From 5aaa785513081ca1f8bf82eb10c9afd7ab97956f Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Fri, 12 Jun 2026 16:09:24 +0200
Subject: [PATCH 1/4] Test package installed with requireNamespace()

---
 R/install.R   | 2 +-
 R/utilities.R | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/install.R b/R/install.R
index e681b9d5..e58e4688 100644
--- a/R/install.R
+++ b/R/install.R
@@ -99,7 +99,7 @@
 .install_github_load_remotes <-
     function(pkgs, lib.loc = NULL)
 {
-    if (!"remotes" %in% rownames(installed.packages(lib.loc))) {
+    if (!requireNamespace("remotes", lib.loc = lib.loc, quietly = TRUE)) {
         if (is.null(lib.loc))
             lib.loc <- .libPaths()
         .stop(
diff --git a/R/utilities.R b/R/utilities.R
index 68071942..2e27c64a 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -129,6 +129,6 @@ isRelease <-
 .skip_if_BiocVersion_not_available <-
     function()
 {
-    if (!"BiocVersion" %in% rownames(installed.packages()))
+    if (!requireNamespace("BiocVersion", quietly = TRUE))
         testthat::skip("BiocVersion not installed")
 }

From 8e913db7771a1b70eba155f9c3983831db1a12dc Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Fri, 12 Jun 2026 16:10:37 +0200
Subject: [PATCH 2/4] Mark some regexes as fixed

---
 R/inet.R    | 5 +++--
 R/version.R | 6 +++---
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/R/inet.R b/R/inet.R
index f5b6f887..d611d402 100644
--- a/R/inet.R
+++ b/R/inet.R
@@ -91,11 +91,12 @@ NULL
         })
     }, warning = function(w) {
         msg <- conditionMessage(w)
-        if (grepl("not available", msg)) {
+        if (grepl("not available", msg, fixed = TRUE)) {
             msg <- gsub(
                 "this version of R",
                 paste0("Bioconductor version ", "'", version(), "'"),
-                msg
+                msg,
+                fixed = TRUE
             )
             w <- simpleWarning(msg, conditionCall(w))
         }
diff --git a/R/version.R b/R/version.R
index 77371144..fc25ef7f 100644
--- a/R/version.R
+++ b/R/version.R
@@ -108,7 +108,7 @@ format.version_sentinel <-
     txt <- tryCatch(.inet_readLines(config), error = identity)
     if (inherits(txt, "error")) {
         if (startsWith(config, "https://"))
-            config <- sub("https", "http", config)
+            config <- sub("https", "http", config, fixed = TRUE)
         else if (!startsWith(config, "http"))
             config <- paste0("file://", config)
         txt <- tryCatch(.inet_readLines(config), error = identity)
@@ -125,7 +125,7 @@ format.version_sentinel <-
         return(setNames(character(), character()))
     end <- ifelse(length(grps) < start + 1L, length(txt), grps[start + 1] - 1L)
     map <- txt[seq(grps[start] + 1, end)]
-    map <- trimws(gsub("\"", "", sub(" #.*", "", map)))
+    map <- trimws(gsub("\"", "", sub(" #.*", "", map), fixed = TRUE))
 
     pattern <- "(.*): (.*)"
     key <- sub(pattern, "\\1", map)
@@ -263,7 +263,7 @@ format.version_sentinel <-
     sprintf(
         "Bioconductor version %s (BiocManager %s), %s",
         bioc_version, packageVersion("BiocManager"),
-        sub(" version", "", R.version.string)
+        sub(" version", "", R.version.string, fixed = TRUE)
     )
 }
 

From 6c0aa3ab589ec125fd1cb1e816c1278f93ecbcab Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Fri, 12 Jun 2026 16:11:08 +0200
Subject: [PATCH 3/4] Use nzchar() instead of nchar()

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

diff --git a/R/version.R b/R/version.R
index fc25ef7f..8b297e3f 100644
--- a/R/version.R
+++ b/R/version.R
@@ -215,7 +215,7 @@ format.version_sentinel <-
     if (!.version_validity_online_check())
         .version_map_get_offline()
     else {
-        if (is.null(config) || !nchar(config))
+        if (is.null(config) || !nzchar(config))
             config <- "https://bioconductor.org/config.yaml"
         .version_map_get_online(config)
     }

From a1fcc45189dc7de7e20b9634ca832b330327c36d Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Fri, 12 Jun 2026 16:17:25 +0200
Subject: [PATCH 4/4] Simplify if/else chaining

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

diff --git a/R/install.R b/R/install.R
index e58e4688..2f8b9fb7 100644
--- a/R/install.R
+++ b/R/install.R
@@ -146,7 +146,7 @@
     function(pkgs, lib, lib.loc, repos, update, ask, force, ...)
 {
     doing <- .install_filter_github_repos(pkgs)
-    ask <- if (!update) "never" else if (update && !ask) "always" else "default"
+    ask <- if (!update) "never" else if (!ask) "always" else "default"
 
     oopts <- options(repos = repos)     # required by remotes::
     on.exit(options(oopts))