From ccfbc19630465aaa666588417d38b56a557a1bff Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 22 Mar 2023 09:41:32 +1100
Subject: [PATCH] rPackages.Rhdf5lib: fix build

use nixpkgs provided hdf5 and libaec to resolve failing vendored code
---
 pkgs/development/r-modules/default.nix        |  6 ++--
 .../r-modules/patches/Rhdf5lib.patch          | 28 +++++++++++++++++++
 2 files changed, 32 insertions(+), 2 deletions(-)
 create mode 100644 pkgs/development/r-modules/patches/Rhdf5lib.patch

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 0966c96cbde13..8913591d645f1 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -389,7 +389,7 @@ let
     Rglpk = [ pkgs.glpk ];
     RGtk2 = [ pkgs.gtk2.dev ];
     rhdf5 = [ pkgs.zlib ];
-    Rhdf5lib = with pkgs; [ zlib.dev hdf5.dev ];
+    Rhdf5lib = with pkgs; [ zlib.dev ];
     Rhpc = with pkgs; [ zlib bzip2.dev icu xz.dev mpi pcre.dev ];
     Rhtslib = with pkgs; [ zlib.dev automake autoconf bzip2.dev xz.dev curl.dev ];
     rjags = [ pkgs.jags ];
@@ -1320,7 +1320,9 @@ let
     });
 
     Rhdf5lib = old.Rhdf5lib.overrideAttrs (attrs: {
-      propagatedBuildInputs = attrs.propagatedBuildInputs ++ [ pkgs.hdf5.dev ];
+      propagatedBuildInputs = attrs.propagatedBuildInputs ++ [ pkgs.hdf5_1_10.dev pkgs.libaec ];
+      patches = [ ./patches/Rhdf5lib.patch ];
+    });
     });
   };
 in
diff --git a/pkgs/development/r-modules/patches/Rhdf5lib.patch b/pkgs/development/r-modules/patches/Rhdf5lib.patch
new file mode 100644
index 0000000000000..424dea79d7ee4
--- /dev/null
+++ b/pkgs/development/r-modules/patches/Rhdf5lib.patch
@@ -0,0 +1,28 @@
+diff --git a/src/Makevars.in b/src/Makevars.in
+index addb6a0..590784a 100644
+--- a/src/Makevars.in
++++ b/src/Makevars.in
+@@ -18,7 +18,7 @@ USER_LIB_DIR = ${R_PACKAGE_DIR}/lib${R_ARCH}/
+ 
+ PKG_CPPFLAGS = -I${USER_INCLUDE_DIR} ${ZLIB_INCLUDE}
+ PKG_CFLAGS = ${ZLIB_LIB}
+-PKG_LIBS = "${USER_LIB_DIR}libhdf5.a" @SZIP_LIB@ -lz
++PKG_LIBS = -lhdf5 -lsz
+ 
+ 
+ 
+@@ -26,12 +26,12 @@ all: $(SHLIB)
+ 
+ $(SHLIB): Rhdf5lib.o
+ 
+-Rhdf5lib.o: copy-hdf5 @COPY_SZIP@
++Rhdf5lib.o:
+ 
+ copy-szip: copy-hdf5
+ 	cp hdf5/libaec-1.0.4/build/szip/lib/libsz.a "${USER_LIB_DIR}"
+ 	cp hdf5/libaec-1.0.4/build/szip/lib/libaec.a "${USER_LIB_DIR}"
+-	
++
+ #copy hdf5 library headers to package include
+ copy-hdf5: @BUILD_HDF5@
+ 	mkdir -p "${USER_INCLUDE_DIR}"