPackages.buildRPackage {\n      name = \"fusen\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/ThinkR-open/fusen\";\n        rev = \"d617172447d2947efb20ad6a4463742b8a5d79dc\";\n        sha256 = \"sha256-TOHA1ymLUSgZMYIA1a2yvuv0799svaDOl3zOhNRxcmw=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          attachment\n          cli\n          desc\n          devtools\n          glue\n          here\n          magrittr\n          parsermd\n          roxygen2\n          stringi\n          tibble\n          tidyr\n          usethis\n          yaml;\n      };\n    })\n\n\n    (pkgs.rPackages.buildRPackage {\n      name = \"housing\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/rap4all/housing/\";\n        rev = \"1c860959310b80e67c41f7bbdc3e84cef00df18e\";\n        sha256 = \"sha256-s4KGtfKQ7hL0sfDhGb4BpBpspfefBN6hf+XlslqyEn4=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          dplyr\n          ggplot2\n          janitor\n          purrr\n          readxl\n          rlang\n          rvest\n          stringr\n          tidyr;\n      };\n    })\n \n    (pkgs.rPackages.buildRPackage {\n      name = \"AER\";\n      src = pkgs.fetchzip {\n       url = \"https://cran.r-project.org/src/contrib/Archive/AER/AER_1.2-8.tar.gz\";\n       sha256 = \"sha256-OqxXcnUX/2C6wfD5fuNayc8OU+mstI3tt4eBVGQZ2S0=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          car\n          lmtest\n          sandwich\n          survival\n          zoo\n          Formula;\n      };\n    })\n\n\n    (pkgs.rPackages.buildRPackage {\n      name = \"dplyr\";\n      src = pkgs.fetchzip {\n       url = \"https://cran.r-project.org/src/contrib/Archive/dplyr/dplyr_0.8.0.tar.gz\";\n       sha256 = \"sha256-f30raalLd9KoZKZSxeTN71PG6BczXRIiP6g7EZeH09U=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          assertthat\n          glue\n          magrittr\n          pkgconfig\n          R6\n          Rcpp\n          rlang\n          tibble\n          tidyselect\n          BH\n          plogr;\n      };\n    })\n  ];\n"
   )
 })
diff --git a/tests/testthat/test-get_sri_hash_deps.R b/tests/testthat/test-get_sri_hash_deps.R
index a62299fc..f280943f 100644
--- a/tests/testthat/test-get_sri_hash_deps.R
+++ b/tests/testthat/test-get_sri_hash_deps.R
@@ -8,8 +8,10 @@ testthat::test_that("get_sri_hash_deps returns correct sri hash and dependencies
       "sri_hash" = "sha256-s4KGtfKQ7hL0sfDhGb4BpBpspfefBN6hf+XlslqyEn4=",
       "deps" = list(
         "package" = "housing",
-        "imports" = c("dplyr", "ggplot2", "janitor", "purrr",
-                      "readxl", "rlang", "rvest", "stringr", "tidyr"),
+        "imports" = c(
+          "dplyr", "ggplot2", "janitor", "purrr",
+          "readxl", "rlang", "rvest", "stringr", "tidyr"
+        ),
         "remotes" = character(0)
       )
     )

From e409014c196d74a4a8550d1bd69009ebe01e2e01 Mon Sep 17 00:00:00 2001
From: mischko <mhem@mailbox.org>
Date: Sun, 5 Jan 2025 13:16:16 +0100
Subject: [PATCH 09/31] try fix handle_remote_deps

if there was a git_pkgs but not a cran_pkgs archive, the previous code would fail.
---
 R/rix.R | 28 ++++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/R/rix.R b/R/rix.R
index 64574f10..0b55b150 100644
--- a/R/rix.R
+++ b/R/rix.R
@@ -282,21 +282,21 @@ for more details."
 
   # If there are R packages from Git, passes the string "git_archive_pkgs" to buildInputs
   flag_git_archive <- if (
-    !is.null(cran_pkgs$archive_pkgs) || !is.null(git_pkgs)
+    !is.null(git_pkgs) || !is.null(cran_pkgs$archive_pkgs)
   ) {
-    # If git_pkgs is a list of lists, then sapply will succeed
-    # if not, then we can access "package_name" directly
-    git_pkgs_names <- tryCatch(
-      sapply(git_pkgs, function(x) x$package_name),
-      error = function(e) git_pkgs$package_name
-    )
-    # CRAN archive pkgs are written as "AER@123"
-    # so we need to split at the '@' character and then
-    # walk through the list to grab the first element
-    # which will be the name of the package
-    pkgs <- strsplit(cran_pkgs$archive_pkg, split = "@")
-    pkgs_names <- sapply(pkgs, function(x) x[[1]])
-    paste0(c(pkgs_names, git_pkgs_names), collapse = " ")
+    git_pkgs_names <- if (!is.null(git_pkgs)) {
+      tryCatch(
+        sapply(git_pkgs, function(x) x$package_name),
+        error = function(e) git_pkgs$package_name
+      )
+    }
+
+    cran_archive_names <- if (!is.null(cran_pkgs$archive_pkgs)) {
+      pkgs <- strsplit(cran_pkgs$archive_pkgs, split = "@")
+      sapply(pkgs, function(x) x[[1]])
+    }
+
+    paste0(c(git_pkgs_names, cran_archive_names), collapse = " ")
   } else {
     ""
   }

From 8e375a936bc590aa41cda2f9e59f01baffc78130 Mon Sep 17 00:00:00 2001
From: mischko <mhem@mailbox.org>
Date: Sun, 5 Jan 2025 14:24:09 +0100
Subject: [PATCH 10/31] add comments back

---
 R/rix.R | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/R/rix.R b/R/rix.R
index 0b55b150..5ec23034 100644
--- a/R/rix.R
+++ b/R/rix.R
@@ -290,7 +290,11 @@ for more details."
         error = function(e) git_pkgs$package_name
       )
     }
-
+    # CRAN archive pkgs are written as "AER@123"
+    # so we need to split at the '@' character and then
+    # walk through the list to grab the first element
+    # which will be the name of the package
+    pkgs <- strsplit(cran_pkgs$archive_pkg, split = "@")
     cran_archive_names <- if (!is.null(cran_pkgs$archive_pkgs)) {
       pkgs <- strsplit(cran_pkgs$archive_pkgs, split = "@")
       sapply(pkgs, function(x) x[[1]])

From da8543eac73514da5419347352c0dbd19be13a66 Mon Sep 17 00:00:00 2001
From: mischko <mhem@mailbox.org>
Date: Sun, 5 Jan 2025 14:25:27 +0100
Subject: [PATCH 11/31] add second comment back

---
 R/rix.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/R/rix.R b/R/rix.R
index 5ec23034..ff8757f1 100644
--- a/R/rix.R
+++ b/R/rix.R
@@ -284,6 +284,8 @@ for more details."
   flag_git_archive <- if (
     !is.null(git_pkgs) || !is.null(cran_pkgs$archive_pkgs)
   ) {
+    # If git_pkgs is a list of lists, then sapply will succeed
+    # if not, then we can access "package_name" directly
     git_pkgs_names <- if (!is.null(git_pkgs)) {
       tryCatch(
         sapply(git_pkgs, function(x) x$package_name),

From a0ff8c8b972e244583ca6a1fb423b54e06bb202a Mon Sep 17 00:00:00 2001
From: mischko <mhem@mailbox.org>
Date: Sun, 5 Jan 2025 14:27:44 +0100
Subject: [PATCH 12/31] fix bug

---
 R/rix.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/R/rix.R b/R/rix.R
index ff8757f1..9327a1aa 100644
--- a/R/rix.R
+++ b/R/rix.R
@@ -296,7 +296,6 @@ for more details."
     # so we need to split at the '@' character and then
     # walk through the list to grab the first element
     # which will be the name of the package
-    pkgs <- strsplit(cran_pkgs$archive_pkg, split = "@")
     cran_archive_names <- if (!is.null(cran_pkgs$archive_pkgs)) {
       pkgs <- strsplit(cran_pkgs$archive_pkgs, split = "@")
       sapply(pkgs, function(x) x[[1]])

From 56efb98753793f9d31a0fe087653e7628aca1782 Mon Sep 17 00:00:00 2001
From: Bruno Rodrigues <bruno@brodrigues.co>
Date: Sun, 5 Jan 2025 15:51:43 +0100
Subject: [PATCH 13/31] tests passing

---
 .../_snaps/renv_helpers/default_v0-14-0.nix    | 10 ++++------
 .../_snaps/renv_helpers/default_v0-15-5.nix    | 14 ++++++--------
 .../_snaps/renv_helpers/default_v0-17-3.nix    | 10 ++++------
 .../_snaps/rix/bleeding-edge_default.nix       | 16 +++++++---------
 tests/testthat/_snaps/rix/code_default.nix     | 16 +++++++---------
 tests/testthat/_snaps/rix/date_default.nix     | 16 +++++++---------
 .../_snaps/rix/frozen-edge_default.nix         | 16 +++++++---------
 tests/testthat/_snaps/rix/one_git_default.nix  | 10 ++++------
 tests/testthat/_snaps/rix/other_default.nix    | 16 +++++++---------
 tests/testthat/_snaps/rix/rstudio_default.nix  | 18 ++++++++----------
 tests/testthat/test-fetchers.R                 | 17 ++++++++---------
 tests/testthat/test-get_sri_hash_deps.R        |  2 +-
 12 files changed, 70 insertions(+), 91 deletions(-)

diff --git a/tests/testthat/_snaps/renv_helpers/default_v0-14-0.nix b/tests/testthat/_snaps/renv_helpers/default_v0-14-0.nix
index 6f5833ea..386ace20 100644
--- a/tests/testthat/_snaps/renv_helpers/default_v0-14-0.nix
+++ b/tests/testthat/_snaps/renv_helpers/default_v0-14-0.nix
@@ -167,8 +167,7 @@ let
       zip;
   };
  
-  git_archive_pkgs = [
-    (pkgs.rPackages.buildRPackage {
+    colourScaleR = (pkgs.rPackages.buildRPackage {
       name = "colourScaleR";
       src = pkgs.fetchgit {
         url = "https://github.com/richardjacton/colourScaleR";
@@ -185,9 +184,8 @@ let
           gridExtra
           purrr;
       };
-    })
-   ];
-   
+    });
+    
   system_packages = builtins.attrValues {
     inherit (pkgs) 
       R
@@ -206,6 +204,6 @@ pkgs.mkShell {
    LC_PAPER = "en_US.UTF-8";
    LC_MEASUREMENT = "en_US.UTF-8";
 
-  buildInputs = [ git_archive_pkgs rpkgs  system_packages   ];
+  buildInputs = [ colourScaleR rpkgs  system_packages   ];
   
 }
diff --git a/tests/testthat/_snaps/renv_helpers/default_v0-15-5.nix b/tests/testthat/_snaps/renv_helpers/default_v0-15-5.nix
index 52c8d571..928fd0ad 100644
--- a/tests/testthat/_snaps/renv_helpers/default_v0-15-5.nix
+++ b/tests/testthat/_snaps/renv_helpers/default_v0-15-5.nix
@@ -135,8 +135,7 @@ let
       zip;
   };
  
-  git_archive_pkgs = [
-    (pkgs.rPackages.buildRPackage {
+    colorblindr = (pkgs.rPackages.buildRPackage {
       name = "colorblindr";
       src = pkgs.fetchgit {
         url = "https://github.com/clauswilke/colorblindr";
@@ -151,10 +150,10 @@ let
           shiny
           scales;
       };
-    })
+    });
 
 
-    (pkgs.rPackages.buildRPackage {
+    colourScaleR = (pkgs.rPackages.buildRPackage {
       name = "colourScaleR";
       src = pkgs.fetchgit {
         url = "https://github.com/RichardJActon/colourScaleR";
@@ -171,9 +170,8 @@ let
           gridExtra
           purrr;
       };
-    })
-   ];
-   
+    });
+    
   system_packages = builtins.attrValues {
     inherit (pkgs) 
       R
@@ -192,6 +190,6 @@ pkgs.mkShell {
    LC_PAPER = "en_US.UTF-8";
    LC_MEASUREMENT = "en_US.UTF-8";
 
-  buildInputs = [ git_archive_pkgs rpkgs  system_packages   ];
+  buildInputs = [ colorblindr colourScaleR rpkgs  system_packages   ];
   
 }
diff --git a/tests/testthat/_snaps/renv_helpers/default_v0-17-3.nix b/tests/testthat/_snaps/renv_helpers/default_v0-17-3.nix
index 018d304f..d4079db5 100644
--- a/tests/testthat/_snaps/renv_helpers/default_v0-17-3.nix
+++ b/tests/testthat/_snaps/renv_helpers/default_v0-17-3.nix
@@ -132,8 +132,7 @@ let
       zip;
   };
  
-  git_archive_pkgs = [
-    (pkgs.rPackages.buildRPackage {
+    emo = (pkgs.rPackages.buildRPackage {
       name = "emo";
       src = pkgs.fetchgit {
         url = "https://github.com/hadley/emo";
@@ -151,9 +150,8 @@ let
           rlang
           purrr;
       };
-    })
-   ];
-   
+    });
+    
   system_packages = builtins.attrValues {
     inherit (pkgs) 
       R
@@ -172,6 +170,6 @@ pkgs.mkShell {
    LC_PAPER = "en_US.UTF-8";
    LC_MEASUREMENT = "en_US.UTF-8";
 
-  buildInputs = [ git_archive_pkgs rpkgs  system_packages   ];
+  buildInputs = [ emo rpkgs  system_packages   ];
   
 }
diff --git a/tests/testthat/_snaps/rix/bleeding-edge_default.nix b/tests/testthat/_snaps/rix/bleeding-edge_default.nix
index e97eefee..fb62e039 100644
--- a/tests/testthat/_snaps/rix/bleeding-edge_default.nix
+++ b/tests/testthat/_snaps/rix/bleeding-edge_default.nix
@@ -9,8 +9,7 @@ let
       quarto;
   };
  
-  git_archive_pkgs = [
-    (pkgs.rPackages.buildRPackage {
+    fusen = (pkgs.rPackages.buildRPackage {
       name = "fusen";
       src = pkgs.fetchgit {
         url = "https://github.com/ThinkR-open/fusen";
@@ -34,10 +33,10 @@ let
           usethis
           yaml;
       };
-    })
+    });
 
 
-    (pkgs.rPackages.buildRPackage {
+    housing = (pkgs.rPackages.buildRPackage {
       name = "housing";
       src = pkgs.fetchgit {
         url = "https://github.com/rap4all/housing/";
@@ -56,9 +55,9 @@ let
           stringr
           tidyr;
       };
-    })
+    });
  
-    (pkgs.rPackages.buildRPackage {
+    AER = (pkgs.rPackages.buildRPackage {
       name = "AER";
       src = pkgs.fetchzip {
        url = "https://cran.r-project.org/src/contrib/Archive/AER/AER_1.2-8.tar.gz";
@@ -73,8 +72,7 @@ let
           zoo
           Formula;
       };
-    })
-  ];
+    }),
  
   tex = (pkgs.texlive.combine {
     inherit (pkgs.texlive) 
@@ -102,6 +100,6 @@ pkgs.mkShell {
    LC_PAPER = "en_US.UTF-8";
    LC_MEASUREMENT = "en_US.UTF-8";
 
-  buildInputs = [ git_archive_pkgs rpkgs tex system_packages   ];
+  buildInputs = [ housing fusen AER rpkgs tex system_packages   ];
   
 }
diff --git a/tests/testthat/_snaps/rix/code_default.nix b/tests/testthat/_snaps/rix/code_default.nix
index ac15f813..4e757041 100644
--- a/tests/testthat/_snaps/rix/code_default.nix
+++ b/tests/testthat/_snaps/rix/code_default.nix
@@ -10,8 +10,7 @@ let
       quarto;
   };
  
-  git_archive_pkgs = [
-    (pkgs.rPackages.buildRPackage {
+    fusen = (pkgs.rPackages.buildRPackage {
       name = "fusen";
       src = pkgs.fetchgit {
         url = "https://github.com/ThinkR-open/fusen";
@@ -35,10 +34,10 @@ let
           usethis
           yaml;
       };
-    })
+    });
 
 
-    (pkgs.rPackages.buildRPackage {
+    housing = (pkgs.rPackages.buildRPackage {
       name = "housing";
       src = pkgs.fetchgit {
         url = "https://github.com/rap4all/housing/";
@@ -57,9 +56,9 @@ let
           stringr
           tidyr;
       };
-    })
+    });
  
-    (pkgs.rPackages.buildRPackage {
+    AER = (pkgs.rPackages.buildRPackage {
       name = "AER";
       src = pkgs.fetchzip {
        url = "https://cran.r-project.org/src/contrib/Archive/AER/AER_1.2-8.tar.gz";
@@ -74,8 +73,7 @@ let
           zoo
           Formula;
       };
-    })
-  ];
+    }),
  
   tex = (pkgs.texlive.combine {
     inherit (pkgs.texlive) 
@@ -102,6 +100,6 @@ pkgs.mkShell {
    LC_PAPER = "en_US.UTF-8";
    LC_MEASUREMENT = "en_US.UTF-8";
 
-  buildInputs = [ git_archive_pkgs rpkgs tex system_packages   ];
+  buildInputs = [ housing fusen AER rpkgs tex system_packages   ];
   
 }
diff --git a/tests/testthat/_snaps/rix/date_default.nix b/tests/testthat/_snaps/rix/date_default.nix
index 646fdd9a..39c0c46d 100644
--- a/tests/testthat/_snaps/rix/date_default.nix
+++ b/tests/testthat/_snaps/rix/date_default.nix
@@ -9,8 +9,7 @@ let
       quarto;
   };
  
-  git_archive_pkgs = [
-    (pkgs.rPackages.buildRPackage {
+    fusen = (pkgs.rPackages.buildRPackage {
       name = "fusen";
       src = pkgs.fetchgit {
         url = "https://github.com/ThinkR-open/fusen";
@@ -34,10 +33,10 @@ let
           usethis
           yaml;
       };
-    })
+    });
 
 
-    (pkgs.rPackages.buildRPackage {
+    housing = (pkgs.rPackages.buildRPackage {
       name = "housing";
       src = pkgs.fetchgit {
         url = "https://github.com/rap4all/housing/";
@@ -56,9 +55,9 @@ let
           stringr
           tidyr;
       };
-    })
+    });
  
-    (pkgs.rPackages.buildRPackage {
+    AER = (pkgs.rPackages.buildRPackage {
       name = "AER";
       src = pkgs.fetchzip {
        url = "https://cran.r-project.org/src/contrib/Archive/AER/AER_1.2-8.tar.gz";
@@ -73,8 +72,7 @@ let
           zoo
           Formula;
       };
-    })
-  ];
+    }),
  
   tex = (pkgs.texlive.combine {
     inherit (pkgs.texlive) 
@@ -102,6 +100,6 @@ pkgs.mkShell {
    LC_PAPER = "en_US.UTF-8";
    LC_MEASUREMENT = "en_US.UTF-8";
 
