From 7b39a5b06e7454a406e5268dd4db821f2b37601b Mon Sep 17 00:00:00 2001
From: agw <cla@weircon.dk>
Date: Tue, 1 Sep 2026 21:55:00 +0200
Subject: [PATCH] Fix R bundling: SIGPIPE abort and wrong R_HOME path

Two bugs found by the first real build:

- 'R --version | head -1' aborted the script with exit 141 under
  'set -o pipefail': head closes the pipe and R dies of SIGPIPE. Use
  'sed -n 1p', which consumes all input.
- R installed to lib64/R, not the lib/R the script assumed. Pin --libdir
  and ask 'R RHOME' for the real path instead of guessing.

Also stop exporting R_HOME. R.cmake warns that a set R_HOME makes R emit
'WARNING: ignoring environment value of R_HOME', which corrupts the output
cmake parses; CUSTOM_R_PATH is the supported way to select an R.
---
 build/build-jasp.sh | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

diff --git a/build/build-jasp.sh b/build/build-jasp.sh
index 91fe7c1..1dc17fa 100755
--- a/build/build-jasp.sh
+++ b/build/build-jasp.sh
@@ -99,9 +99,13 @@ tar -xzf "R-${R_VERSION}.tar.gz"
 cd "R-${R_VERSION}"
 
 # --enable-R-shlib is required: JASP embeds R through RInside/libR.
-# rpath is set to $ORIGIN-relative so the tree stays relocatable after install.
+# --libdir is pinned so R lands in lib/R rather than the lib64/R that Arch's
+# config.site would otherwise pick, which keeps the rpath below predictable.
+# The install prefix equals the final install path, so the rpath stays valid
+# once the tarball is unpacked on the user's machine.
 ./configure \
   --prefix="${R_HOME_DIR}" \
+  --libdir="${R_HOME_DIR}/lib" \
   --enable-R-shlib \
   --enable-memory-profiling \
   --with-blas \
@@ -112,9 +116,14 @@ cd "R-${R_VERSION}"
 make -j"$JOBS"
 make install
 
-export R_HOME="${R_HOME_DIR}/lib/R"
 export PATH="${R_HOME_DIR}/bin:${PATH}"
-R --version | head -1
+# Ask R where it actually put itself rather than assuming lib vs lib64.
+# Deliberately NOT exported: R.cmake notes that a set R_HOME makes R print
+# "WARNING: ignoring environment value of R_HOME", which corrupts the output it
+# parses. CUSTOM_R_PATH is the supported way to point JASP at a specific R.
+JASP_R_HOME="$("${R_HOME_DIR}/bin/R" RHOME)"
+log "bundled R_HOME is ${JASP_R_HOME}"
+"${R_HOME_DIR}/bin/R" --version | sed -n 1p || true
 
 # ------------------------------------------------------------------- checkout
 log "cloning jasp-desktop $JASP_TAG"
@@ -140,7 +149,7 @@ cmake -S "$SRC_DIR" -B "$BUILD_DIR" -G Ninja \
   -DCMAKE_BUILD_TYPE=Release \
   -DCMAKE_INSTALL_PREFIX="$PREFIX" \
   -DLINUX_LOCAL_BUILD=OFF \
-  -DCUSTOM_R_PATH="${R_HOME}" \
+  -DCUSTOM_R_PATH="${JASP_R_HOME}" \
   -Wno-dev
 
 log "compiling JASP (-j$JOBS)"