From 913217572b5a2985fa47374a8599afcbc6e9b327 Mon Sep 17 00:00:00 2001
From: ryanstraight <ryanstraight@arizona.edu>
Date: Mon, 21 Sep 2026 16:43:34 -0700
Subject: [PATCH] Recommend remotes for installing from GitHub

---
 README.md                     | 4 ++--
 README.qmd                    | 4 ++--
 concordance/about.qmd         | 7 +------
 concordance/start/install.qmd | 4 ++--
 vignettes/getting-started.Rmd | 4 ++--
 5 files changed, 9 insertions(+), 14 deletions(-)

diff --git a/README.md b/README.md
index b1c932e..3ea0e26 100644
--- a/README.md
+++ b/README.md
@@ -899,8 +899,8 @@ framework text needs to be staged for this path.
 ### R
 
 ``` r
-# install.packages("pak")
-pak::pak("ryanstraight/cybedtools")
+# install.packages("remotes")
+remotes::install_github("ryanstraight/cybedtools")
 ```
 
 ### Python
diff --git a/README.qmd b/README.qmd
index 174fb35..82fc068 100644
--- a/README.qmd
+++ b/README.qmd
@@ -553,8 +553,8 @@ Install the package, then fetch the public data release: hash-verified per-frame
 ### R
 
 ```r
-# install.packages("pak")
-pak::pak("ryanstraight/cybedtools")
+# install.packages("remotes")
+remotes::install_github("ryanstraight/cybedtools")
 ```
 
 ### Python
diff --git a/concordance/about.qmd b/concordance/about.qmd
index 5cb71fa..7273360 100644
--- a/concordance/about.qmd
+++ b/concordance/about.qmd
@@ -33,16 +33,11 @@ Every number, table, and lookup widget on this site is derived from the same pac
 ## Install cybedtools
 
 ```r
-# Option A: remotes
 install.packages("remotes")
 remotes::install_github("ryanstraight/cybedtools")
-
-# Option B: pak (faster on first install)
-install.packages("pak")
-pak::pkg_install("ryanstraight/cybedtools")
 ```
 
-The package depends on `rdflib`, `jsonlite`, `dplyr`, `purrr`, and `tibble`. See [Start](start/install.qmd) for the full staging pipeline (framework source data, ingestion, graph assembly, query loading).
+Python: `pip install cybedtools`. See [Start](start/install.qmd) for fetching the data release and a first query.
 
 ## How to cite
 
diff --git a/concordance/start/install.qmd b/concordance/start/install.qmd
index 4b4d394..4c50c7a 100644
--- a/concordance/start/install.qmd
+++ b/concordance/start/install.qmd
@@ -8,8 +8,8 @@ subtitle: "Install the package, fetch the data, run your first query"
 ### R
 
 ```{.r}
-install.packages("pak")
-pak::pak("ryanstraight/cybedtools")
+install.packages("remotes")
+remotes::install_github("ryanstraight/cybedtools")
 ```
 
 ### Python
diff --git a/vignettes/getting-started.Rmd b/vignettes/getting-started.Rmd
index 70c1658..faf049e 100644
--- a/vignettes/getting-started.Rmd
+++ b/vignettes/getting-started.Rmd
@@ -37,8 +37,8 @@ A single SPARQL query targeting `cybed:RoleElement` returns atomic elements acro
 ```{r}
 #| eval: false
 # Install from GitHub (not yet on CRAN)
-# install.packages("pak")
-pak::pak("ryanstraight/cybedtools")
+# install.packages("remotes")
+remotes::install_github("ryanstraight/cybedtools")
 ```
 
 The package depends on `rdflib` for RDF/SPARQL, `jsonlite` for JSON-LD I/O, and a small subset of the tidyverse (`dplyr`, `purrr`, `tibble`). A native Python package with the same API is on PyPI: `pip install cybedtools`.