-  buildInputs = [ git_archive_pkgs rpkgs tex system_packages   ];
+  buildInputs = [ housing fusen AER rpkgs tex system_packages   ];
   
 }
diff --git a/tests/testthat/_snaps/rix/frozen-edge_default.nix b/tests/testthat/_snaps/rix/frozen-edge_default.nix
index 1b706b46..5169f364 100644
--- a/tests/testthat/_snaps/rix/frozen-edge_default.nix
+++ b/tests/testthat/_snaps/rix/frozen-edge_default.nix
@@ -9,8 +9,7 @@ let
       quarto;
   };
  
-  git_archive_pkgs = [
-    (pkgs.rPackages.buildRPackage {
+    fusen = (pkgs.rPackages.buildRPackage {
       name = "fusen";
       src = pkgs.fetchgit {
         url = "https://github.com/ThinkR-open/fusen";
@@ -34,10 +33,10 @@ let
           usethis
           yaml;
       };
-    })
+    });
 
 
-    (pkgs.rPackages.buildRPackage {
+    housing = (pkgs.rPackages.buildRPackage {
       name = "housing";
       src = pkgs.fetchgit {
         url = "https://github.com/rap4all/housing/";
@@ -56,9 +55,9 @@ let
           stringr
           tidyr;
       };
-    })
+    });
  
-    (pkgs.rPackages.buildRPackage {
+    AER = (pkgs.rPackages.buildRPackage {
       name = "AER";
       src = pkgs.fetchzip {
        url = "https://cran.r-project.org/src/contrib/Archive/AER/AER_1.2-8.tar.gz";
@@ -73,8 +72,7 @@ let
           zoo
           Formula;
       };
-    })
-  ];
+    }),
  
   tex = (pkgs.texlive.combine {
     inherit (pkgs.texlive) 
@@ -101,6 +99,6 @@ pkgs.mkShell {
    LC_PAPER = "en_US.UTF-8";
    LC_MEASUREMENT = "en_US.UTF-8";
 
-  buildInputs = [ git_archive_pkgs rpkgs tex system_packages   ];
+  buildInputs = [ housing fusen AER rpkgs tex system_packages   ];
   
 }
diff --git a/tests/testthat/_snaps/rix/one_git_default.nix b/tests/testthat/_snaps/rix/one_git_default.nix
index eed8ead8..0f688b46 100644
--- a/tests/testthat/_snaps/rix/one_git_default.nix
+++ b/tests/testthat/_snaps/rix/one_git_default.nix
@@ -2,8 +2,7 @@
 let
   pkgs = import (fetchTarball "https://github.com/rstats-on-nix/nixpkgs/archive/2023-10-30.tar.gz") {};
   
-  git_archive_pkgs = [
-    (pkgs.rPackages.buildRPackage {
+    housing = (pkgs.rPackages.buildRPackage {
       name = "housing";
       src = pkgs.fetchgit {
         url = "https://github.com/rap4all/housing/";
@@ -22,9 +21,8 @@ let
           stringr
           tidyr;
       };
-    })
-   ];
-   
+    });
+    
   system_packages = builtins.attrValues {
     inherit (pkgs) 
       R
@@ -43,6 +41,6 @@ pkgs.mkShell {
    LC_PAPER = "en_US.UTF-8";
    LC_MEASUREMENT = "en_US.UTF-8";
 
-  buildInputs = [ git_archive_pkgs   system_packages   ];
+  buildInputs = [ housing   system_packages   ];
   
 }
diff --git a/tests/testthat/_snaps/rix/other_default.nix b/tests/testthat/_snaps/rix/other_default.nix
index db4b417a..b6ae5141 100644
--- a/tests/testthat/_snaps/rix/other_default.nix
+++ b/tests/testthat/_snaps/rix/other_default.nix
@@ -9,8 +9,7 @@ let
       quarto;
   };
  
-  git_archive_pkgs = [
-    (pkgs.rPackages.buildRPackage {
+    fusen = (pkgs.rPackages.buildRPackage {
       name = "fusen";
       src = pkgs.fetchgit {
         url = "https://github.com/ThinkR-open/fusen";
@@ -34,10 +33,10 @@ let
           usethis
           yaml;
       };
-    })
+    });
 
 
-    (pkgs.rPackages.buildRPackage {
+    housing = (pkgs.rPackages.buildRPackage {
       name = "housing";
       src = pkgs.fetchgit {
         url = "https://github.com/rap4all/housing/";
@@ -56,9 +55,9 @@ let
           stringr
           tidyr;
       };
-    })
+    });
  
-    (pkgs.rPackages.buildRPackage {
+    AER = (pkgs.rPackages.buildRPackage {
       name = "AER";
       src = pkgs.fetchzip {
        url = "https://cran.r-project.org/src/contrib/Archive/AER/AER_1.2-8.tar.gz";
@@ -73,8 +72,7 @@ let
           zoo
           Formula;
       };
-    })
-  ];
+    }),
  
   tex = (pkgs.texlive.combine {
     inherit (pkgs.texlive) 
@@ -101,6 +99,6 @@ pkgs.mkShell {
    LC_PAPER = "en_US.UTF-8";
    LC_MEASUREMENT = "en_US.UTF-8";
 
-  buildInputs = [ git_archive_pkgs rpkgs tex system_packages   ];
+  buildInputs = [ housing fusen AER rpkgs tex system_packages   ];
   
 }
diff --git a/tests/testthat/_snaps/rix/rstudio_default.nix b/tests/testthat/_snaps/rix/rstudio_default.nix
index 1177817b..b91e9a4d 100644
--- a/tests/testthat/_snaps/rix/rstudio_default.nix
+++ b/tests/testthat/_snaps/rix/rstudio_default.nix
@@ -9,8 +9,7 @@ let
       quarto;
   };
  
-  git_archive_pkgs = [
-    (pkgs.rPackages.buildRPackage {
+    fusen = (pkgs.rPackages.buildRPackage {
       name = "fusen";
       src = pkgs.fetchgit {
         url = "https://github.com/ThinkR-open/fusen";
@@ -34,10 +33,10 @@ let
           usethis
           yaml;
       };
-    })
+    });
 
 
-    (pkgs.rPackages.buildRPackage {
+    housing = (pkgs.rPackages.buildRPackage {
       name = "housing";
       src = pkgs.fetchgit {
         url = "https://github.com/rap4all/housing/";
@@ -56,9 +55,9 @@ let
           stringr
           tidyr;
       };
-    })
+    });
  
-    (pkgs.rPackages.buildRPackage {
+    AER = (pkgs.rPackages.buildRPackage {
       name = "AER";
       src = pkgs.fetchzip {
        url = "https://cran.r-project.org/src/contrib/Archive/AER/AER_1.2-8.tar.gz";
@@ -73,8 +72,7 @@ let
           zoo
           Formula;
       };
-    })
-  ];
+    }),
  
   tex = (pkgs.texlive.combine {
     inherit (pkgs.texlive) 
@@ -91,7 +89,7 @@ let
   };
  
   wrapped_pkgs = pkgs.rstudioWrapper.override {
-    packages = [ git_archive_pkgs rpkgs  ];
+    packages = [ housing fusen AER rpkgs  ];
   };
  
 in
@@ -105,6 +103,6 @@ pkgs.mkShell {
    LC_PAPER = "en_US.UTF-8";
    LC_MEASUREMENT = "en_US.UTF-8";
 
-  buildInputs = [ git_archive_pkgs rpkgs tex system_packages  wrapped_pkgs ];
+  buildInputs = [ housing fusen AER rpkgs tex system_packages  wrapped_pkgs ];
   
 }
diff --git a/tests/testthat/test-fetchers.R b/tests/testthat/test-fetchers.R
index 27873cb4..f40f75be 100644
--- a/tests/testthat/test-fetchers.R
+++ b/tests/testthat/test-fetchers.R
@@ -8,7 +8,7 @@ testthat::test_that("Test fetchgit works", {
         commit = "1c860959310b80e67c41f7bbdc3e84cef00df18e"
       )
     ),
-    "\n    (pkgs.rPackages.buildRPackage {\n      name = \"housing\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/rap4all/housing/\";\n        rev = \"1c860959310b80e67c41f7bbdc3e84cef00df18e\";\n        sha256 = \"sha256-s4KGtfKQ7hL0sfDhGb4BpBpspfefBN6hf+XlslqyEn4=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          dplyr\n          ggplot2\n          janitor\n          purrr\n          readxl\n          rlang\n          rvest\n          stringr\n          tidyr;\n      };\n    })\n"
+"\n    housing = (pkgs.rPackages.buildRPackage {\n      name = \"housing\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/rap4all/housing/\";\n        rev = \"1c860959310b80e67c41f7bbdc3e84cef00df18e\";\n        sha256 = \"sha256-s4KGtfKQ7hL0sfDhGb4BpBpspfefBN6hf+XlslqyEn4=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          dplyr\n          ggplot2\n          janitor\n          purrr\n          readxl\n          rlang\n          rvest\n          stringr\n          tidyr;\n      };\n    });\n"
   )
 })
 
@@ -35,7 +35,7 @@ testthat::test_that("Test fetchgit works with gitlab packages", {
         commit = "9442aa63d352d3c900f1c6f5a06f7930cdf702c4"
       )
     ),
-    "\n    (pkgs.rPackages.buildRPackage {\n      name = \"housing\";\n      src = pkgs.fetchgit {\n        url = \"https://gitlab.com/b-rodrigues/housing/\";\n        rev = \"9442aa63d352d3c900f1c6f5a06f7930cdf702c4\";\n        sha256 = \"sha256-3V9XbNbq/YpbgnzkEu3XH7QKSDY8yNNd1vpOeR9ER0w=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          dplyr\n          ggplot2\n          janitor\n          purrr\n          readxl\n          rlang\n          rvest\n          stringr\n          tidyr;\n      };\n    })\n"
+"\n    housing = (pkgs.rPackages.buildRPackage {\n      name = \"housing\";\n      src = pkgs.fetchgit {\n        url = \"https://gitlab.com/b-rodrigues/housing/\";\n        rev = \"9442aa63d352d3c900f1c6f5a06f7930cdf702c4\";\n        sha256 = \"sha256-3V9XbNbq/YpbgnzkEu3XH7QKSDY8yNNd1vpOeR9ER0w=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          dplyr\n          ggplot2\n          janitor\n          purrr\n          readxl\n          rlang\n          rvest\n          stringr\n          tidyr;\n      };\n    });\n"
   )
 })
 
@@ -49,15 +49,15 @@ testthat::test_that("Test fetchgit works with packages with empty imports", {
         commit = "48ceefdfb4858743454ede71d19999c2e6b38ed2"
       )
     ),
-    "\n    (pkgs.rPackages.buildRPackage {\n      name = \"helloworld\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/jrosell/helloworld/\";\n        rev = \"48ceefdfb4858743454ede71d19999c2e6b38ed2\";\n        sha256 = \"sha256-vaO7ItKMO6PfvNDhWNDdw5ST/K081HplyW3RoQhNsEs=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) ;\n      };\n    })\n"
+"\n    helloworld = (pkgs.rPackages.buildRPackage {\n      name = \"helloworld\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/jrosell/helloworld/\";\n        rev = \"48ceefdfb4858743454ede71d19999c2e6b38ed2\";\n        sha256 = \"sha256-vaO7ItKMO6PfvNDhWNDdw5ST/K081HplyW3RoQhNsEs=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) ;\n      };\n    });\n"
   )
 })
 
 testthat::test_that("Test fetchzip works", {
   testthat::skip_on_cran()
   testthat::expect_equal(
-    fetchzip("AER@1.2-8"),
-    "\n    (pkgs.rPackages.buildRPackage {\n      name = \"AER\";\n      src = pkgs.fetchzip {\n       url = \"https://cran.r-project.org/src/contrib/Archive/AER/AER_1.2-8.tar.gz\";\n       sha256 = \"sha256-OqxXcnUX/2C6wfD5fuNayc8OU+mstI3tt4eBVGQZ2S0=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          car\n          lmtest\n          sandwich\n          survival\n          zoo\n          Formula;\n      };\n    })\n"
+              fetchzip("AER@1.2-8"),
+"\n    AER = (pkgs.rPackages.buildRPackage {\n      name = \"AER\";\n      src = pkgs.fetchzip {\n       url = \"https://cran.r-project.org/src/contrib/Archive/AER/AER_1.2-8.tar.gz\";\n       sha256 = \"sha256-OqxXcnUX/2C6wfD5fuNayc8OU+mstI3tt4eBVGQZ2S0=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          car\n          lmtest\n          sandwich\n          survival\n          zoo\n          Formula;\n      };\n    }),\n"
   )
 })
 
@@ -86,7 +86,7 @@ testthat::test_that("Test fetchgits", {
         )
       )
     ),
-    "\n    (pkgs.rPackages.buildRPackage {\n      name = \"fusen\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/ThinkR-open/fusen\";\n        rev = \"d617172447d2947efb20ad6a4463742b8a5d79dc\";\n        sha256 = \"sha256-TOHA1ymLUSgZMYIA1a2yvuv0799svaDOl3zOhNRxcmw=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          attachment\n          cli\n          desc\n          devtools\n          glue\n          here\n          magrittr\n          parsermd\n          roxygen2\n          stringi\n          tibble\n          tidyr\n          usethis\n          yaml;\n      };\n    })\n\n\n    (pkgs.rPackages.buildRPackage {\n      name = \"housing\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/rap4all/housing/\";\n        rev = \"1c860959310b80e67c41f7bbdc3e84cef00df18e\";\n        sha256 = \"sha256-s4KGtfKQ7hL0sfDhGb4BpBpspfefBN6hf+XlslqyEn4=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          dplyr\n          ggplot2\n          janitor\n          purrr\n          readxl\n          rlang\n          rvest\n          stringr\n          tidyr;\n      };\n    })\n"
+"\n    fusen = (pkgs.rPackages.buildRPackage {\n      name = \"fusen\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/ThinkR-open/fusen\";\n        rev = \"d617172447d2947efb20ad6a4463742b8a5d79dc\";\n        sha256 = \"sha256-TOHA1ymLUSgZMYIA1a2yvuv0799svaDOl3zOhNRxcmw=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          attachment\n          cli\n          desc\n          devtools\n          glue\n          here\n          magrittr\n          parsermd\n          roxygen2\n          stringi\n          tibble\n          tidyr\n          usethis\n          yaml;\n      };\n    });\n\n\n    housing = (pkgs.rPackages.buildRPackage {\n      name = \"housing\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/rap4all/housing/\";\n        rev = \"1c860959310b80e67c41f7bbdc3e84cef00df18e\";\n        sha256 = \"sha256-s4KGtfKQ7hL0sfDhGb4BpBpspfefBN6hf+XlslqyEn4=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          dplyr\n          ggplot2\n          janitor\n          purrr\n          readxl\n          rlang\n          rvest\n          stringr\n          tidyr;\n      };\n    });\n"
   )
 })
 
@@ -96,11 +96,10 @@ testthat::test_that("Test fetchzips works", {
     fetchzips(
       c("dplyr@0.8.0", "AER@1.2-8")
     ),
-    "\n    (pkgs.rPackages.buildRPackage {\n      name = \"AER\";\n      src = pkgs.fetchzip {\n       url = \"https://cran.r-project.org/src/contrib/Archive/AER/AER_1.2-8.tar.gz\";\n       sha256 = \"sha256-OqxXcnUX/2C6wfD5fuNayc8OU+mstI3tt4eBVGQZ2S0=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          car\n          lmtest\n          sandwich\n          survival\n          zoo\n          Formula;\n      };\n    })\n\n\n    (pkgs.rPackages.buildRPackage {\n      name = \"dplyr\";\n      src = pkgs.fetchzip {\n       url = \"https://cran.r-project.org/src/contrib/Archive/dplyr/dplyr_0.8.0.tar.gz\";\n       sha256 = \"sha256-f30raalLd9KoZKZSxeTN71PG6BczXRIiP6g7EZeH09U=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          assertthat\n          glue\n          magrittr\n          pkgconfig\n          R6\n          Rcpp\n          rlang\n          tibble\n          tidyselect\n          BH\n          plogr;\n      };\n    })\n"
+"\n    AER = (pkgs.rPackages.buildRPackage {\n      name = \"AER\";\n      src = pkgs.fetchzip {\n       url = \"https://cran.r-project.org/src/contrib/Archive/AER/AER_1.2-8.tar.gz\";\n       sha256 = \"sha256-OqxXcnUX/2C6wfD5fuNayc8OU+mstI3tt4eBVGQZ2S0=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          car\n          lmtest\n          sandwich\n          survival\n          zoo\n          Formula;\n      };\n    }),\n\n\n    dplyr = (pkgs.rPackages.buildRPackage {\n      name = \"dplyr\";\n      src = pkgs.fetchzip {\n       url = \"https://cran.r-project.org/src/contrib/Archive/dplyr/dplyr_0.8.0.tar.gz\";\n       sha256 = \"sha256-f30raalLd9KoZKZSxeTN71PG6BczXRIiP6g7EZeH09U=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          assertthat\n          glue\n          magrittr\n          pkgconfig\n          R6\n          Rcpp\n          rlang\n          tibble\n          tidyselect\n          BH\n          plogr;\n      };\n    }),\n"
   )
 })
 
