From 28270943368f3071e8f0ec33f06d4733f7a59716 Mon Sep 17 00:00:00 2001
From: TomaSajt <62384384+TomaSajt@users.noreply.github.com>
Date: Tue, 17 Jun 2025 17:07:23 +0200
Subject: [PATCH 1/3] rPackages.{Rhtslib,h2o,rmarkdown,tesseract}: use
 --replace-fail

---
 pkgs/development/r-modules/default.nix | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 78483cd61b7e..7816d8f18d7c 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -2523,7 +2523,7 @@ let
 
     Rhtslib = old.Rhtslib.overrideAttrs (attrs: {
       preConfigure = ''
-        substituteInPlace R/zzz.R --replace "-lcurl" "-L${pkgs.curl.out}/lib -lcurl"
+        substituteInPlace R/zzz.R --replace-fail "-lcurl" "-L${pkgs.curl.out}/lib -lcurl"
       '';
     });
 
@@ -2534,7 +2534,7 @@ let
 
         # during runtime the package directory is not writable as it's in the
         # nix store, so store the jar in the user's cache directory instead
-        substituteInPlace R/connection.R --replace \
+        substituteInPlace R/connection.R --replace-fail \
           'dest_file <- file.path(dest_folder, "h2o.jar")' \
           'dest_file <- file.path("~/.cache/", "h2o.jar")'
       '';
@@ -2674,7 +2674,7 @@ let
     rmarkdown = old.rmarkdown.overrideAttrs (_: {
       preConfigure = ''
         substituteInPlace R/pandoc.R \
-          --replace '"~/opt/pandoc"' '"~/opt/pandoc", "${pkgs.pandoc}/bin"'
+          --replace-fail '"~/opt/pandoc"' '"~/opt/pandoc", "${pkgs.pandoc}/bin"'
       '';
     });
 
@@ -2700,7 +2700,7 @@ let
     tesseract = old.tesseract.overrideAttrs (_: {
       preConfigure = ''
         substituteInPlace configure \
-          --replace 'PKG_CONFIG_NAME="tesseract"' 'PKG_CONFIG_NAME="tesseract lept"'
+          --replace-fail 'PKG_CONFIG_NAME="tesseract"' 'PKG_CONFIG_NAME="tesseract lept"'
       '';
     });
 

From 7fe54ed9e7393c3aed398277a64ee9ea5ef13d83 Mon Sep 17 00:00:00 2001
From: TomaSajt <62384384+TomaSajt@users.noreply.github.com>
Date: Tue, 17 Jun 2025 17:10:47 +0200
Subject: [PATCH 2/3] rPackages.proj4: remove substitution

---
 pkgs/development/r-modules/default.nix | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 7816d8f18d7c..c2532f197e4a 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -2580,13 +2580,6 @@ let
       '';
     });
 
-    proj4 = old.proj4.overrideAttrs (attrs: {
-      preConfigure = ''
-        substituteInPlace configure \
-          --replace "-lsqlite3" "-L${lib.makeLibraryPath [ pkgs.sqlite ]} -lsqlite3"
-      '';
-    });
-
     rrd = old.rrd.overrideAttrs (attrs: {
       preConfigure = ''
         patchShebangs configure

From 0d8030ace63fb06caf481dc58dd21225266199e2 Mon Sep 17 00:00:00 2001
From: TomaSajt <62384384+TomaSajt@users.noreply.github.com>
Date: Tue, 17 Jun 2025 17:11:35 +0200
Subject: [PATCH 3/3] rPackages.sparklyr: improve onLoad logic

---
 pkgs/development/r-modules/default.nix | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index c2532f197e4a..cfe8af1583b3 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -2572,11 +2572,17 @@ let
     sparklyr = old.sparklyr.overrideAttrs (attrs: {
       # Pyspark's spark is full featured and better maintained than pkgs.spark
       preConfigure = ''
-        substituteInPlace R/zzz.R \
-          --replace ".onLoad <- function(...) {" \
-            ".onLoad <- function(...) {
-          Sys.setenv(\"SPARK_HOME\" = Sys.getenv(\"SPARK_HOME\", unset = \"${pkgs.python3Packages.pyspark}/${pkgs.python3Packages.python.sitePackages}/pyspark\"))
-          Sys.setenv(\"JAVA_HOME\" = Sys.getenv(\"JAVA_HOME\", unset = \"${pkgs.jdk}\"))"
+        if grep "onLoad" R/zzz.R; then
+          echo "onLoad is already present, patch needs to be updated!"
+          exit 1
+        fi
+
+        cat >> R/zzz.R <<EOF
+        .onLoad <- function(...) {
+          Sys.setenv("SPARK_HOME" = Sys.getenv("SPARK_HOME", unset = "${pkgs.python3Packages.pyspark}/${pkgs.python3Packages.python.sitePackages}/pyspark"))
+          Sys.setenv("JAVA_HOME" = Sys.getenv("JAVA_HOME", unset = "${pkgs.jdk}"))
+        }
+        EOF
       '';
     });