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feat: add GitHub source to load_library #172

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Merged
WeilerP merged 1 commit into from
Oct 19, 2026
Merged

feat: add GitHub source to load_library #172

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23 changes: 17 additions & 6 deletions {{ cookiecutter.project_name }}/scripts/r/_setup.R
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Original file line number Diff line number Diff line change
@@ -1,8 +1,14 @@
# Install (if missing) and attach packages from CRAN or Bioconductor. When install = FALSE, missing packages raise an
# error instead of being installed, since installing is unsafe/undesired in a multi-worker run, for example.
load_library <- function(packages, source = c("CRAN", "Bioconductor"), install = TRUE) {
# Install (if missing) and attach packages from CRAN, Bioconductor, or GitHub (given as "owner/repo"). When
# install = FALSE, missing packages raise an error instead of being installed, since installing is unsafe/undesired in a
# multi-worker run, for example.
load_library <- function(packages, source = c("CRAN", "Bioconductor", "github"), install = TRUE) {
source <- match.arg(source)
is_installed <- vapply(packages, requireNamespace, logical(1), quietly = TRUE)
if (source == "github") {
package_names <- vapply(strsplit(packages, "/"), `[`, character(1), 2)
} else {
package_names <- packages
}
is_installed <- vapply(package_names, requireNamespace, logical(1), quietly = TRUE)
missing_packages <- packages[!is_installed]
if (length(missing_packages) > 0) {
if (!install) {
Expand All @@ -15,14 +21,19 @@ load_library <- function(packages, source = c("CRAN", "Bioconductor"), install =
}
if (source == "CRAN") {
install.packages(missing_packages, repos = "https://cloud.r-project.org")
} else {
} else if (source == "Bioconductor") {
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager", repos = "https://cloud.r-project.org")
}
BiocManager::install(missing_packages, update = FALSE, ask = FALSE)
} else if (source == "github") {
if (!requireNamespace("pak", quietly = TRUE)) {
install.packages("pak", repos = "https://cloud.r-project.org")
}
pak::pak(missing_packages)
}
}
for (package_name in packages) {
for (package_name in package_names) {
library(package_name, character.only = TRUE)
}
}
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