-
 testthat::test_that("Test fetchpkgs works", {
   testthat::skip_on_cran()
   testthat::expect_equal(
@@ -119,6 +118,6 @@ testthat::test_that("Test fetchpkgs works", {
       ),
       archive_pkgs = c("AER@1.2-8", "dplyr@0.8.0")
     ),
-    "\n  git_archive_pkgs = [\n    (pkgs.rPackages.buildRPackage {\n      name = \"fusen\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/ThinkR-open/fusen\";\n        rev = \"d617172447d2947efb20ad6a4463742b8a5d79dc\";\n        sha256 = \"sha256-TOHA1ymLUSgZMYIA1a2yvuv0799svaDOl3zOhNRxcmw=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          attachment\n          cli\n          desc\n          devtools\n          glue\n          here\n          magrittr\n          parsermd\n          roxygen2\n          stringi\n          tibble\n          tidyr\n          usethis\n          yaml;\n      };\n    })\n\n\n    (pkgs.rPackages.buildRPackage {\n      name = \"housing\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/rap4all/housing/\";\n        rev = \"1c860959310b80e67c41f7bbdc3e84cef00df18e\";\n        sha256 = \"sha256-s4KGtfKQ7hL0sfDhGb4BpBpspfefBN6hf+XlslqyEn4=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          dplyr\n          ggplot2\n          janitor\n          purrr\n          readxl\n          rlang\n          rvest\n          stringr\n          tidyr;\n      };\n    })\n \n    (pkgs.rPackages.buildRPackage {\n      name = \"AER\";\n      src = pkgs.fetchzip {\n       url = \"https://cran.r-project.org/src/contrib/Archive/AER/AER_1.2-8.tar.gz\";\n       sha256 = \"sha256-OqxXcnUX/2C6wfD5fuNayc8OU+mstI3tt4eBVGQZ2S0=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          car\n          lmtest\n          sandwich\n          survival\n          zoo\n          Formula;\n      };\n    })\n\n\n    (pkgs.rPackages.buildRPackage {\n      name = \"dplyr\";\n      src = pkgs.fetchzip {\n       url = \"https://cran.r-project.org/src/contrib/Archive/dplyr/dplyr_0.8.0.tar.gz\";\n       sha256 = \"sha256-f30raalLd9KoZKZSxeTN71PG6BczXRIiP6g7EZeH09U=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          assertthat\n          glue\n          magrittr\n          pkgconfig\n          R6\n          Rcpp\n          rlang\n          tibble\n          tidyselect\n          BH\n          plogr;\n      };\n    })\n  ];\n"
+"\n    fusen = (pkgs.rPackages.buildRPackage {\n      name = \"fusen\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/ThinkR-open/fusen\";\n        rev = \"d617172447d2947efb20ad6a4463742b8a5d79dc\";\n        sha256 = \"sha256-TOHA1ymLUSgZMYIA1a2yvuv0799svaDOl3zOhNRxcmw=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          attachment\n          cli\n          desc\n          devtools\n          glue\n          here\n          magrittr\n          parsermd\n          roxygen2\n          stringi\n          tibble\n          tidyr\n          usethis\n          yaml;\n      };\n    });\n\n\n    housing = (pkgs.rPackages.buildRPackage {\n      name = \"housing\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/rap4all/housing/\";\n        rev = \"1c860959310b80e67c41f7bbdc3e84cef00df18e\";\n        sha256 = \"sha256-s4KGtfKQ7hL0sfDhGb4BpBpspfefBN6hf+XlslqyEn4=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          dplyr\n          ggplot2\n          janitor\n          purrr\n          readxl\n          rlang\n          rvest\n          stringr\n          tidyr;\n      };\n    });\n \n    AER = (pkgs.rPackages.buildRPackage {\n      name = \"AER\";\n      src = pkgs.fetchzip {\n       url = \"https://cran.r-project.org/src/contrib/Archive/AER/AER_1.2-8.tar.gz\";\n       sha256 = \"sha256-OqxXcnUX/2C6wfD5fuNayc8OU+mstI3tt4eBVGQZ2S0=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          car\n          lmtest\n          sandwich\n          survival\n          zoo\n          Formula;\n      };\n    }),\n\n\n    dplyr = (pkgs.rPackages.buildRPackage {\n      name = \"dplyr\";\n      src = pkgs.fetchzip {\n       url = \"https://cran.r-project.org/src/contrib/Archive/dplyr/dplyr_0.8.0.tar.gz\";\n       sha256 = \"sha256-f30raalLd9KoZKZSxeTN71PG6BczXRIiP6g7EZeH09U=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          assertthat\n          glue\n          magrittr\n          pkgconfig\n          R6\n          Rcpp\n          rlang\n          tibble\n          tidyselect\n          BH\n          plogr;\n      };\n    }),\n"
   )
 })
diff --git a/tests/testthat/test-get_sri_hash_deps.R b/tests/testthat/test-get_sri_hash_deps.R
index f280943f..7cbfe692 100644
--- a/tests/testthat/test-get_sri_hash_deps.R
+++ b/tests/testthat/test-get_sri_hash_deps.R
@@ -12,7 +12,7 @@ testthat::test_that("get_sri_hash_deps returns correct sri hash and dependencies
           "dplyr", "ggplot2", "janitor", "purrr",
           "readxl", "rlang", "rvest", "stringr", "tidyr"
         ),
-        "remotes" = character(0)
+        "remotes" = NULL
       )
     )
   )

From 0eacddd41a322bb11d9f1e749ec3990e837a355b Mon Sep 17 00:00:00 2001
From: b-rodrigues <b-rodrigues@users.noreply.github.com>
Date: Sun, 5 Jan 2025 14:54:06 +0000
Subject: [PATCH 14/31] Style via {styler}

---
 tests/testthat/test-fetchers.R | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/tests/testthat/test-fetchers.R b/tests/testthat/test-fetchers.R
index f40f75be..93a8c0cc 100644
--- a/tests/testthat/test-fetchers.R
+++ b/tests/testthat/test-fetchers.R
@@ -8,7 +8,7 @@ testthat::test_that("Test fetchgit works", {
         commit = "1c860959310b80e67c41f7bbdc3e84cef00df18e"
       )
     ),
-"\n    housing = (pkgs.rPackages.buildRPackage {\n      name = \"housing\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/rap4all/housing/\";\n        rev = \"1c860959310b80e67c41f7bbdc3e84cef00df18e\";\n        sha256 = \"sha256-s4KGtfKQ7hL0sfDhGb4BpBpspfefBN6hf+XlslqyEn4=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          dplyr\n          ggplot2\n          janitor\n          purrr\n          readxl\n          rlang\n          rvest\n          stringr\n          tidyr;\n      };\n    });\n"
+    "\n    housing = (pkgs.rPackages.buildRPackage {\n      name = \"housing\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/rap4all/housing/\";\n        rev = \"1c860959310b80e67c41f7bbdc3e84cef00df18e\";\n        sha256 = \"sha256-s4KGtfKQ7hL0sfDhGb4BpBpspfefBN6hf+XlslqyEn4=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          dplyr\n          ggplot2\n          janitor\n          purrr\n          readxl\n          rlang\n          rvest\n          stringr\n          tidyr;\n      };\n    });\n"
   )
 })
 
@@ -35,7 +35,7 @@ testthat::test_that("Test fetchgit works with gitlab packages", {
         commit = "9442aa63d352d3c900f1c6f5a06f7930cdf702c4"
       )
     ),
-"\n    housing = (pkgs.rPackages.buildRPackage {\n      name = \"housing\";\n      src = pkgs.fetchgit {\n        url = \"https://gitlab.com/b-rodrigues/housing/\";\n        rev = \"9442aa63d352d3c900f1c6f5a06f7930cdf702c4\";\n        sha256 = \"sha256-3V9XbNbq/YpbgnzkEu3XH7QKSDY8yNNd1vpOeR9ER0w=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          dplyr\n          ggplot2\n          janitor\n          purrr\n          readxl\n          rlang\n          rvest\n          stringr\n          tidyr;\n      };\n    });\n"
+    "\n    housing = (pkgs.rPackages.buildRPackage {\n      name = \"housing\";\n      src = pkgs.fetchgit {\n        url = \"https://gitlab.com/b-rodrigues/housing/\";\n        rev = \"9442aa63d352d3c900f1c6f5a06f7930cdf702c4\";\n        sha256 = \"sha256-3V9XbNbq/YpbgnzkEu3XH7QKSDY8yNNd1vpOeR9ER0w=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          dplyr\n          ggplot2\n          janitor\n          purrr\n          readxl\n          rlang\n          rvest\n          stringr\n          tidyr;\n      };\n    });\n"
   )
 })
 
@@ -49,15 +49,15 @@ testthat::test_that("Test fetchgit works with packages with empty imports", {
         commit = "48ceefdfb4858743454ede71d19999c2e6b38ed2"
       )
     ),
-"\n    helloworld = (pkgs.rPackages.buildRPackage {\n      name = \"helloworld\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/jrosell/helloworld/\";\n        rev = \"48ceefdfb4858743454ede71d19999c2e6b38ed2\";\n        sha256 = \"sha256-vaO7ItKMO6PfvNDhWNDdw5ST/K081HplyW3RoQhNsEs=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) ;\n      };\n    });\n"
+    "\n    helloworld = (pkgs.rPackages.buildRPackage {\n      name = \"helloworld\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/jrosell/helloworld/\";\n        rev = \"48ceefdfb4858743454ede71d19999c2e6b38ed2\";\n        sha256 = \"sha256-vaO7ItKMO6PfvNDhWNDdw5ST/K081HplyW3RoQhNsEs=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) ;\n      };\n    });\n"
   )
 })
 
 testthat::test_that("Test fetchzip works", {
   testthat::skip_on_cran()
   testthat::expect_equal(
-              fetchzip("AER@1.2-8"),
-"\n    AER = (pkgs.rPackages.buildRPackage {\n      name = \"AER\";\n      src = pkgs.fetchzip {\n       url = \"https://cran.r-project.org/src/contrib/Archive/AER/AER_1.2-8.tar.gz\";\n       sha256 = \"sha256-OqxXcnUX/2C6wfD5fuNayc8OU+mstI3tt4eBVGQZ2S0=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          car\n          lmtest\n          sandwich\n          survival\n          zoo\n          Formula;\n      };\n    }),\n"
+    fetchzip("AER@1.2-8"),
+    "\n    AER = (pkgs.rPackages.buildRPackage {\n      name = \"AER\";\n      src = pkgs.fetchzip {\n       url = \"https://cran.r-project.org/src/contrib/Archive/AER/AER_1.2-8.tar.gz\";\n       sha256 = \"sha256-OqxXcnUX/2C6wfD5fuNayc8OU+mstI3tt4eBVGQZ2S0=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          car\n          lmtest\n          sandwich\n          survival\n          zoo\n          Formula;\n      };\n    }),\n"
   )
 })
 
@@ -86,7 +86,7 @@ testthat::test_that("Test fetchgits", {
         )
       )
     ),
-"\n    fusen = (pkgs.rPackages.buildRPackage {\n      name = \"fusen\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/ThinkR-open/fusen\";\n        rev = \"d617172447d2947efb20ad6a4463742b8a5d79dc\";\n        sha256 = \"sha256-TOHA1ymLUSgZMYIA1a2yvuv0799svaDOl3zOhNRxcmw=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          attachment\n          cli\n          desc\n          devtools\n          glue\n          here\n          magrittr\n          parsermd\n          roxygen2\n          stringi\n          tibble\n          tidyr\n          usethis\n          yaml;\n      };\n    });\n\n\n    housing = (pkgs.rPackages.buildRPackage {\n      name = \"housing\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/rap4all/housing/\";\n        rev = \"1c860959310b80e67c41f7bbdc3e84cef00df18e\";\n        sha256 = \"sha256-s4KGtfKQ7hL0sfDhGb4BpBpspfefBN6hf+XlslqyEn4=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          dplyr\n          ggplot2\n          janitor\n          purrr\n          readxl\n          rlang\n          rvest\n          stringr\n          tidyr;\n      };\n    });\n"
+    "\n    fusen = (pkgs.rPackages.buildRPackage {\n      name = \"fusen\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/ThinkR-open/fusen\";\n        rev = \"d617172447d2947efb20ad6a4463742b8a5d79dc\";\n        sha256 = \"sha256-TOHA1ymLUSgZMYIA1a2yvuv0799svaDOl3zOhNRxcmw=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          attachment\n          cli\n          desc\n          devtools\n          glue\n          here\n          magrittr\n          parsermd\n          roxygen2\n          stringi\n          tibble\n          tidyr\n          usethis\n          yaml;\n      };\n    });\n\n\n    housing = (pkgs.rPackages.buildRPackage {\n      name = \"housing\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/rap4all/housing/\";\n        rev = \"1c860959310b80e67c41f7bbdc3e84cef00df18e\";\n        sha256 = \"sha256-s4KGtfKQ7hL0sfDhGb4BpBpspfefBN6hf+XlslqyEn4=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          dplyr\n          ggplot2\n          janitor\n          purrr\n          readxl\n          rlang\n          rvest\n          stringr\n          tidyr;\n      };\n    });\n"
   )
 })
 
@@ -96,7 +96,7 @@ testthat::test_that("Test fetchzips works", {
     fetchzips(
       c("dplyr@0.8.0", "AER@1.2-8")
     ),
-"\n    AER = (pkgs.rPackages.buildRPackage {\n      name = \"AER\";\n      src = pkgs.fetchzip {\n       url = \"https://cran.r-project.org/src/contrib/Archive/AER/AER_1.2-8.tar.gz\";\n       sha256 = \"sha256-OqxXcnUX/2C6wfD5fuNayc8OU+mstI3tt4eBVGQZ2S0=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          car\n          lmtest\n          sandwich\n          survival\n          zoo\n          Formula;\n      };\n    }),\n\n\n    dplyr = (pkgs.rPackages.buildRPackage {\n      name = \"dplyr\";\n      src = pkgs.fetchzip {\n       url = \"https://cran.r-project.org/src/contrib/Archive/dplyr/dplyr_0.8.0.tar.gz\";\n       sha256 = \"sha256-f30raalLd9KoZKZSxeTN71PG6BczXRIiP6g7EZeH09U=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          assertthat\n          glue\n          magrittr\n          pkgconfig\n          R6\n          Rcpp\n          rlang\n          tibble\n          tidyselect\n          BH\n          plogr;\n      };\n    }),\n"
+    "\n    AER = (pkgs.rPackages.buildRPackage {\n      name = \"AER\";\n      src = pkgs.fetchzip {\n       url = \"https://cran.r-project.org/src/contrib/Archive/AER/AER_1.2-8.tar.gz\";\n       sha256 = \"sha256-OqxXcnUX/2C6wfD5fuNayc8OU+mstI3tt4eBVGQZ2S0=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          car\n          lmtest\n          sandwich\n          survival\n          zoo\n          Formula;\n      };\n    }),\n\n\n    dplyr = (pkgs.rPackages.buildRPackage {\n      name = \"dplyr\";\n      src = pkgs.fetchzip {\n       url = \"https://cran.r-project.org/src/contrib/Archive/dplyr/dplyr_0.8.0.tar.gz\";\n       sha256 = \"sha256-f30raalLd9KoZKZSxeTN71PG6BczXRIiP6g7EZeH09U=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          assertthat\n          glue\n          magrittr\n          pkgconfig\n          R6\n          Rcpp\n          rlang\n          tibble\n          tidyselect\n          BH\n          plogr;\n      };\n    }),\n"
   )
 })
 
@@ -118,6 +118,6 @@ testthat::test_that("Test fetchpkgs works", {
       ),
       archive_pkgs = c("AER@1.2-8", "dplyr@0.8.0")
     ),
-"\n    fusen = (pkgs.rPackages.buildRPackage {\n      name = \"fusen\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/ThinkR-open/fusen\";\n        rev = \"d617172447d2947efb20ad6a4463742b8a5d79dc\";\n        sha256 = \"sha256-TOHA1ymLUSgZMYIA1a2yvuv0799svaDOl3zOhNRxcmw=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          attachment\n          cli\n          desc\n          devtools\n          glue\n          here\n          magrittr\n          parsermd\n          roxygen2\n          stringi\n          tibble\n          tidyr\n          usethis\n          yaml;\n      };\n    });\n\n\n    housing = (pkgs.rPackages.buildRPackage {\n      name = \"housing\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/rap4all/housing/\";\n        rev = \"1c860959310b80e67c41f7bbdc3e84cef00df18e\";\n        sha256 = \"sha256-s4KGtfKQ7hL0sfDhGb4BpBpspfefBN6hf+XlslqyEn4=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          dplyr\n          ggplot2\n          janitor\n          purrr\n          readxl\n          rlang\n          rvest\n          stringr\n          tidyr;\n      };\n    });\n \n    AER = (pkgs.rPackages.buildRPackage {\n      name = \"AER\";\n      src = pkgs.fetchzip {\n       url = \"https://cran.r-project.org/src/contrib/Archive/AER/AER_1.2-8.tar.gz\";\n       sha256 = \"sha256-OqxXcnUX/2C6wfD5fuNayc8OU+mstI3tt4eBVGQZ2S0=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          car\n          lmtest\n          sandwich\n          survival\n          zoo\n          Formula;\n      };\n    }),\n\n\n    dplyr = (pkgs.rPackages.buildRPackage {\n      name = \"dplyr\";\n      src = pkgs.fetchzip {\n       url = \"https://cran.r-project.org/src/contrib/Archive/dplyr/dplyr_0.8.0.tar.gz\";\n       sha256 = \"sha256-f30raalLd9KoZKZSxeTN71PG6BczXRIiP6g7EZeH09U=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          assertthat\n          glue\n          magrittr\n          pkgconfig\n          R6\n          Rcpp\n          rlang\n          tibble\n          tidyselect\n          BH\n          plogr;\n      };\n    }),\n"
+    "\n    fusen = (pkgs.rPackages.buildRPackage {\n      name = \"fusen\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/ThinkR-open/fusen\";\n        rev = \"d617172447d2947efb20ad6a4463742b8a5d79dc\";\n        sha256 = \"sha256-TOHA1ymLUSgZMYIA1a2yvuv0799svaDOl3zOhNRxcmw=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          attachment\n          cli\n          desc\n          devtools\n          glue\n          here\n          magrittr\n          parsermd\n          roxygen2\n          stringi\n          tibble\n          tidyr\n          usethis\n          yaml;\n      };\n    });\n\n\n    housing = (pkgs.rPackages.buildRPackage {\n      name = \"housing\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/rap4all/housing/\";\n        rev = \"1c860959310b80e67c41f7bbdc3e84cef00df18e\";\n        sha256 = \"sha256-s4KGtfKQ7hL0sfDhGb4BpBpspfefBN6hf+XlslqyEn4=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          dplyr\n          ggplot2\n          janitor\n          purrr\n          readxl\n          rlang\n          rvest\n          stringr\n          tidyr;\n      };\n    });\n \n    AER = (pkgs.rPackages.buildRPackage {\n      name = \"AER\";\n      src = pkgs.fetchzip {\n       url = \"https://cran.r-project.org/src/contrib/Archive/AER/AER_1.2-8.tar.gz\";\n       sha256 = \"sha256-OqxXcnUX/2C6wfD5fuNayc8OU+mstI3tt4eBVGQZ2S0=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          car\n          lmtest\n          sandwich\n          survival\n          zoo\n          Formula;\n      };\n    }),\n\n\n    dplyr = (pkgs.rPackages.buildRPackage {\n      name = \"dplyr\";\n      src = pkgs.fetchzip {\n       url = \"https://cran.r-project.org/src/contrib/Archive/dplyr/dplyr_0.8.0.tar.gz\";\n       sha256 = \"sha256-f30raalLd9KoZKZSxeTN71PG6BczXRIiP6g7EZeH09U=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          assertthat\n          glue\n          magrittr\n          pkgconfig\n          R6\n          Rcpp\n          rlang\n          tibble\n          tidyselect\n          BH\n          plogr;\n      };\n    }),\n"
   )
 })

From 04c3028dc3058915cce13be9f3b051e2a851082c Mon Sep 17 00:00:00 2001
From: mischko <mhem@mailbox.org>
Date: Sun, 5 Jan 2025 16:14:37 +0100
Subject: [PATCH 15/31] try to fix double installation of remote packages

---
 R/fetchers.R | 22 +++++++++++++++++++++-
 1 file changed, 21 insertions(+), 1 deletion(-)

diff --git a/R/fetchers.R b/R/fetchers.R
index fe4a7ed6..4366168e 100644
--- a/R/fetchers.R
+++ b/R/fetchers.R
@@ -369,8 +369,28 @@ fetchzips <- function(archive_pkgs) {
 #' from the CRAN archives.
 #' @noRd
 fetchpkgs <- function(git_pkgs, archive_pkgs) {
-  paste(fetchgits(git_pkgs),
+  # This removes all packages that are already included
+  # because they are remote packages from another package
+  all_remote_package_names <- unlist(lapply(git_pkgs, get_remote))
+  package_names <- sapply(git_pkgs, `[[`, "package_name")
+  git_pkgs_corrected <- setdiff(package_names, all_remote_package_names)
+  paste(fetchgits(git_pkgs_corrected),
     fetchzips(archive_pkgs),
     collapse = "\n"
   )
 }
+
+#' get_remote Retrieves the names of remote dependencies for a given Git package
+#' @param git_pkg A list of three elements: "package_name", the name of the
+#'   package, "repo_url", the repository's URL, and "commit", the commit hash of
+#'   interest.
+#' @return A character vector containing the names of remote dependencies.
+#' @noRd
+get_remote <- function(git_pkg) {
+  repo_url <- git_pkg$repo_url
+  commit <- git_pkg$commit
+  output <- get_sri_hash_deps(repo_url, commit)
+  remotes <- output$deps$remotes
+  remote_package_names <- sapply(remotes, `[[`, "package_name")
+  return(remote_package_names)
+}
\ No newline at end of file

From 4e2f1145f3422bb45c2cea63e2074cdf7a0955ac Mon Sep 17 00:00:00 2001
From: Bruno Rodrigues <bruno@brodrigues.co>
Date: Sun, 5 Jan 2025 16:19:48 +0100
Subject: [PATCH 16/31] added tests for handling remote deps

---
 tests/testthat/test-fetchers.R | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/tests/testthat/test-fetchers.R b/tests/testthat/test-fetchers.R
index 93a8c0cc..e3043a5e 100644
--- a/tests/testthat/test-fetchers.R
+++ b/tests/testthat/test-fetchers.R
@@ -121,3 +121,32 @@ testthat::test_that("Test fetchpkgs works", {
     "\n    fusen = (pkgs.rPackages.buildRPackage {\n      name = \"fusen\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/ThinkR-open/fusen\";\n        rev = \"d617172447d2947efb20ad6a4463742b8a5d79dc\";\n        sha256 = \"sha256-TOHA1ymLUSgZMYIA1a2yvuv0799svaDOl3zOhNRxcmw=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          attachment\n          cli\n          desc\n          devtools\n          glue\n          here\n          magrittr\n          parsermd\n          roxygen2\n          stringi\n          tibble\n          tidyr\n          usethis\n          yaml;\n      };\n    });\n\n\n    housing = (pkgs.rPackages.buildRPackage {\n      name = \"housing\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/rap4all/housing/\";\n        rev = \"1c860959310b80e67c41f7bbdc3e84cef00df18e\";\n        sha256 = \"sha256-s4KGtfKQ7hL0sfDhGb4BpBpspfefBN6hf+XlslqyEn4=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          dplyr\n          ggplot2\n          janitor\n          purrr\n          readxl\n          rlang\n          rvest\n          stringr\n          tidyr;\n      };\n    });\n \n    AER = (pkgs.rPackages.buildRPackage {\n      name = \"AER\";\n      src = pkgs.fetchzip {\n       url = \"https://cran.r-project.org/src/contrib/Archive/AER/AER_1.2-8.tar.gz\";\n       sha256 = \"sha256-OqxXcnUX/2C6wfD5fuNayc8OU+mstI3tt4eBVGQZ2S0=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          car\n          lmtest\n          sandwich\n          survival\n          zoo\n          Formula;\n      };\n    }),\n\n\n    dplyr = (pkgs.rPackages.buildRPackage {\n      name = \"dplyr\";\n      src = pkgs.fetchzip {\n       url = \"https://cran.r-project.org/src/contrib/Archive/dplyr/dplyr_0.8.0.tar.gz\";\n       sha256 = \"sha256-f30raalLd9KoZKZSxeTN71PG6BczXRIiP6g7EZeH09U=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          assertthat\n          glue\n          magrittr\n          pkgconfig\n          R6\n          Rcpp\n          rlang\n          tibble\n          tidyselect\n          BH\n          plogr;\n      };\n    }),\n"
   )
 })
+
+testthat::test_that("Test fetchgit gets a package with several remote deps", {
+  testthat::skip_on_cran()
+  testthat::expect_equal(
+    fetchgit(
+      list(
+        package_name = "lookup",
+        repo_url = "https://github.com/jimhester/lookup/",
+        commit = "eba63db477dd2f20153b75e2949eb333a36cccfc"
+      )
+    ),
+"\n    httr2 = (pkgs.rPackages.buildRPackage {\n      name = \"httr2\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/r-lib/httr2\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-rPMn+MvN/KCnhulS0Itv2g58fRYQw75SBJC15cSBxBI=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          cli\n          curl\n          glue\n          lifecycle\n          magrittr\n          openssl\n          R6\n          rappdirs\n          rlang\n          vctrs\n          withr;\n      };\n    });\n\n    gh = (pkgs.rPackages.buildRPackage {\n      name = \"gh\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/gaborcsardi/gh\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-VpxFIfUEk0PudytQ3boMhEJhT0AnelWkSU++WD/HAyo=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          cli\n          gitcreds\n          glue\n          ini\n          jsonlite\n          lifecycle\n          rlang;\n      } ++ [ httr2 ];\n    });\n\n\n    highlite = (pkgs.rPackages.buildRPackage {\n      name = \"highlite\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/jimhester/highlite\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-lkWMlAi75MYxiBUYnLwxLK9ApXkWanA4Mt7g4qtLpxM=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          Rcpp\n          BH;\n      };\n    });\n\n\n    memoise = (pkgs.rPackages.buildRPackage {\n      name = \"memoise\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/hadley/memoise\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-FDMNgrgctzkN8dXKRoWsOKe3tXxmm8Cqdu/Sh6WKx/Q=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          rlang\n          cachem;\n      };\n    });\n\n    lookup = (pkgs.rPackages.buildRPackage {\n      name = \"lookup\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/jimhester/lookup/\";\n        rev = \"eba63db477dd2f20153b75e2949eb333a36cccfc\";\n        sha256 = \"sha256-arl7LVxL8xGUW3LhuDCSUjcfswX0rdofL/7v8Klw8FM=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          Rcpp\n          codetools\n          crayon\n          rex\n          jsonlite\n          rstudioapi\n          withr\n          httr;\n      } ++ [ highlite gh memoise ];\n    });\n"
+  )
+})
+
+
+testthat::test_that("Test fetchgit gets a package with one remote dep", {
+  testthat::skip_on_cran()
+  testthat::expect_equal(
+    fetchgit(
+      list(
+        package_name = "scMisc",
+        repo_url = "https://github.com/mihem/scMisc/",
+        commit = "e2ebddcb779b935551f14216514c0429616fc91d"
+      )
+    ),
+"\n    enrichR = (pkgs.rPackages.buildRPackage {\n      name = \"enrichR\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/wjawaid/enrichR\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-Jm6Z46ARyp+geSY4RLb/x9zV6uvlyjnFdLh4/c6uGoI=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          httr\n          curl\n          rjson\n          ggplot2\n          WriteXLS;\n      };\n    });\n\n    scMisc = (pkgs.rPackages.buildRPackage {\n      name = \"scMisc\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/mihem/scMisc/\";\n        rev = \"e2ebddcb779b935551f14216514c0429616fc91d\";\n        sha256 = \"sha256-Atmr+vGfJxNc5HK+UgpnSIeZ1fYKWEzD3Dt2va1xoFE=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          Seurat\n          readr\n          glue\n          viridis\n          ggplot2\n          pheatmap\n          homologene\n          dplyr\n          tibble\n          magrittr\n          clustifyr\n          ggrepel\n          writexl\n          ggsignif\n          patchwork\n          rstatix\n          readxl\n          tidyr\n          speckle\n          limma\n          RColorBrewer\n          factoextra\n          FactoMineR\n          Matrix\n          ggpubr\n          tidyselect\n          stringr\n          forcats;\n      } ++ [ enrichR ];\n    });\n"
+  )
+})

From f4483a54c51655246441a73a60398cfd96569090 Mon Sep 17 00:00:00 2001
From: b-rodrigues <b-rodrigues@users.noreply.github.com>
Date: Sun, 5 Jan 2025 15:23:07 +0000
Subject: [PATCH 17/31] Style via {styler}

---
 tests/testthat/test-fetchers.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-fetchers.R b/tests/testthat/test-fetchers.R
index e3043a5e..c5b95a13 100644
--- a/tests/testthat/test-fetchers.R
+++ b/tests/testthat/test-fetchers.R
@@ -132,7 +132,7 @@ testthat::test_that("Test fetchgit gets a package with several remote deps", {
         commit = "eba63db477dd2f20153b75e2949eb333a36cccfc"
       )
     ),
-"\n    httr2 = (pkgs.rPackages.buildRPackage {\n      name = \"httr2\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/r-lib/httr2\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-rPMn+MvN/KCnhulS0Itv2g58fRYQw75SBJC15cSBxBI=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          cli\n          curl\n          glue\n          lifecycle\n          magrittr\n          openssl\n          R6\n          rappdirs\n          rlang\n          vctrs\n          withr;\n      };\n    });\n\n    gh = (pkgs.rPackages.buildRPackage {\n      name = \"gh\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/gaborcsardi/gh\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-VpxFIfUEk0PudytQ3boMhEJhT0AnelWkSU++WD/HAyo=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          cli\n          gitcreds\n          glue\n          ini\n          jsonlite\n          lifecycle\n          rlang;\n      } ++ [ httr2 ];\n    });\n\n\n    highlite = (pkgs.rPackages.buildRPackage {\n      name = \"highlite\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/jimhester/highlite\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-lkWMlAi75MYxiBUYnLwxLK9ApXkWanA4Mt7g4qtLpxM=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          Rcpp\n          BH;\n      };\n    });\n\n\n    memoise = (pkgs.rPackages.buildRPackage {\n      name = \"memoise\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/hadley/memoise\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-FDMNgrgctzkN8dXKRoWsOKe3tXxmm8Cqdu/Sh6WKx/Q=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          rlang\n          cachem;\n      };\n    });\n\n    lookup = (pkgs.rPackages.buildRPackage {\n      name = \"lookup\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/jimhester/lookup/\";\n        rev = \"eba63db477dd2f20153b75e2949eb333a36cccfc\";\n        sha256 = \"sha256-arl7LVxL8xGUW3LhuDCSUjcfswX0rdofL/7v8Klw8FM=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          Rcpp\n          codetools\n          crayon\n          rex\n          jsonlite\n          rstudioapi\n          withr\n          httr;\n      } ++ [ highlite gh memoise ];\n    });\n"
+    "\n    httr2 = (pkgs.rPackages.buildRPackage {\n      name = \"httr2\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/r-lib/httr2\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-rPMn+MvN/KCnhulS0Itv2g58fRYQw75SBJC15cSBxBI=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          cli\n          curl\n          glue\n          lifecycle\n          magrittr\n          openssl\n          R6\n          rappdirs\n          rlang\n          vctrs\n          withr;\n      };\n    });\n\n    gh = (pkgs.rPackages.buildRPackage {\n      name = \"gh\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/gaborcsardi/gh\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-VpxFIfUEk0PudytQ3boMhEJhT0AnelWkSU++WD/HAyo=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          cli\n          gitcreds\n          glue\n          ini\n          jsonlite\n          lifecycle\n          rlang;\n      } ++ [ httr2 ];\n    });\n\n\n    highlite = (pkgs.rPackages.buildRPackage {\n      name = \"highlite\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/jimhester/highlite\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-lkWMlAi75MYxiBUYnLwxLK9ApXkWanA4Mt7g4qtLpxM=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          Rcpp\n          BH;\n      };\n    });\n\n\n    memoise = (pkgs.rPackages.buildRPackage {\n      name = \"memoise\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/hadley/memoise\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-FDMNgrgctzkN8dXKRoWsOKe3tXxmm8Cqdu/Sh6WKx/Q=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          rlang\n          cachem;\n      };\n    });\n\n    lookup = (pkgs.rPackages.buildRPackage {\n      name = \"lookup\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/jimhester/lookup/\";\n        rev = \"eba63db477dd2f20153b75e2949eb333a36cccfc\";\n        sha256 = \"sha256-arl7LVxL8xGUW3LhuDCSUjcfswX0rdofL/7v8Klw8FM=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          Rcpp\n          codetools\n          crayon\n          rex\n          jsonlite\n          rstudioapi\n          withr\n          httr;\n      } ++ [ highlite gh memoise ];\n    });\n"
   )
 })
 
@@ -147,6 +147,6 @@ testthat::test_that("Test fetchgit gets a package with one remote dep", {
         commit = "e2ebddcb779b935551f14216514c0429616fc91d"
       )
     ),
-"\n    enrichR = (pkgs.rPackages.buildRPackage {\n      name = \"enrichR\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/wjawaid/enrichR\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-Jm6Z46ARyp+geSY4RLb/x9zV6uvlyjnFdLh4/c6uGoI=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          httr\n          curl\n          rjson\n          ggplot2\n          WriteXLS;\n      };\n    });\n\n    scMisc = (pkgs.rPackages.buildRPackage {\n      name = \"scMisc\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/mihem/scMisc/\";\n        rev = \"e2ebddcb779b935551f14216514c0429616fc91d\";\n        sha256 = \"sha256-Atmr+vGfJxNc5HK+UgpnSIeZ1fYKWEzD3Dt2va1xoFE=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          Seurat\n          readr\n          glue\n          viridis\n          ggplot2\n          pheatmap\n          homologene\n          dplyr\n          tibble\n          magrittr\n          clustifyr\n          ggrepel\n          writexl\n          ggsignif\n          patchwork\n          rstatix\n          readxl\n          tidyr\n          speckle\n          limma\n          RColorBrewer\n          factoextra\n          FactoMineR\n          Matrix\n          ggpubr\n          tidyselect\n          stringr\n          forcats;\n      } ++ [ enrichR ];\n    });\n"
+    "\n    enrichR = (pkgs.rPackages.buildRPackage {\n      name = \"enrichR\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/wjawaid/enrichR\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-Jm6Z46ARyp+geSY4RLb/x9zV6uvlyjnFdLh4/c6uGoI=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          httr\n          curl\n          rjson\n          ggplot2\n          WriteXLS;\n      };\n    });\n\n    scMisc = (pkgs.rPackages.buildRPackage {\n      name = \"scMisc\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/mihem/scMisc/\";\n        rev = \"e2ebddcb779b935551f14216514c0429616fc91d\";\n        sha256 = \"sha256-Atmr+vGfJxNc5HK+UgpnSIeZ1fYKWEzD3Dt2va1xoFE=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          Seurat\n          readr\n          glue\n          viridis\n          ggplot2\n          pheatmap\n          homologene\n          dplyr\n          tibble\n          magrittr\n          clustifyr\n          ggrepel\n          writexl\n          ggsignif\n          patchwork\n          rstatix\n          readxl\n          tidyr\n          speckle\n          limma\n          RColorBrewer\n          factoextra\n          FactoMineR\n          Matrix\n          ggpubr\n          tidyselect\n          stringr\n          forcats;\n      } ++ [ enrichR ];\n    });\n"
   )
 })

From 388beb5f4a4656f73bbb8d44030b2867a1969fdc Mon Sep 17 00:00:00 2001
From: mischko <mhem@mailbox.org>
Date: Sun, 5 Jan 2025 16:34:55 +0100
Subject: [PATCH 18/31] try to get git_pgk expression instead of name

---
 R/fetchers.R | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/R/fetchers.R b/R/fetchers.R
index 4366168e..a2550a37 100644
--- a/R/fetchers.R
+++ b/R/fetchers.R
@@ -371,9 +371,10 @@ fetchzips <- function(archive_pkgs) {
 fetchpkgs <- function(git_pkgs, archive_pkgs) {
   # This removes all packages that are already included
   # because they are remote packages from another package
-  all_remote_package_names <- unlist(lapply(git_pkgs, get_remote))
-  package_names <- sapply(git_pkgs, `[[`, "package_name")
-  git_pkgs_corrected <- setdiff(package_names, all_remote_package_names)
+  remote_package_names <- unlist(lapply(git_pkgs, get_remote))
+  git_pkgs_names <- sapply(git_pkgs, `[[`, "package_name")
+  git_pkgs_name_corrected <- setdiff(git_pkgs_names, remote_package_names)
+  git_pkgs_corrected <- git_pkgs[sapply(git_pkgs, function(pkg) pkg$package_name %in% git_pkgs_name_corrected)]
   paste(fetchgits(git_pkgs_corrected),
     fetchzips(archive_pkgs),
     collapse = "\n"

From 5f2d536f62cdf0928dbcaf5027ae267b33a09532 Mon Sep 17 00:00:00 2001
From: mischko <mhem@mailbox.org>
Date: Sun, 5 Jan 2025 16:51:24 +0100
Subject: [PATCH 19/31] simplify fetchpkgs

---
 R/fetchers.R | 29 ++++++++++++++---------------
 1 file changed, 14 insertions(+), 15 deletions(-)

diff --git a/R/fetchers.R b/R/fetchers.R
index a2550a37..804366ba 100644
--- a/R/fetchers.R
+++ b/R/fetchers.R
@@ -359,23 +359,22 @@ fetchzips <- function(archive_pkgs) {
   }
 }
 
-#' fetchpkgs Downloads and installs packages hosted in the CRAN archives or
-#' Github.
-#' @param git_pkgs A list of three elements: "package_name", the name of the
-#' package, "repo_url", the repository's url and "commit", the commit hash of
-#' interest. This argument can also be a list of lists of these four elements.
-#' @param archive_pkgs A character, or an atomic vector of characters.
-#' @return A character. The Nix definition to download and build the R package
-#' from the CRAN archives.
+#' fetchpkgs Downloads and installs packages from CRAN archives or Github
+#' @param git_pkgs List of Git packages with name, url and commit
+#' @param archive_pkgs Vector of CRAN archive package names
+#' @return Nix definition string for building the packages
 #' @noRd
 fetchpkgs <- function(git_pkgs, archive_pkgs) {
-  # This removes all packages that are already included
-  # because they are remote packages from another package
-  remote_package_names <- unlist(lapply(git_pkgs, get_remote))
-  git_pkgs_names <- sapply(git_pkgs, `[[`, "package_name")
-  git_pkgs_name_corrected <- setdiff(git_pkgs_names, remote_package_names)
-  git_pkgs_corrected <- git_pkgs[sapply(git_pkgs, function(pkg) pkg$package_name %in% git_pkgs_name_corrected)]
-  paste(fetchgits(git_pkgs_corrected),
+  all_remotes <- unique(unlist(lapply(git_pkgs, get_remote)))
+  
+  # Only include git packages that aren't already remote dependencies
+  needed_git_pkgs <- git_pkgs[!sapply(git_pkgs, function(pkg) {
+    pkg$package_name %in% all_remotes
+  })]
+
+  # Combine git and archive package definitions
+  paste(
+    fetchgits(needed_git_pkgs),
     fetchzips(archive_pkgs),
     collapse = "\n"
   )

From 7422f341098e97dd72652e1e3e17c94f62b86a76 Mon Sep 17 00:00:00 2001
From: Bruno Rodrigues <bruno@brodrigues.co>
Date: Sun, 5 Jan 2025 16:59:17 +0100
Subject: [PATCH 20/31] support for revisions in DESCRIPTION

---
 R/fetchers.R                   | 32 ++++++++++++++++++++++++++++----
 tests/testthat/test-fetchers.R | 14 ++++++++++++++
 2 files changed, 42 insertions(+), 4 deletions(-)

diff --git a/R/fetchers.R b/R/fetchers.R
index fe4a7ed6..5f7cb638 100644
--- a/R/fetchers.R
+++ b/R/fetchers.R
@@ -203,14 +203,38 @@ get_imports <- function(path) {
     # remotes are of the form username/packagename so we need
     # to only keep packagename
     remotes <- gsub("\n", "", x = unlist(strsplit(remotes$Remotes, ",")))
-    remote_pkgs_names <- sub(".*?/", "", remotes)
-    urls <- paste0("https://github.com/", remotes)
-    commits <- rep("HEAD", length(remotes))
+    # Get user names
+    remote_pkgs_usernames <- strsplit(remotes, "/") |>
+      sapply(function(x)x[[1]])
+
+    # Now remove user name and
+    # split at "@" or "#" character to get name and commit or PR separated
+    remote_pkgs_names_and_refs <- sub(".*?/", "", remotes)
+    remote_pkgs_names_and_refs <- strsplit(remote_pkgs_names_and_refs, "(@|#)")
+
+    remote_pkgs_names <- remote_pkgs_names_and_refs |>
+      sapply(function(x)x[[1]])
+
+    # Check if we have a list of lists of two elements: a package name
+    # and a ref. If not, add "HEAD" to it.
+    remote_pkgs_refs <- lapply(remote_pkgs_names_and_refs, function(sublist) {
+      if (length(sublist) == 1) {
+        c(sublist, "HEAD")
+      } else {
+        sublist
+      }
+    }) |>
+      sapply(function(x)x[[2]])
+
+    urls <- paste0("https://github.com/",
+                   remote_pkgs_usernames, "/",
+                   remote_pkgs_names)
+
     remote_pkgs <- lapply(seq_along(remote_pkgs_names), function(i) {
       list(
         "package_name" = remote_pkgs_names[i],
         "repo_url" = urls[i],
-        "commit" = commits[i]
+        "commit" = remote_pkgs_refs[i]
       )
     })
   } else {
diff --git a/tests/testthat/test-fetchers.R b/tests/testthat/test-fetchers.R
index c5b95a13..925a1110 100644
--- a/tests/testthat/test-fetchers.R
+++ b/tests/testthat/test-fetchers.R
@@ -150,3 +150,17 @@ testthat::test_that("Test fetchgit gets a package with one remote dep", {
     "\n    enrichR = (pkgs.rPackages.buildRPackage {\n      name = \"enrichR\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/wjawaid/enrichR\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-Jm6Z46ARyp+geSY4RLb/x9zV6uvlyjnFdLh4/c6uGoI=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          httr\n          curl\n          rjson\n          ggplot2\n          WriteXLS;\n      };\n    });\n\n    scMisc = (pkgs.rPackages.buildRPackage {\n      name = \"scMisc\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/mihem/scMisc/\";\n        rev = \"e2ebddcb779b935551f14216514c0429616fc91d\";\n        sha256 = \"sha256-Atmr+vGfJxNc5HK+UgpnSIeZ1fYKWEzD3Dt2va1xoFE=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          Seurat\n          readr\n          glue\n          viridis\n          ggplot2\n          pheatmap\n          homologene\n          dplyr\n          tibble\n          magrittr\n          clustifyr\n          ggrepel\n          writexl\n          ggsignif\n          patchwork\n          rstatix\n          readxl\n          tidyr\n          speckle\n          limma\n          RColorBrewer\n          factoextra\n          FactoMineR\n          Matrix\n          ggpubr\n          tidyselect\n          stringr\n          forcats;\n      } ++ [ enrichR ];\n    });\n"
   )
 })
+
+testthat::test_that("Test fetchgit gets a package with several remote deps and commits", {
+  testthat::skip_on_cran()
+  testthat::expect_equal(
+    fetchgit(
+      list(
+        package_name = "lookup",
+        repo_url = "https://github.com/b-rodrigues/lookup/",
+        commit = "a36973c87ec0f24e4b1bf2884c7cc99dc442f8ff"
+      )
+    ),
+"\n    glue = (pkgs.rPackages.buildRPackage {\n      name = \"glue\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/tidyverse/glue\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-HuYKjZYVd2RF16F3HsYE7xGQHvV45z6YIe5K6OlDFLo=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) ;\n      };\n    });\n\n\n    httr = (pkgs.rPackages.buildRPackage {\n      name = \"httr\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/hadley/httr\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-DtgrlVyPhp0V3bgpwzvJMH7luxqPJJ37ObMIeZnUDX8=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          curl\n          jsonlite\n          mime\n          openssl\n          R6;\n      };\n    });\n\n    httrmock = (pkgs.rPackages.buildRPackage {\n      name = \"httrmock\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/gaborcsardi/httrmock\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-+Sncxv83N/FB0mL1KJSTtwFoZb6zxULncmr00cv7Fuc=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          assertthat\n          base64enc\n          debugme\n          digest\n          lintr\n          R6\n          rprojroot\n          whoami;\n      } ++ [ httr glue ];\n    });\n\n    gh = (pkgs.rPackages.buildRPackage {\n      name = \"gh\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/gaborcsardi/gh\";\n        rev = \"8237a88\";\n        sha256 = \"sha256-yZofcmA+mpYsi81DcEQsA2vtVcaTvK1FDXfpJEiLqVY=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          ini\n          jsonlite\n          httr;\n      } ++ [ httrmock ];\n    });\n\n\n    highlite = (pkgs.rPackages.buildRPackage {\n      name = \"highlite\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/jimhester/highlite\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-lkWMlAi75MYxiBUYnLwxLK9ApXkWanA4Mt7g4qtLpxM=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          Rcpp\n          BH;\n      };\n    });\n\n\n    memoise = (pkgs.rPackages.buildRPackage {\n      name = \"memoise\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/hadley/memoise\";\n        rev = \"74d62c8\";\n        sha256 = \"sha256-fsdop66VglkOIYrJ0LKZKikIZmzQ2gqEATLy9tTJ/B8=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          digest;\n      };\n    });\n\n    lookup = (pkgs.rPackages.buildRPackage {\n      name = \"lookup\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/b-rodrigues/lookup/\";\n        rev = \"a36973c87ec0f24e4b1bf2884c7cc99dc442f8ff\";\n        sha256 = \"sha256-zE5LcjeO5xcABo+ZfHLh6N1bWbH9rJYLfL0ewZe7/bk=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          Rcpp\n          codetools\n          crayon\n          rex\n          jsonlite\n          rstudioapi\n          withr\n          httr;\n      } ++ [ highlite gh memoise ];\n    });\n"
+  )
+})

From f9a138356b90143e77faad808dd2c0615d1405c5 Mon Sep 17 00:00:00 2001
From: mischko <mhem@mailbox.org>
Date: Sun, 5 Jan 2025 16:59:37 +0100
Subject: [PATCH 21/31] exclude git_pkgs with one pkgs for correction

---
 R/fetchers.R | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/R/fetchers.R b/R/fetchers.R
index 804366ba..38493697 100644
--- a/R/fetchers.R
+++ b/R/fetchers.R
@@ -365,12 +365,13 @@ fetchzips <- function(archive_pkgs) {
 #' @return Nix definition string for building the packages
 #' @noRd
 fetchpkgs <- function(git_pkgs, archive_pkgs) {
-  all_remotes <- unique(unlist(lapply(git_pkgs, get_remote)))
-  
   # Only include git packages that aren't already remote dependencies
-  needed_git_pkgs <- git_pkgs[!sapply(git_pkgs, function(pkg) {
-    pkg$package_name %in% all_remotes
-  })]
+  if (all(sapply(git_pkgs, is.list))) {
+    all_remotes <- unique(unlist(lapply(git_pkgs, get_remote)))
+    git_pkgs <- git_pkgs[!sapply(git_pkgs, function(pkg) {
+      pkg$package_name %in% all_remotes
+    })]
+  }
 
   # Combine git and archive package definitions
   paste(

From 2a7eeba5831f94063683b97fd9f84e89813fa175 Mon Sep 17 00:00:00 2001
From: mischko <mhem@mailbox.org>
Date: Sun, 5 Jan 2025 17:01:31 +0100
Subject: [PATCH 22/31] fix small bug

---
 R/fetchers.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/fetchers.R b/R/fetchers.R
index 38493697..cf2d1b60 100644
--- a/R/fetchers.R
+++ b/R/fetchers.R
@@ -375,7 +375,7 @@ fetchpkgs <- function(git_pkgs, archive_pkgs) {
 
   # Combine git and archive package definitions
   paste(
-    fetchgits(needed_git_pkgs),
+    fetchgits(git_pkgs),
     fetchzips(archive_pkgs),
     collapse = "\n"
   )

From 8a8ecb61d44d27d07654cfc4300d83024ae661ef Mon Sep 17 00:00:00 2001
From: b-rodrigues <b-rodrigues@users.noreply.github.com>
Date: Sun, 5 Jan 2025 16:01:44 +0000
Subject: [PATCH 23/31] Style via {styler}

---
 R/fetchers.R                   | 14 ++++++++------
 tests/testthat/test-fetchers.R |  2 +-
 2 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/R/fetchers.R b/R/fetchers.R
index 5f7cb638..ad7d7c60 100644
--- a/R/fetchers.R
+++ b/R/fetchers.R
@@ -205,7 +205,7 @@ get_imports <- function(path) {
     remotes <- gsub("\n", "", x = unlist(strsplit(remotes$Remotes, ",")))
     # Get user names
     remote_pkgs_usernames <- strsplit(remotes, "/") |>
-      sapply(function(x)x[[1]])
+      sapply(function(x) x[[1]])
 
     # Now remove user name and
     # split at "@" or "#" character to get name and commit or PR separated
@@ -213,7 +213,7 @@ get_imports <- function(path) {
     remote_pkgs_names_and_refs <- strsplit(remote_pkgs_names_and_refs, "(@|#)")
 
     remote_pkgs_names <- remote_pkgs_names_and_refs |>
-      sapply(function(x)x[[1]])
+      sapply(function(x) x[[1]])
 
     # Check if we have a list of lists of two elements: a package name
     # and a ref. If not, add "HEAD" to it.
@@ -224,11 +224,13 @@ get_imports <- function(path) {
         sublist
       }
     }) |>
-      sapply(function(x)x[[2]])
+      sapply(function(x) x[[2]])
 
-    urls <- paste0("https://github.com/",
-                   remote_pkgs_usernames, "/",
-                   remote_pkgs_names)
+    urls <- paste0(
+      "https://github.com/",
+      remote_pkgs_usernames, "/",
+      remote_pkgs_names
+    )
 
     remote_pkgs <- lapply(seq_along(remote_pkgs_names), function(i) {
       list(
diff --git a/tests/testthat/test-fetchers.R b/tests/testthat/test-fetchers.R
index 925a1110..91f40011 100644
--- a/tests/testthat/test-fetchers.R
+++ b/tests/testthat/test-fetchers.R
@@ -161,6 +161,6 @@ testthat::test_that("Test fetchgit gets a package with several remote deps and c
         commit = "a36973c87ec0f24e4b1bf2884c7cc99dc442f8ff"
       )
     ),
-"\n    glue = (pkgs.rPackages.buildRPackage {\n      name = \"glue\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/tidyverse/glue\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-HuYKjZYVd2RF16F3HsYE7xGQHvV45z6YIe5K6OlDFLo=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) ;\n      };\n    });\n\n\n    httr = (pkgs.rPackages.buildRPackage {\n      name = \"httr\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/hadley/httr\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-DtgrlVyPhp0V3bgpwzvJMH7luxqPJJ37ObMIeZnUDX8=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          curl\n          jsonlite\n          mime\n          openssl\n          R6;\n      };\n    });\n\n    httrmock = (pkgs.rPackages.buildRPackage {\n      name = \"httrmock\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/gaborcsardi/httrmock\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-+Sncxv83N/FB0mL1KJSTtwFoZb6zxULncmr00cv7Fuc=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          assertthat\n          base64enc\n          debugme\n          digest\n          lintr\n          R6\n          rprojroot\n          whoami;\n      } ++ [ httr glue ];\n    });\n\n    gh = (pkgs.rPackages.buildRPackage {\n      name = \"gh\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/gaborcsardi/gh\";\n        rev = \"8237a88\";\n        sha256 = \"sha256-yZofcmA+mpYsi81DcEQsA2vtVcaTvK1FDXfpJEiLqVY=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          ini\n          jsonlite\n          httr;\n      } ++ [ httrmock ];\n    });\n\n\n    highlite = (pkgs.rPackages.buildRPackage {\n      name = \"highlite\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/jimhester/highlite\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-lkWMlAi75MYxiBUYnLwxLK9ApXkWanA4Mt7g4qtLpxM=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          Rcpp\n          BH;\n      };\n    });\n\n\n    memoise = (pkgs.rPackages.buildRPackage {\n      name = \"memoise\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/hadley/memoise\";\n        rev = \"74d62c8\";\n        sha256 = \"sha256-fsdop66VglkOIYrJ0LKZKikIZmzQ2gqEATLy9tTJ/B8=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          digest;\n      };\n    });\n\n    lookup = (pkgs.rPackages.buildRPackage {\n      name = \"lookup\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/b-rodrigues/lookup/\";\n        rev = \"a36973c87ec0f24e4b1bf2884c7cc99dc442f8ff\";\n        sha256 = \"sha256-zE5LcjeO5xcABo+ZfHLh6N1bWbH9rJYLfL0ewZe7/bk=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          Rcpp\n          codetools\n          crayon\n          rex\n          jsonlite\n          rstudioapi\n          withr\n          httr;\n      } ++ [ highlite gh memoise ];\n    });\n"
+    "\n    glue = (pkgs.rPackages.buildRPackage {\n      name = \"glue\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/tidyverse/glue\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-HuYKjZYVd2RF16F3HsYE7xGQHvV45z6YIe5K6OlDFLo=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) ;\n      };\n    });\n\n\n    httr = (pkgs.rPackages.buildRPackage {\n      name = \"httr\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/hadley/httr\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-DtgrlVyPhp0V3bgpwzvJMH7luxqPJJ37ObMIeZnUDX8=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          curl\n          jsonlite\n          mime\n          openssl\n          R6;\n      };\n    });\n\n    httrmock = (pkgs.rPackages.buildRPackage {\n      name = \"httrmock\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/gaborcsardi/httrmock\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-+Sncxv83N/FB0mL1KJSTtwFoZb6zxULncmr00cv7Fuc=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          assertthat\n          base64enc\n          debugme\n          digest\n          lintr\n          R6\n          rprojroot\n          whoami;\n      } ++ [ httr glue ];\n    });\n\n    gh = (pkgs.rPackages.buildRPackage {\n      name = \"gh\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/gaborcsardi/gh\";\n        rev = \"8237a88\";\n        sha256 = \"sha256-yZofcmA+mpYsi81DcEQsA2vtVcaTvK1FDXfpJEiLqVY=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          ini\n          jsonlite\n          httr;\n      } ++ [ httrmock ];\n    });\n\n\n    highlite = (pkgs.rPackages.buildRPackage {\n      name = \"highlite\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/jimhester/highlite\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-lkWMlAi75MYxiBUYnLwxLK9ApXkWanA4Mt7g4qtLpxM=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          Rcpp\n          BH;\n      };\n    });\n\n\n    memoise = (pkgs.rPackages.buildRPackage {\n      name = \"memoise\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/hadley/memoise\";\n        rev = \"74d62c8\";\n        sha256 = \"sha256-fsdop66VglkOIYrJ0LKZKikIZmzQ2gqEATLy9tTJ/B8=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          digest;\n      };\n    });\n\n    lookup = (pkgs.rPackages.buildRPackage {\n      name = \"lookup\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/b-rodrigues/lookup/\";\n        rev = \"a36973c87ec0f24e4b1bf2884c7cc99dc442f8ff\";\n        sha256 = \"sha256-zE5LcjeO5xcABo+ZfHLh6N1bWbH9rJYLfL0ewZe7/bk=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          Rcpp\n          codetools\n          crayon\n          rex\n          jsonlite\n          rstudioapi\n          withr\n          httr;\n      } ++ [ highlite gh memoise ];\n    });\n"
   )
 })

From fed503f954e1da9af8b1f5654cb7a260994f207b Mon Sep 17 00:00:00 2001
From: b-rodrigues <b-rodrigues@users.noreply.github.com>
Date: Sun, 5 Jan 2025 16:26:02 +0000
Subject: [PATCH 24/31] Style via {styler}

---
 R/fetchers.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/fetchers.R b/R/fetchers.R
index 31a6d8a5..32535567 100644
--- a/R/fetchers.R
+++ b/R/fetchers.R
@@ -420,4 +420,4 @@ get_remote <- function(git_pkg) {
   remotes <- output$deps$remotes
   remote_package_names <- sapply(remotes, `[[`, "package_name")
   return(remote_package_names)
-}
\ No newline at end of file
+}

From f39a76ff05b5d82a6bf0584ae057307335f525c6 Mon Sep 17 00:00:00 2001
From: Bruno Rodrigues <bruno@brodrigues.co>
Date: Sun, 5 Jan 2025 20:35:05 +0100
Subject: [PATCH 25/31] added test for double entry in renv.lock file

---
 .../_snaps/renv_helpers/default_datathin.nix  |  413 ++
 tests/testthat/test-renv_helpers.R            |   12 +
 .../testdata/renv-samples/renv_datathin.lock  | 5013 +++++++++++++++++
 3 files changed, 5438 insertions(+)
 create mode 100644 tests/testthat/_snaps/renv_helpers/default_datathin.nix
 create mode 100644 tests/testthat/testdata/renv-samples/renv_datathin.lock

diff --git a/tests/testthat/_snaps/renv_helpers/default_datathin.nix b/tests/testthat/_snaps/renv_helpers/default_datathin.nix
new file mode 100644
index 00000000..c67774fb
--- /dev/null
+++ b/tests/testthat/_snaps/renv_helpers/default_datathin.nix
@@ -0,0 +1,413 @@
+
+let
+  pkgs = import (fetchTarball "https://github.com/rstats-on-nix/nixpkgs/archive/2024-12-14.tar.gz") {};
+ 
+  rpkgs = builtins.attrValues {
+    inherit (pkgs.rPackages) 
+      AsioHeaders
+      BH
+      Biobase
+      BiocGenerics
+      BiocManager
+      BiocVersion
+      DBI
+      DT
+      DiceDesign
+      FNN
+      GPfit
+      ICD10gm
+      KMsurv
+      KernSmooth
+      LambertW
+      MASS
+      Matrix
+      MatrixModels
+      Polychrome
+      R_cache
+      R_methodsS3
+      R_oo
+      R_utils
+      R6
+      RANN
+      RApiSerialize
+      RColorBrewer
+      ROCR
+      RProtoBufLib
+      RSpectra
+      Rcpp
+      RcppAnnoy
+      RcppArmadillo
+      RcppEigen
+      RcppHNSW
+      RcppParallel
+      RcppProgress
+      RcppTOML
+      Rhdf5lib
+      Rtsne
+      S4Vectors
+      SQUAREM
+      Seurat
+      SeuratObject
+      SoupX
+      SparseM
+      VGAM
+      WRS2
+      abind
+      askpass
+      backports
+      base64enc
+      bestNormalize
+      bit
+      bit64
+      bitops
+      blob
+      boot
+      brew
+      brio
+      broom
+      bslib
+      butcher
+      caTools
+      cachem
+      callr
+      car
+      carData
+      cellranger
+      class
+      cli
+      clipr
+      clock
+      cluster
+      codetools
+      collections
+      colorspace
+      commonmark
+      conflicted
+      corrplot
+      cowplot
+      cpp11
+      crayon
+      crosstalk
+      curl
+      cyclocomp
+      cytolib
+      data_table
+      datawizard
+      dbplyr
+      deldir
+      desc
+      diagram
+      dials
+      dichromat
+      diffobj
+      digest
+      doFuture
+      doMC
+      doParallel
+      doRNG
+      dotCall64
+      dplyr
+      dqrng
+      dtplyr
+      ellipsis
+      emmeans
+      estimability
+      evaluate
+      exactRankTests
+      extraDistr
+      fansi
+      farver
+      fastDummies
+      fastmap
+      finetune
+      fitdistrplus
+      flowCore
+      fontawesome
+      forcats
+      foreach
+      fs
+      furrr
+      future
+      future_apply
+      fuzzyjoin
+      gargle
+      generics
+      geosphere
+      ggplot2
+      ggpubr
+      ggrepel
+      ggridges
+      ggsci
+      ggsignif
+      ggtext
+      glmnet
+      globals
+      glue
+      goftest
+      googledrive
+      googlesheets4
+      gower
+      gplots
+      gridExtra
+      gridtext
+      gtable
+      gtools
+      hardhat
+      haven
+      here
+      highr
+      hms
+      htmltools
+      htmlwidgets
+      httpgd
+      httpuv
+      httr
+      ica
+      ids
+      igraph
+      infer
+      insight
+      ipred
+      irlba
+      isoband
+      iterators
+      janitor
+      jomo
+      jpeg
+      jquerylib
+      jsonlite
+      km_ci
+      knitr
+      labeling
+      lamW
+      languageserver
+      later
+      lattice
+      lava
+      lazyeval
+      leiden
+      lhs
+      lifecycle
+      lintr
+      listenv
+      lme4
+      lmtest
+      lobstr
+      lubridate
+      magrittr
+      mapproj
+      maps
+      markdown
+      matrixStats
+      maxstat
+      mclust
+      memoise
+      mgcv
+      mice
+      mime
+      miniUI
+      minqa
+      mitml
+      modeldata
+      modelenv
+      modelr
+      munsell
+      mvtnorm
+      nlme
+      nloptr
+      nnet
+      nortest
+      numDeriv
+      openssl
+      ordinal
+      pals
+      pan
+      parallelly
+      parsnip
+      patchwork
+      pbapply
+      pbkrtest
+      pheatmap
+      pillar
+      pkgbuild
+      pkgconfig
+      pkgload
+      plotly
+      plyr
+      png
+      polyclip
+      polynom
+      praise
+      prettyunits
+      processx
+      prodlim
+      progress
+      progressr
+      promises
+      ps
+      purrr
+      qs
+      quantreg
+      ragg
+      rappdirs
+      readr
+      readxl
+      recipes
+      rematch
+      rematch2
+      remotes
+      renv
+      repr
+      reprex
+      reshape
+      reshape2
+      reticulate
+      rex
+      rlang
+      rmarkdown
+      rngtools
+      roxygen2
+      rpart
+      rprojroot
+      rsample
+      rstatix
+      rstudioapi
+      rvest
+      sass
+      scales
+      scattermore
+      scatterplot3d
+      sctransform
+      selectr
+      shape
+      shiny
+      sitmo
+      skimr
+      slider
+      snakecase
+      sourcetools
+      sp
+      spam
+      spatstat_data
+      spatstat_explore
+      spatstat_geom
+      spatstat_random
+      spatstat_sparse
+      spatstat_utils
+      stringdist
+      stringfish
+      stringi
+      stringr
+      styler
+      survMisc
+      survival
+      survminer
+      sys
+      systemfonts
+      tensor
+      testthat
+      textshaping
+      tibble
+      tidymodels
+      tidyr
+      tidyselect
+      tidyverse
+      timeDate
+      timechange
+      tinytex
+      tune
+      tzdb
+      ucminf
+      unigd
+      utf8
+      uuid
+      uwot
+      vctrs
+      vip
+      viridis
+      viridisLite
+      vroom
+      waldo
+      warp
+      withr
+      workflows
+      workflowsets
+      writexl
+      xfun
+      xgboost
+      xml2
+      xmlparsedata
+      xtable
+      yaml
+      yardstick
+      zoo;
+  };
+ 
+    datathin = (pkgs.rPackages.buildRPackage {
+      name = "datathin";
+      src = pkgs.fetchgit {
+        url = "https://github.com/anna-neufeld/datathin";
+        rev = "HEAD";
+        sha256 = "sha256-rtRpwFI+JggX8SwnfH4SPDaMPK2yLhJFTgzvWT+Zll4=";
+      };
+      propagatedBuildInputs = builtins.attrValues {
+        inherit (pkgs.rPackages) 
+          VGAM
+          knitr
+          extraDistr
+          mvtnorm;
+      };
+    });
+
+    CSFAtlasTools = (pkgs.rPackages.buildRPackage {
+      name = "CSFAtlasTools";
+      src = pkgs.fetchgit {
+        url = "https://github.com/mihem/CSFAtlasTools";
+        rev = "02d485896d383e2a876f0f3bbae7265c017e7e92";
+        sha256 = "sha256-q9qBYrGrn96lG5I9xUuWCLw0CSnh7BA5Qs9AAcRtz0E=";
+      };
+      propagatedBuildInputs = builtins.attrValues {
+        inherit (pkgs.rPackages) 
+          dplyr
+          glue
+          readr
+          ggplot2
+          tidyr
+          RColorBrewer
+          bestNormalize
+          pheatmap
+          recipes
+          tibble
+          viridis
+          broom
+          WRS2
+          Seurat
+          abind
+          mclust
+          tune
+          yardstick
+          ggsignif;
+      } ++ [ datathin ];
+    });
+    
+  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 = [ CSFAtlasTools datathin rpkgs  system_packages   ];
+  
+}
diff --git a/tests/testthat/test-renv_helpers.R b/tests/testthat/test-renv_helpers.R
index f686a717..83a91f98 100644
--- a/tests/testthat/test-renv_helpers.R
+++ b/tests/testthat/test-renv_helpers.R
@@ -222,6 +222,18 @@ testthat::test_that("testing renv_helpers", {
       name = "default_v1-0-7.nix"
     )
 
+    # This should not get datathin twice in the generated
+    # default.nix
+    testthat::expect_snapshot_file(
+      path = save_renv2nix_test(
+        "testdata/renv-samples/renv_datathin.lock",
+        path_env_nix,
+        "/default_datathin.nix",
+        override_r_ver = "4.4.2",
+        ),
+      name = "default_datathin.nix"
+    )
+
     on.exit(unlink(path_env_nix))
   })
 })
diff --git a/tests/testthat/testdata/renv-samples/renv_datathin.lock b/tests/testthat/testdata/renv-samples/renv_datathin.lock
new file mode 100644
index 00000000..f591b597
--- /dev/null
+++ b/tests/testthat/testdata/renv-samples/renv_datathin.lock
@@ -0,0 +1,5013 @@
+{
+  "R": {
+    "Version": "4.3.1",
+    "Repositories": [
+      {
+        "Name": "BioCsoft",
+        "URL": "https://bioconductor.org/packages/3.18/bioc"
+      },
+      {
+        "Name": "BioCann",
+        "URL": "https://bioconductor.org/packages/3.18/data/annotation"
+      },
+      {
+        "Name": "BioCexp",
+        "URL": "https://bioconductor.org/packages/3.18/data/experiment"
+      },
+      {
+        "Name": "BioCworkflows",
+        "URL": "https://bioconductor.org/packages/3.18/workflows"
+      },
+      {
+        "Name": "BioCbooks",
+        "URL": "https://bioconductor.org/packages/3.18/books"
+      },
+      {
+        "Name": "RSPM",
+        "URL": "https://packagemanager.rstudio.com/cran/latest"
+      }
+    ]
+  },
+  "Bioconductor": {
+    "Version": "3.18"
+  },
+  "Packages": {
+    "AsioHeaders": {
+      "Package": "AsioHeaders",
+      "Version": "1.22.1-2",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Hash": "85bf3bd8fa58da21a22d84fd4f4ef0a8"
+    },
+    "BH": {
+      "Package": "BH",
+      "Version": "1.84.0-0",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Hash": "a8235afbcd6316e6e91433ea47661013"
+    },
+    "Biobase": {
+      "Package": "Biobase",
+      "Version": "2.62.0",
+      "Source": "Bioconductor",
+      "Requirements": [
+        "BiocGenerics",
+        "R",
+        "methods",
+        "utils"
+      ],
+      "Hash": "38252a34e82d3ff6bb46b4e2252d2dce"
+    },
+    "BiocGenerics": {
+      "Package": "BiocGenerics",
+      "Version": "0.48.1",
+      "Source": "Bioconductor",
+      "Requirements": [
+        "R",
+        "graphics",
+        "methods",
+        "stats",
+        "utils"
+      ],
+      "Hash": "e34278c65d7dffcc08f737bf0944ca9a"
+    },
+    "BiocManager": {
+      "Package": "BiocManager",
+      "Version": "1.30.25",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "utils"
+      ],
+      "Hash": "3aec5928ca10897d7a0a1205aae64627"
+    },
+    "BiocVersion": {
+      "Package": "BiocVersion",
+      "Version": "3.18.1",
+      "Source": "Bioconductor",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "2ecaed86684f5fae76ed5530f9d29c4a"
+    },
+    "CSFAtlasTools": {
+      "Package": "CSFAtlasTools",
+      "Version": "2.0.0",
+      "Source": "GitHub",
+      "RemoteType": "github",
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+    "xmlparsedata": {
+      "Package": "xmlparsedata",
+      "Version": "1.0.5",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "45e4bf3c46476896e821fc0a408fb4fc"
+    },
+    "xtable": {
+      "Package": "xtable",
+      "Version": "1.8-4",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "stats",
+        "utils"
+      ],
+      "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2"
+    },
+    "yaml": {
+      "Package": "yaml",
+      "Version": "2.3.8",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Hash": "29240487a071f535f5e5d5a323b7afbd"
+    },
+    "yardstick": {
+      "Package": "yardstick",
+      "Version": "1.3.1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "cli",
+        "dplyr",
+        "generics",
+        "hardhat",
+        "lifecycle",
+        "rlang",
+        "tibble",
+        "tidyselect",
+        "utils",
+        "vctrs",
+        "withr"
+      ],
+      "Hash": "9ce4117141b326c4fffc7c42e56e0f88"
+    },
+    "zoo": {
+      "Package": "zoo",
+      "Version": "1.8-12",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "grDevices",
+        "graphics",
+        "lattice",
+        "stats",
+        "utils"
+      ],
+      "Hash": "5c715954112b45499fb1dadc6ee6ee3e"
+    }
+  }
+}

From 903054826e321e03536ef585e9037d410d47d4d9 Mon Sep 17 00:00:00 2001
From: b-rodrigues <b-rodrigues@users.noreply.github.com>
Date: Sun, 5 Jan 2025 19:37:30 +0000
Subject: [PATCH 26/31] Style via {styler}

---
 tests/testthat/test-renv_helpers.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-renv_helpers.R b/tests/testthat/test-renv_helpers.R
index 83a91f98..19ef6c44 100644
--- a/tests/testthat/test-renv_helpers.R
+++ b/tests/testthat/test-renv_helpers.R
@@ -230,7 +230,7 @@ testthat::test_that("testing renv_helpers", {
         path_env_nix,
         "/default_datathin.nix",
         override_r_ver = "4.4.2",
-        ),
+      ),
       name = "default_datathin.nix"
     )
 

From 66721f0a2556fd19921638bbf83745cc69224fc8 Mon Sep 17 00:00:00 2001
From: Bruno Rodrigues <bruno@brodrigues.co>
Date: Tue, 7 Jan 2025 20:13:49 +0100
Subject: [PATCH 27/31] updated vignette to reflect changes

---
 ...ling-packages-with-remote-dependencies.Rmd | 183 +++++-------------
 1 file changed, 52 insertions(+), 131 deletions(-)

diff --git a/vignettes/z-advanced-topic-handling-packages-with-remote-dependencies.Rmd b/vignettes/z-advanced-topic-handling-packages-with-remote-dependencies.Rmd
index 645dc1b4..ee1278f3 100644
--- a/vignettes/z-advanced-topic-handling-packages-with-remote-dependencies.Rmd
+++ b/vignettes/z-advanced-topic-handling-packages-with-remote-dependencies.Rmd
@@ -24,12 +24,11 @@ Packages published on CRAN must have their dependencies on either CRAN or
 BioConductor, but not on GitHub. However, there are many packages available on
 GitHub that never get published on CRAN, and some of these packages may even
 depend on other packages that are also only available on GitHub. `{rix}` makes
-it possible to install packages from GitHub, but in case one of the package's
-dependencies has also only been released on GitHub, building the Nix environment
-will fail. This is because Nix will be looking for these packages on `nixpkgs`,
-but only packages released on CRAN and Bioconductor are available through
-`nixpkgs`. This vignette explains how to install such a packages that have
-dependencies only available on GitHub.
+it possible to install packages from GitHub and if these packages have
+dependencies that are also on Github, these also get correctly added to the
+generated `default.nix`.
+
+There are however certain caveats you should be aware of.
 
 ## The {lookup} package
 
@@ -62,17 +61,13 @@ rix(
 )
 ```
 
-Trying to build this environment will fail with following error message:
+This will generate the following `default.nix`:
 
-```
-error: attribute 'highlite' missing
-```
 
-## Building remote dependencies
 
-`{highlite}` is a dependency of [{lookup}](https://github.com/jimhester/lookup)
-that is only available on GitHub. This can be checked by looking at the
-`DESCRIPTION` file of [{lookup}](https://github.com/jimhester/lookup):
+as you can see, several other packages hosted on Github were added
+automatically. This is because these were listed as remote dependencies in
+`{lookup}`'s `DESCRIPTION` file:
 
 ```
 Remotes:
@@ -81,131 +76,57 @@ Remotes:
     hadley/memoise
 ```
 
-We see that there are actually three packages that come from GitHub: but `{gh}`
-and `{memoise}` have in the meantime been released on CRAN, which means that
-they are also available through `nixpkgs`. We have to deal with `{highlite}`
-however, because it never got released on CRAN. Doing so is fairly easy: first,
-create a new expression using `{rix}` to install `{highlite}`:
-
-```{r, eval = F}
-path_default_nix <- tempdir()
-
-rix(
-  r_ver = "latest-upstream",
-  r_pkgs = NULL,
-  system_pkgs = NULL,
-  git_pkgs = list(
-    package_name = "highlite",
-    repo_url = "https://github.com/jimhester/highlite/",
-    commit = "767b122ef47a60a01e1707e4093cf3635a99c86b"
-  ),
-  ide = "other",
-  project_path = path_default_nix,
-  overwrite = FALSE,
-  print = TRUE
-)
-```
-
-(you don't need to overwrite the previous expression, simply printing this
-one on screen will do). Copy the following lines:
-
-```
-git_archive_pkgs = [(pkgs.rPackages.buildRPackage {
-  name = "highlite";
-  src = pkgs.fetchgit {
-    url = "https://github.com/jimhester/highlite/";
-    rev = "767b122ef47a60a01e1707e4093cf3635a99c86b";
-    sha256 = "sha256-lkWMlAi75MYxiBUYnLwxLK9ApXkWanA4Mt7g4qtLpxM=";
-  };
-  propagatedBuildInputs = builtins.attrValues {
-    inherit (pkgs.rPackages) Rcpp BH;
-  };
-}) ];
-```
+## Caveats
 
-into the previous expression (and change `git_archive_pkgs` into `highlite`).
-The file should look like this now:
-
-```
-let
- pkgs = import (fetchTarball "https://github.com/NixOS/nixpkgs/archive/b200e0df08f80c32974a6108ce431d8a8a5e6547.tar.gz") {};
-
-  highlite = [(pkgs.rPackages.buildRPackage {
-    name = "highlite";
-    src = pkgs.fetchgit {
-      url = "https://github.com/jimhester/highlite/";
-      rev = "767b122ef47a60a01e1707e4093cf3635a99c86b";
-      sha256 = "sha256-lkWMlAi75MYxiBUYnLwxLK9ApXkWanA4Mt7g4qtLpxM=";
-    };
-    propagatedBuildInputs = builtins.attrValues {
-      inherit (pkgs.rPackages) Rcpp BH;
-    };
-  }) ];
-  git_archive_pkgs = [(pkgs.rPackages.buildRPackage {
-    name = "lookup";
-    src = pkgs.fetchgit {
-      url = "https://github.com/jimhester/lookup/";
-      rev = "eba63db477dd2f20153b75e2949eb333a36cccfc";
-      sha256 = "sha256-arl7LVxL8xGUW3LhuDCSUjcfswX0rdofL/7v8Klw8FM=";
-    };
-    propagatedBuildInputs = builtins.attrValues {
-      inherit (pkgs.rPackages) gh memoise Rcpp codetools crayon rex highlite jsonlite rstudioapi withr httr;
-    };
-  }) ];
- system_packages = builtins.attrValues {
-  inherit (pkgs) R ;
-};
-  in
-  pkgs.mkShell {
-    buildInputs = [ git_archive_pkgs  system_packages  ];
-      shellHook = ''
-R --vanilla
-'';
-  }
-
-```
-
-The only thing that we need to change is this line:
-
-```
-propagatedBuildInputs = builtins.attrValues {
-      inherit (pkgs.rPackages) gh memoise Rcpp codetools crayon rex highlite jsonlite rstudioapi withr httr;
-    };
-```
-
-into:
-
-```
-propagatedBuildInputs = builtins.attrValues {
-      inherit (pkgs.rPackages) gh memoise Rcpp codetools crayon rex jsonlite rstudioapi withr httr;
-    } ++ [highlite];
-
-```
-
-and this line:
+`{highlite}` is a dependency of [{lookup}](https://github.com/jimhester/lookup)
+that is only available on GitHub. `{gh}` and `{memoise}` are also listed as
+remote dependencies, however, they are also available on CRAN. What likely happened
+here was that `{gh}` and `{memoise}` were not yet available on CRAN at the time
+when `{lookup}` was written (which was more than 6 years ago now). Because they
+are listed as remote dependencies, they will also be built from Github instead of 
+CRAN. Here, it is up to you to decide if you want to keep the Github version of 
+these packages, or if you should instead include the released CRAN version. Depending
+on what you want to do, going for the CRAN release of the packages might be advisable.
+For example here, trying to build this expression will not work:
+
+This is because `{httr2}` is a package that needs to be compiled from source and will
+not benefit from the Nix-specific fixes that it needs to compile successfully. Change 
+your `default.nix` from:
+
+to:
+
+and then trying to build it will work. In the second, manually edited
+expression, `{httr2}` will now build successfully because Nix is instructed to
+build the CRAN version by applying [this
+fix](https://github.com/NixOS/nixpkgs/blob/7b87fced8bc525d466c7258a042bd12ea336a3c6/pkgs/development/r-modules/default.nix#L1817)
+which was added there by packagers and maintainers of the R programming language
+for `nixpkgs` (it is exactly the same if you tried to install `{httr2}` from Github
+on Windows: you would need to build it from source and thus make
+sure that you have the required system-level dependencies to build it. Instead, it is
+easier to install a pre-compiled binary from CRAN).
+
+Another important point to address is that if remote dependincies are listed in 
+a `DESCRIPTION` file like this:
 
 ```
-buildInputs = [ git_archive_pkgs  system_packages  ];
+Remotes:
+    jimhester/highlite,
+    gaborcsardi/gh,
+    hadley/memoise
 ```
 
-into:
+`{rix}` will automatically use the latest commit from these repositories as the revision.
+If instead the remotes are listed like this:
 
 ```
-buildInputs = [ git_archive_pkgs  system_packages highlite ];
+Remotes:
+    jimhester/highlite@abc123,
+    gaborcsardi/gh@def123,
+    hadley/memoise@ghi123
 ```
 
-Building the expression now succeeds.
-
-We know that this is quite tedious, but at the moment there are no plans to make
-`{rix}` handle remote dependencies automatically. This is for mainly three
-reasons:
-
-- packages with remote dependencies are rare, and never on CRAN on Bioconductor;
-- packages may have remote dependencies, but these dependencies may later be available on CRAN (such as with `{memoise}` and `{gh}` for [{lookup}](https://github.com/jimhester/lookup));
-- `{rix}` cannot decide for the user which commit to use for a remote dependency (or whether to use the released version of that dependency from CRAN).
+then the listed commits will be used. Only commits can be used, anything else
+listed there (such as pull request numbers or release tags) will not work with
+`{rix}`.
 
-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/ropensci/rix/issues) if you require
-assistance.
 

From d9e38de4e89e12ca49611163181ab33f5386dc2d Mon Sep 17 00:00:00 2001
From: Bruno Rodrigues <bruno@brodrigues.co>
Date: Tue, 7 Jan 2025 20:23:30 +0100
Subject: [PATCH 28/31] finished vignetet

---
 ...ling-packages-with-remote-dependencies.Rmd | 242 +++++++++++++++++-
 1 file changed, 229 insertions(+), 13 deletions(-)

diff --git a/vignettes/z-advanced-topic-handling-packages-with-remote-dependencies.Rmd b/vignettes/z-advanced-topic-handling-packages-with-remote-dependencies.Rmd
index ee1278f3..f1cdae8a 100644
--- a/vignettes/z-advanced-topic-handling-packages-with-remote-dependencies.Rmd
+++ b/vignettes/z-advanced-topic-handling-packages-with-remote-dependencies.Rmd
@@ -63,6 +63,124 @@ rix(
 
 This will generate the following `default.nix`:
 
+```
+let
+ pkgs = import (fetchTarball "https://github.com/NixOS/nixpkgs/archive/6a25f33c843a45b8d67ba782b6782973a7265774.tar.gz") {};
+  
+    httr2 = (pkgs.rPackages.buildRPackage {
+      name = "httr2";
+      src = pkgs.fetchgit {
+        url = "https://github.com/r-lib/httr2";
+        rev = "HEAD";
+        sha256 = "sha256-UgJCFPO47mgUt3esRRPhXjr0oNDRrR9XAAIxMhZYbFc=";
+      };
+      propagatedBuildInputs = builtins.attrValues {
+        inherit (pkgs.rPackages) 
+          cli
+          curl
+          glue
+          lifecycle
+          magrittr
+          openssl
+          R6
+          rappdirs
+          rlang
+          vctrs
+          withr;
+      };
+    });
+
+    gh = (pkgs.rPackages.buildRPackage {
+      name = "gh";
+      src = pkgs.fetchgit {
+        url = "https://github.com/gaborcsardi/gh";
+        rev = "HEAD";
+        sha256 = "sha256-VpxFIfUEk0PudytQ3boMhEJhT0AnelWkSU++WD/HAyo=";
+      };
+      propagatedBuildInputs = builtins.attrValues {
+        inherit (pkgs.rPackages) 
+          cli
+          gitcreds
+          glue
+          ini
+          jsonlite
+          lifecycle
+          rlang;
+      } ++ [ httr2 ];
+    });
+
+
+    highlite = (pkgs.rPackages.buildRPackage {
+      name = "highlite";
+      src = pkgs.fetchgit {
+        url = "https://github.com/jimhester/highlite";
+        rev = "HEAD";
+        sha256 = "sha256-lkWMlAi75MYxiBUYnLwxLK9ApXkWanA4Mt7g4qtLpxM=";
+      };
+      propagatedBuildInputs = builtins.attrValues {
+        inherit (pkgs.rPackages) 
+          Rcpp
+          BH;
+      };
+    });
+
+
+    memoise = (pkgs.rPackages.buildRPackage {
+      name = "memoise";
+      src = pkgs.fetchgit {
+        url = "https://github.com/hadley/memoise";
+        rev = "HEAD";
+        sha256 = "sha256-FDMNgrgctzkN8dXKRoWsOKe3tXxmm8Cqdu/Sh6WKx/Q=";
+      };
+      propagatedBuildInputs = builtins.attrValues {
+        inherit (pkgs.rPackages) 
+          rlang
+          cachem;
+      };
+    });
+
+    lookup = (pkgs.rPackages.buildRPackage {
+      name = "lookup";
+      src = pkgs.fetchgit {
+        url = "https://github.com/jimhester/lookup/";
+        rev = "eba63db477dd2f20153b75e2949eb333a36cccfc";
+        sha256 = "sha256-arl7LVxL8xGUW3LhuDCSUjcfswX0rdofL/7v8Klw8FM=";
+      };
+      propagatedBuildInputs = builtins.attrValues {
+        inherit (pkgs.rPackages) 
+          Rcpp
+          codetools
+          crayon
+          rex
+          jsonlite
+          rstudioapi
+          withr
+          httr;
+      } ++ [ highlite gh memoise ];
+    });
+    
+  system_packages = builtins.attrValues {
+    inherit (pkgs) 
+      glibcLocales
+      nix
+      R;
+  };
+  
+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 = [ lookup   system_packages   ];
+  
+}
+```
 
 
 as you can see, several other packages hosted on Github were added
@@ -89,23 +207,121 @@ these packages, or if you should instead include the released CRAN version. Depe
 on what you want to do, going for the CRAN release of the packages might be advisable.
 For example here, trying to build this expression will not work:
 
-This is because `{httr2}` is a package that needs to be compiled from source and will
-not benefit from the Nix-specific fixes that it needs to compile successfully. Change 
-your `default.nix` from:
+This is because `{httr2}` is a package that needs to be compiled from source and
+will not benefit from the Nix-specific fixes that need to be applied to its
+source code for it to build successfully. In order to install the version of
+`{httr2}` from CRAN which will build successfully, change the `default.nix`
+manually to this (essentially remove the definition of `{httr2}` and put it
+as a `propagatedBuildInput` to `{gh}`):
+
+```
+let
+ pkgs = import (fetchTarball "https://github.com/NixOS/nixpkgs/archive/6a25f33c843a45b8d67ba782b6782973a7265774.tar.gz") {};
+
+    gh = (pkgs.rPackages.buildRPackage {
+      name = "gh";
+      src = pkgs.fetchgit {
+        url = "https://github.com/gaborcsardi/gh";
+        rev = "HEAD";
+        sha256 = "sha256-VpxFIfUEk0PudytQ3boMhEJhT0AnelWkSU++WD/HAyo=";
+      };
+      propagatedBuildInputs = builtins.attrValues {
+        inherit (pkgs.rPackages)
+          cli
+          gitcreds
+          glue
+          httr2 # <- httr2 is now declared here, so it's the CRAN version
+          ini
+          jsonlite
+          lifecycle
+          rlang;
+      };
+    });
+
+
+    highlite = (pkgs.rPackages.buildRPackage {
+      name = "highlite";
+      src = pkgs.fetchgit {
+        url = "https://github.com/jimhester/highlite";
+        rev = "HEAD";
+        sha256 = "sha256-lkWMlAi75MYxiBUYnLwxLK9ApXkWanA4Mt7g4qtLpxM=";
+      };
+      propagatedBuildInputs = builtins.attrValues {
+        inherit (pkgs.rPackages) 
+          Rcpp
+          BH;
+      };
+    });
+
+
+    memoise = (pkgs.rPackages.buildRPackage {
+      name = "memoise";
+      src = pkgs.fetchgit {
+        url = "https://github.com/hadley/memoise";
+        rev = "HEAD";
+        sha256 = "sha256-FDMNgrgctzkN8dXKRoWsOKe3tXxmm8Cqdu/Sh6WKx/Q=";
+      };
+      propagatedBuildInputs = builtins.attrValues {
+        inherit (pkgs.rPackages)
+          rlang
+          cachem;
+      };
+    });
 
-to:
+    lookup = (pkgs.rPackages.buildRPackage {
+      name = "lookup";
+      src = pkgs.fetchgit {
+        url = "https://github.com/jimhester/lookup/";
+        rev = "eba63db477dd2f20153b75e2949eb333a36cccfc";
+        sha256 = "sha256-arl7LVxL8xGUW3LhuDCSUjcfswX0rdofL/7v8Klw8FM=";
+      };
+      propagatedBuildInputs = builtins.attrValues {
+        inherit (pkgs.rPackages)
+          Rcpp
+          codetools
+          crayon
+          rex
+          jsonlite
+          rstudioapi
+          withr
+          httr;
+      } ++ [ highlite gh memoise ];
+    });
+
+  system_packages = builtins.attrValues {
+    inherit (pkgs)
+      glibcLocales
+      nix
+      R;
+  };
+
+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 = [ lookup   system_packages   ];
+  
+}
+```
 
-and then trying to build it will work. In the second, manually edited
-expression, `{httr2}` will now build successfully because Nix is instructed to
-build the CRAN version by applying [this
+and then try to build it will work. In the second, manually edited expression,
+`{httr2}` will now build successfully because Nix is instructed to build the
+CRAN version by applying [this
 fix](https://github.com/NixOS/nixpkgs/blob/7b87fced8bc525d466c7258a042bd12ea336a3c6/pkgs/development/r-modules/default.nix#L1817)
 which was added there by packagers and maintainers of the R programming language
-for `nixpkgs` (it is exactly the same if you tried to install `{httr2}` from Github
-on Windows: you would need to build it from source and thus make
-sure that you have the required system-level dependencies to build it. Instead, it is
+for `nixpkgs` (it is exactly the same if you tried to install `{httr2}` from
+Github on Windows: you would need to build it from source and thus make sure
+that you have the required system-level dependencies to build it. Instead, it is
 easier to install a pre-compiled binary from CRAN).
 
-Another important point to address is that if remote dependincies are listed in 
+Another important point to address is that if remote dependencies are listed in
 a `DESCRIPTION` file like this:
 
 ```
@@ -115,8 +331,8 @@ Remotes:
     hadley/memoise
 ```
 
-`{rix}` will automatically use the latest commit from these repositories as the revision.
-If instead the remotes are listed like this:
+`{rix}` will automatically use the latest commit from these repositories as the
+revision. If instead the remotes are listed like this:
 
 ```
 Remotes:

From d3fe565d64975b0015df1e5feb902767bc22a1b2 Mon Sep 17 00:00:00 2001
From: Bruno Rodrigues <brodriguesco@protonmail.com>
Date: Wed, 8 Jan 2025 13:48:12 +0100
Subject: [PATCH 29/31] changed b-rodrigues/lookup commit

---
 tests/testthat/test-fetchers.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-fetchers.R b/tests/testthat/test-fetchers.R
index 91f40011..be3f8d45 100644
--- a/tests/testthat/test-fetchers.R
+++ b/tests/testthat/test-fetchers.R
@@ -158,7 +158,7 @@ testthat::test_that("Test fetchgit gets a package with several remote deps and c
       list(
         package_name = "lookup",
         repo_url = "https://github.com/b-rodrigues/lookup/",
-        commit = "a36973c87ec0f24e4b1bf2884c7cc99dc442f8ff"
+        commit = "f7c836fae9bddf7da298f7b7fb311ce0fb33488b"
       )
     ),
     "\n    glue = (pkgs.rPackages.buildRPackage {\n      name = \"glue\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/tidyverse/glue\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-HuYKjZYVd2RF16F3HsYE7xGQHvV45z6YIe5K6OlDFLo=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) ;\n      };\n    });\n\n\n    httr = (pkgs.rPackages.buildRPackage {\n      name = \"httr\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/hadley/httr\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-DtgrlVyPhp0V3bgpwzvJMH7luxqPJJ37ObMIeZnUDX8=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          curl\n          jsonlite\n          mime\n          openssl\n          R6;\n      };\n    });\n\n    httrmock = (pkgs.rPackages.buildRPackage {\n      name = \"httrmock\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/gaborcsardi/httrmock\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-+Sncxv83N/FB0mL1KJSTtwFoZb6zxULncmr00cv7Fuc=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          assertthat\n          base64enc\n          debugme\n          digest\n          lintr\n          R6\n          rprojroot\n          whoami;\n      } ++ [ httr glue ];\n    });\n\n    gh = (pkgs.rPackages.buildRPackage {\n      name = \"gh\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/gaborcsardi/gh\";\n        rev = \"8237a88\";\n        sha256 = \"sha256-yZofcmA+mpYsi81DcEQsA2vtVcaTvK1FDXfpJEiLqVY=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          ini\n          jsonlite\n          httr;\n      } ++ [ httrmock ];\n    });\n\n\n    highlite = (pkgs.rPackages.buildRPackage {\n      name = \"highlite\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/jimhester/highlite\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-lkWMlAi75MYxiBUYnLwxLK9ApXkWanA4Mt7g4qtLpxM=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          Rcpp\n          BH;\n      };\n    });\n\n\n    memoise = (pkgs.rPackages.buildRPackage {\n      name = \"memoise\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/hadley/memoise\";\n        rev = \"74d62c8\";\n        sha256 = \"sha256-fsdop66VglkOIYrJ0LKZKikIZmzQ2gqEATLy9tTJ/B8=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          digest;\n      };\n    });\n\n    lookup = (pkgs.rPackages.buildRPackage {\n      name = \"lookup\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/b-rodrigues/lookup/\";\n        rev = \"a36973c87ec0f24e4b1bf2884c7cc99dc442f8ff\";\n        sha256 = \"sha256-zE5LcjeO5xcABo+ZfHLh6N1bWbH9rJYLfL0ewZe7/bk=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          Rcpp\n          codetools\n          crayon\n          rex\n          jsonlite\n          rstudioapi\n          withr\n          httr;\n      } ++ [ highlite gh memoise ];\n    });\n"

From 35abfd721603489a9c1c55d1d4676e265e8d97a0 Mon Sep 17 00:00:00 2001
From: Bruno Rodrigues <bruno@brodrigues.co>
Date: Wed, 8 Jan 2025 21:05:43 +0100
Subject: [PATCH 30/31] updated test and vignett

---
 tests/testthat/test-fetchers.R                |  33 +----
 ...ling-packages-with-remote-dependencies.Rmd | 118 +++++++++++++-----
 2 files changed, 88 insertions(+), 63 deletions(-)

diff --git a/tests/testthat/test-fetchers.R b/tests/testthat/test-fetchers.R
index be3f8d45..0bcc23a4 100644
--- a/tests/testthat/test-fetchers.R
+++ b/tests/testthat/test-fetchers.R
@@ -122,35 +122,6 @@ testthat::test_that("Test fetchpkgs works", {
   )
 })
 
-testthat::test_that("Test fetchgit gets a package with several remote deps", {
-  testthat::skip_on_cran()
-  testthat::expect_equal(
-    fetchgit(
-      list(
-        package_name = "lookup",
-        repo_url = "https://github.com/jimhester/lookup/",
-        commit = "eba63db477dd2f20153b75e2949eb333a36cccfc"
-      )
-    ),
-    "\n    httr2 = (pkgs.rPackages.buildRPackage {\n      name = \"httr2\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/r-lib/httr2\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-rPMn+MvN/KCnhulS0Itv2g58fRYQw75SBJC15cSBxBI=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          cli\n          curl\n          glue\n          lifecycle\n          magrittr\n          openssl\n          R6\n          rappdirs\n          rlang\n          vctrs\n          withr;\n      };\n    });\n\n    gh = (pkgs.rPackages.buildRPackage {\n      name = \"gh\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/gaborcsardi/gh\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-VpxFIfUEk0PudytQ3boMhEJhT0AnelWkSU++WD/HAyo=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          cli\n          gitcreds\n          glue\n          ini\n          jsonlite\n          lifecycle\n          rlang;\n      } ++ [ httr2 ];\n    });\n\n\n    highlite = (pkgs.rPackages.buildRPackage {\n      name = \"highlite\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/jimhester/highlite\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-lkWMlAi75MYxiBUYnLwxLK9ApXkWanA4Mt7g4qtLpxM=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          Rcpp\n          BH;\n      };\n    });\n\n\n    memoise = (pkgs.rPackages.buildRPackage {\n      name = \"memoise\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/hadley/memoise\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-FDMNgrgctzkN8dXKRoWsOKe3tXxmm8Cqdu/Sh6WKx/Q=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          rlang\n          cachem;\n      };\n    });\n\n    lookup = (pkgs.rPackages.buildRPackage {\n      name = \"lookup\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/jimhester/lookup/\";\n        rev = \"eba63db477dd2f20153b75e2949eb333a36cccfc\";\n        sha256 = \"sha256-arl7LVxL8xGUW3LhuDCSUjcfswX0rdofL/7v8Klw8FM=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          Rcpp\n          codetools\n          crayon\n          rex\n          jsonlite\n          rstudioapi\n          withr\n          httr;\n      } ++ [ highlite gh memoise ];\n    });\n"
-  )
-})
-
-
-testthat::test_that("Test fetchgit gets a package with one remote dep", {
-  testthat::skip_on_cran()
-  testthat::expect_equal(
-    fetchgit(
-      list(
-        package_name = "scMisc",
-        repo_url = "https://github.com/mihem/scMisc/",
-        commit = "e2ebddcb779b935551f14216514c0429616fc91d"
-      )
-    ),
-    "\n    enrichR = (pkgs.rPackages.buildRPackage {\n      name = \"enrichR\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/wjawaid/enrichR\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-Jm6Z46ARyp+geSY4RLb/x9zV6uvlyjnFdLh4/c6uGoI=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          httr\n          curl\n          rjson\n          ggplot2\n          WriteXLS;\n      };\n    });\n\n    scMisc = (pkgs.rPackages.buildRPackage {\n      name = \"scMisc\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/mihem/scMisc/\";\n        rev = \"e2ebddcb779b935551f14216514c0429616fc91d\";\n        sha256 = \"sha256-Atmr+vGfJxNc5HK+UgpnSIeZ1fYKWEzD3Dt2va1xoFE=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          Seurat\n          readr\n          glue\n          viridis\n          ggplot2\n          pheatmap\n          homologene\n          dplyr\n          tibble\n          magrittr\n          clustifyr\n          ggrepel\n          writexl\n          ggsignif\n          patchwork\n          rstatix\n          readxl\n          tidyr\n          speckle\n          limma\n          RColorBrewer\n          factoextra\n          FactoMineR\n          Matrix\n          ggpubr\n          tidyselect\n          stringr\n          forcats;\n      } ++ [ enrichR ];\n    });\n"
-  )
-})
-
 testthat::test_that("Test fetchgit gets a package with several remote deps and commits", {
   testthat::skip_on_cran()
   testthat::expect_equal(
@@ -158,9 +129,9 @@ testthat::test_that("Test fetchgit gets a package with several remote deps and c
       list(
         package_name = "lookup",
         repo_url = "https://github.com/b-rodrigues/lookup/",
-        commit = "f7c836fae9bddf7da298f7b7fb311ce0fb33488b"
+        commit = "ee5505c817b19b59d37236ed35a81a65aa376124"
       )
     ),
-    "\n    glue = (pkgs.rPackages.buildRPackage {\n      name = \"glue\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/tidyverse/glue\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-HuYKjZYVd2RF16F3HsYE7xGQHvV45z6YIe5K6OlDFLo=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) ;\n      };\n    });\n\n\n    httr = (pkgs.rPackages.buildRPackage {\n      name = \"httr\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/hadley/httr\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-DtgrlVyPhp0V3bgpwzvJMH7luxqPJJ37ObMIeZnUDX8=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          curl\n          jsonlite\n          mime\n          openssl\n          R6;\n      };\n    });\n\n    httrmock = (pkgs.rPackages.buildRPackage {\n      name = \"httrmock\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/gaborcsardi/httrmock\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-+Sncxv83N/FB0mL1KJSTtwFoZb6zxULncmr00cv7Fuc=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          assertthat\n          base64enc\n          debugme\n          digest\n          lintr\n          R6\n          rprojroot\n          whoami;\n      } ++ [ httr glue ];\n    });\n\n    gh = (pkgs.rPackages.buildRPackage {\n      name = \"gh\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/gaborcsardi/gh\";\n        rev = \"8237a88\";\n        sha256 = \"sha256-yZofcmA+mpYsi81DcEQsA2vtVcaTvK1FDXfpJEiLqVY=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          ini\n          jsonlite\n          httr;\n      } ++ [ httrmock ];\n    });\n\n\n    highlite = (pkgs.rPackages.buildRPackage {\n      name = \"highlite\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/jimhester/highlite\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-lkWMlAi75MYxiBUYnLwxLK9ApXkWanA4Mt7g4qtLpxM=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          Rcpp\n          BH;\n      };\n    });\n\n\n    memoise = (pkgs.rPackages.buildRPackage {\n      name = \"memoise\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/hadley/memoise\";\n        rev = \"74d62c8\";\n        sha256 = \"sha256-fsdop66VglkOIYrJ0LKZKikIZmzQ2gqEATLy9tTJ/B8=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          digest;\n      };\n    });\n\n    lookup = (pkgs.rPackages.buildRPackage {\n      name = \"lookup\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/b-rodrigues/lookup/\";\n        rev = \"a36973c87ec0f24e4b1bf2884c7cc99dc442f8ff\";\n        sha256 = \"sha256-zE5LcjeO5xcABo+ZfHLh6N1bWbH9rJYLfL0ewZe7/bk=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          Rcpp\n          codetools\n          crayon\n          rex\n          jsonlite\n          rstudioapi\n          withr\n          httr;\n      } ++ [ highlite gh memoise ];\n    });\n"
+"\n    httr2 = (pkgs.rPackages.buildRPackage {\n      name = \"httr2\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/b-rodrigues/httr2\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-ny4J2WqUL4LPLWRKS8rgVqwvgMOQ2Rm/lbBWtF+99PE=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          cli\n          curl\n          glue\n          lifecycle\n          magrittr\n          openssl\n          R6\n          rappdirs\n          rlang\n          vctrs\n          withr;\n      };\n    });\n\n    gh = (pkgs.rPackages.buildRPackage {\n      name = \"gh\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/b-rodrigues/gh\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-POXEMZv8kqHokAxK8LoWkS0qYrcIcVdQi5xyGD992KU=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          cli\n          gitcreds\n          glue\n          ini\n          jsonlite\n          lifecycle\n          rlang;\n      } ++ [ httr2 ];\n    });\n\n\n    highlite = (pkgs.rPackages.buildRPackage {\n      name = \"highlite\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/jimhester/highlite\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-lkWMlAi75MYxiBUYnLwxLK9ApXkWanA4Mt7g4qtLpxM=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          Rcpp\n          BH;\n      };\n    });\n\n\n    memoise = (pkgs.rPackages.buildRPackage {\n      name = \"memoise\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/b-rodrigues/memoise\";\n        rev = \"74d62c8\";\n        sha256 = \"sha256-fsdop66VglkOIYrJ0LKZKikIZmzQ2gqEATLy9tTJ/B8=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          digest;\n      };\n    });\n\n    lookup = (pkgs.rPackages.buildRPackage {\n      name = \"lookup\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/b-rodrigues/lookup/\";\n        rev = \"ee5505c817b19b59d37236ed35a81a65aa376124\";\n        sha256 = \"sha256-jiSBuC1vzJbN6OckgVX0E+XuMCeZS5LKsldIVL7DNgo=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          Rcpp\n          codetools\n          crayon\n          rex\n          jsonlite\n          rstudioapi\n          withr\n          httr;\n      } ++ [ highlite gh memoise ];\n    });\n"
   )
 })
diff --git a/vignettes/z-advanced-topic-handling-packages-with-remote-dependencies.Rmd b/vignettes/z-advanced-topic-handling-packages-with-remote-dependencies.Rmd
index f1cdae8a..377c123b 100644
--- a/vignettes/z-advanced-topic-handling-packages-with-remote-dependencies.Rmd
+++ b/vignettes/z-advanced-topic-handling-packages-with-remote-dependencies.Rmd
@@ -21,7 +21,7 @@ library(rix)
 ## Introduction
 
 Packages published on CRAN must have their dependencies on either CRAN or
-BioConductor, but not on GitHub. However, there are many packages available on
+Bioconductor, but not on GitHub. However, there are many packages available on
 GitHub that never get published on CRAN, and some of these packages may even
 depend on other packages that are also only available on GitHub. `{rix}` makes
 it possible to install packages from GitHub and if these packages have
@@ -66,7 +66,7 @@ This will generate the following `default.nix`:
 ```
 let
  pkgs = import (fetchTarball "https://github.com/NixOS/nixpkgs/archive/6a25f33c843a45b8d67ba782b6782973a7265774.tar.gz") {};
-  
+
     httr2 = (pkgs.rPackages.buildRPackage {
       name = "httr2";
       src = pkgs.fetchgit {
@@ -75,7 +75,7 @@ let
         sha256 = "sha256-UgJCFPO47mgUt3esRRPhXjr0oNDRrR9XAAIxMhZYbFc=";
       };
       propagatedBuildInputs = builtins.attrValues {
-        inherit (pkgs.rPackages) 
+        inherit (pkgs.rPackages)
           cli
           curl
           glue
@@ -158,14 +158,14 @@ let
           httr;
       } ++ [ highlite gh memoise ];
     });
-    
+
   system_packages = builtins.attrValues {
-    inherit (pkgs) 
+    inherit (pkgs)
       glibcLocales
       nix
       R;
   };
-  
+
 in
 
 pkgs.mkShell {
@@ -178,11 +178,10 @@ pkgs.mkShell {
    LC_MEASUREMENT = "en_US.UTF-8";
 
   buildInputs = [ lookup   system_packages   ];
-  
+ 
 }
 ```
 
-
 as you can see, several other packages hosted on Github were added
 automatically. This is because these were listed as remote dependencies in
 `{lookup}`'s `DESCRIPTION` file:
@@ -198,21 +197,22 @@ Remotes:
 
 `{highlite}` is a dependency of [{lookup}](https://github.com/jimhester/lookup)
 that is only available on GitHub. `{gh}` and `{memoise}` are also listed as
-remote dependencies, however, they are also available on CRAN. What likely happened
-here was that `{gh}` and `{memoise}` were not yet available on CRAN at the time
-when `{lookup}` was written (which was more than 6 years ago now). Because they
-are listed as remote dependencies, they will also be built from Github instead of 
-CRAN. Here, it is up to you to decide if you want to keep the Github version of 
-these packages, or if you should instead include the released CRAN version. Depending
-on what you want to do, going for the CRAN release of the packages might be advisable.
-For example here, trying to build this expression will not work:
+remote dependencies, however, they are also available on CRAN. What likely
+happened here was that `{gh}` and `{memoise}` were not yet available on CRAN at
+the time when `{lookup}` was written (which was more than 6 years ago as of
+2025). Because they are listed as remote dependencies, they will also be built
+from GitHub instead of CRAN. Here, it is up to you to decide if you want to keep
+the GitHub version of these packages, or if you should instead include the
+released CRAN version. Depending on what you want to do, going for the CRAN
+release of the packages might be advisable. For example in this case, trying to
+build this expression will not work.
 
 This is because `{httr2}` is a package that needs to be compiled from source and
-will not benefit from the Nix-specific fixes that need to be applied to its
-source code for it to build successfully. In order to install the version of
-`{httr2}` from CRAN which will build successfully, change the `default.nix`
-manually to this (essentially remove the definition of `{httr2}` and put it
-as a `propagatedBuildInput` to `{gh}`):
+which needs some Nix-specific fixes applied to its source code for it to build
+successfully. Installing the version provided by `nixpkgs`, which builds upon
+the released CRAN version will succeed however. To do so, change the
+`default.nix` manually to this (essentially remove the definition of `{httr2}`
+and put it as a `propagatedBuildInput` to `{gh}`):
 
 ```
 let
@@ -238,7 +238,6 @@ let
       };
     });
 
-
     highlite = (pkgs.rPackages.buildRPackage {
       name = "highlite";
       src = pkgs.fetchgit {
@@ -253,7 +252,6 @@ let
       };
     });
 
-
     memoise = (pkgs.rPackages.buildRPackage {
       name = "memoise";
       src = pkgs.fetchgit {
@@ -307,17 +305,16 @@ pkgs.mkShell {
    LC_MEASUREMENT = "en_US.UTF-8";
 
   buildInputs = [ lookup   system_packages   ];
-  
+
 }
 ```
 
-and then try to build it will work. In the second, manually edited expression,
-`{httr2}` will now build successfully because Nix is instructed to build the
-CRAN version by applying [this
+In this manually edited expression, `{httr2}` will now build successfully
+because Nix is instructed to build the CRAN version by applying [this
 fix](https://github.com/NixOS/nixpkgs/blob/7b87fced8bc525d466c7258a042bd12ea336a3c6/pkgs/development/r-modules/default.nix#L1817)
 which was added there by packagers and maintainers of the R programming language
 for `nixpkgs` (it is exactly the same if you tried to install `{httr2}` from
-Github on Windows: you would need to build it from source and thus make sure
+GitHub on Windows: you would need to build it from source and thus make sure
 that you have the required system-level dependencies to build it. Instead, it is
 easier to install a pre-compiled binary from CRAN).
 
@@ -332,7 +329,57 @@ Remotes:
 ```
 
 `{rix}` will automatically use the latest commit from these repositories as the
-revision. If instead the remotes are listed like this:
+revision. This also means that if these repositories are being actively worked on,
+rebuilding these environments will actually pull another version of these packages.
+Instead, it is advisable to edit the `default.nix` yet again, and replace mentions
+of `HEAD` with an actual commit. For example, edit this:
+
+```
+    gh = (pkgs.rPackages.buildRPackage {
+      name = "gh";
+      src = pkgs.fetchgit {
+        url = "https://github.com/gaborcsardi/gh";
+        rev = "HEAD";
+        sha256 = "sha256-VpxFIfUEk0PudytQ3boMhEJhT0AnelWkSU++WD/HAyo=";
+      };
+      propagatedBuildInputs = builtins.attrValues {
+        inherit (pkgs.rPackages) 
+          cli
+          gitcreds
+          glue
+          ini
+          jsonlite
+          lifecycle
+          rlang;
+      } ++ [ httr2 ];
+    });
+```
+
+to this:
+
+```
+    gh = (pkgs.rPackages.buildRPackage {
+      name = "gh";
+      src = pkgs.fetchgit {
+        url = "https://github.com/gaborcsardi/gh";
+        rev = "27db16cf363dc";
+        sha256 = ""; # <- You will need to try to build the expression once, and then
+      };             # <- put the sha256 that nix-build returns
+      propagatedBuildInputs = builtins.attrValues {
+        inherit (pkgs.rPackages)
+          cli
+          gitcreds
+          glue
+          ini
+          jsonlite
+          lifecycle
+          rlang;
+      } ++ [ httr2 ];
+    });
+```
+
+
+However, if instead the remotes are listed like this:
 
 ```
 Remotes:
@@ -341,8 +388,15 @@ Remotes:
     hadley/memoise@ghi123
 ```
 
-then the listed commits will be used. Only commits can be used, anything else
-listed there (such as pull request numbers or release tags) will not work with
-`{rix}`.
+then the listed commits will be used, which will make sure that the build
+process is reproducible. Only commits can be used, anything else listed there
+(such as pull request numbers or release tags) will not work with `{rix}`.
+
+In conclusion, `{rix}` makes it easier to build packages from GitHub which
+have themselves dependencies hosted on GitHub, you should however make sure
+that the expression that is generated uses fixed commits instead of `HEAD`
+for the packages being built from GitHub, and you should also decide if you
+want to use the version of a packages hosted on GitHub instead of the CRAN
+release. These are decisions that `{rix}` cannot take for you.
 
 

From 43233481da30171517aaf517e4cb44aaa9a50a2b Mon Sep 17 00:00:00 2001
From: b-rodrigues <b-rodrigues@users.noreply.github.com>
Date: Wed, 8 Jan 2025 20:08:08 +0000
Subject: [PATCH 31/31] Style via {styler}

---
 tests/testthat/test-fetchers.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-fetchers.R b/tests/testthat/test-fetchers.R
index 0bcc23a4..29747980 100644
--- a/tests/testthat/test-fetchers.R
+++ b/tests/testthat/test-fetchers.R
@@ -132,6 +132,6 @@ testthat::test_that("Test fetchgit gets a package with several remote deps and c
         commit = "ee5505c817b19b59d37236ed35a81a65aa376124"
       )
     ),
-"\n    httr2 = (pkgs.rPackages.buildRPackage {\n      name = \"httr2\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/b-rodrigues/httr2\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-ny4J2WqUL4LPLWRKS8rgVqwvgMOQ2Rm/lbBWtF+99PE=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          cli\n          curl\n          glue\n          lifecycle\n          magrittr\n          openssl\n          R6\n          rappdirs\n          rlang\n          vctrs\n          withr;\n      };\n    });\n\n    gh = (pkgs.rPackages.buildRPackage {\n      name = \"gh\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/b-rodrigues/gh\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-POXEMZv8kqHokAxK8LoWkS0qYrcIcVdQi5xyGD992KU=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          cli\n          gitcreds\n          glue\n          ini\n          jsonlite\n          lifecycle\n          rlang;\n      } ++ [ httr2 ];\n    });\n\n\n    highlite = (pkgs.rPackages.buildRPackage {\n      name = \"highlite\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/jimhester/highlite\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-lkWMlAi75MYxiBUYnLwxLK9ApXkWanA4Mt7g4qtLpxM=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          Rcpp\n          BH;\n      };\n    });\n\n\n    memoise = (pkgs.rPackages.buildRPackage {\n      name = \"memoise\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/b-rodrigues/memoise\";\n        rev = \"74d62c8\";\n        sha256 = \"sha256-fsdop66VglkOIYrJ0LKZKikIZmzQ2gqEATLy9tTJ/B8=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          digest;\n      };\n    });\n\n    lookup = (pkgs.rPackages.buildRPackage {\n      name = \"lookup\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/b-rodrigues/lookup/\";\n        rev = \"ee5505c817b19b59d37236ed35a81a65aa376124\";\n        sha256 = \"sha256-jiSBuC1vzJbN6OckgVX0E+XuMCeZS5LKsldIVL7DNgo=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          Rcpp\n          codetools\n          crayon\n          rex\n          jsonlite\n          rstudioapi\n          withr\n          httr;\n      } ++ [ highlite gh memoise ];\n    });\n"
+    "\n    httr2 = (pkgs.rPackages.buildRPackage {\n      name = \"httr2\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/b-rodrigues/httr2\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-ny4J2WqUL4LPLWRKS8rgVqwvgMOQ2Rm/lbBWtF+99PE=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          cli\n          curl\n          glue\n          lifecycle\n          magrittr\n          openssl\n          R6\n          rappdirs\n          rlang\n          vctrs\n          withr;\n      };\n    });\n\n    gh = (pkgs.rPackages.buildRPackage {\n      name = \"gh\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/b-rodrigues/gh\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-POXEMZv8kqHokAxK8LoWkS0qYrcIcVdQi5xyGD992KU=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          cli\n          gitcreds\n          glue\n          ini\n          jsonlite\n          lifecycle\n          rlang;\n      } ++ [ httr2 ];\n    });\n\n\n    highlite = (pkgs.rPackages.buildRPackage {\n      name = \"highlite\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/jimhester/highlite\";\n        rev = \"HEAD\";\n        sha256 = \"sha256-lkWMlAi75MYxiBUYnLwxLK9ApXkWanA4Mt7g4qtLpxM=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          Rcpp\n          BH;\n      };\n    });\n\n\n    memoise = (pkgs.rPackages.buildRPackage {\n      name = \"memoise\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/b-rodrigues/memoise\";\n        rev = \"74d62c8\";\n        sha256 = \"sha256-fsdop66VglkOIYrJ0LKZKikIZmzQ2gqEATLy9tTJ/B8=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          digest;\n      };\n    });\n\n    lookup = (pkgs.rPackages.buildRPackage {\n      name = \"lookup\";\n      src = pkgs.fetchgit {\n        url = \"https://github.com/b-rodrigues/lookup/\";\n        rev = \"ee5505c817b19b59d37236ed35a81a65aa376124\";\n        sha256 = \"sha256-jiSBuC1vzJbN6OckgVX0E+XuMCeZS5LKsldIVL7DNgo=\";\n      };\n      propagatedBuildInputs = builtins.attrValues {\n        inherit (pkgs.rPackages) \n          Rcpp\n          codetools\n          crayon\n          rex\n          jsonlite\n          rstudioapi\n          withr\n          httr;\n      } ++ [ highlite gh memoise ];\n    });\n"
   )
 })