From 442e1b87d1bf0134f0fdea1ca7697e08e0b04627 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 22 Mar 2023 09:43:03 +1100
Subject: rPackages.rhdf5filters: fix build

- use hdf5-blosc from nixpkgs to fix failing vendored build
- add missing build dependencies
---
 pkgs/development/r-modules/default.nix             |  7 +++-
 .../r-modules/patches/rhdf5filters.patch           | 46 ++++++++++++++++++++++
 2 files changed, 52 insertions(+), 1 deletion(-)
 create mode 100644 pkgs/development/r-modules/patches/rhdf5filters.patch

(limited to 'pkgs/development/r-modules')

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 8913591d645f1..d89a788b5f12d 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -582,7 +582,7 @@ let
     podkat = [ pkgs.zlib.dev ];
     qrqc = [ pkgs.zlib.dev ];
     rJPSGCS = [ pkgs.zlib.dev ];
-    rhdf5filters = [ pkgs.zlib.dev ];
+    rhdf5filters = with pkgs; [ zlib.dev bzip2.dev ];
     rtk = [ pkgs.zlib.dev ];
     scPipe = [ pkgs.zlib.dev ];
     seqTools = [ pkgs.zlib.dev ];
@@ -1323,6 +1323,11 @@ let
       propagatedBuildInputs = attrs.propagatedBuildInputs ++ [ pkgs.hdf5_1_10.dev pkgs.libaec ];
       patches = [ ./patches/Rhdf5lib.patch ];
     });
+
+    rhdf5filters = old.rhdf5filters.overrideAttrs (attrs: {
+      propagatedBuildInputs = with pkgs; attrs.propagatedBuildInputs ++ [ (hdf5-blosc.override {hdf5 = hdf5_1_10;}) ];
+      patches = [ ./patches/rhdf5filters.patch ];
+    });
     });
   };
 in
diff --git a/pkgs/development/r-modules/patches/rhdf5filters.patch b/pkgs/development/r-modules/patches/rhdf5filters.patch
new file mode 100644
index 0000000000000..39f09f54ceef8
--- /dev/null
+++ b/pkgs/development/r-modules/patches/rhdf5filters.patch
@@ -0,0 +1,46 @@
+diff --git a/src/Makevars.in b/src/Makevars.in
+index 4441634..665a2dd 100644
+--- a/src/Makevars.in
++++ b/src/Makevars.in
+@@ -20,10 +20,9 @@ export PKG_LDFLAGS=@LDFLAGS@
+ all: copying $(SHLIB)
+ 
+ #copy hdf5 library headers to package include
+-copying: blosc/libH5Zblosc.so bzip2/libH5Zbz2.so lzf/libH5Zlzf.so
++copying: bzip2/libH5Zbz2.so lzf/libH5Zlzf.so
+ 	mkdir -p "${USER_LIB_DIR}"
+ 	cp ${BZIP2_LIB} "${USER_LIB_DIR}"
+-	cp ${BLOSC_LIB} "${USER_LIB_DIR}"
+ 	cp ${LZF_LIB} "${USER_LIB_DIR}"
+ 
+ blosc/libH5Zblosc.so:
+diff --git a/src/bzip2/Makefile b/src/bzip2/Makefile
+index 449bbe7..154354e 100644
+--- a/src/bzip2/Makefile
++++ b/src/bzip2/Makefile
+@@ -1,9 +1,9 @@
+ 
+ all: libH5Zbz2.so
+ 
+-libH5Zbz2.so: bzip2-1.0.8/libbz2.a
+-	${CC} ${PKG_CFLAGS} ${PKG_CPICFLAGS} -shared H5Zbzip2.c $(PKG_CPPFLAGS) \
+-	-I./bzip2-1.0.8/ ./bzip2-1.0.8/libbz2.a ${PKG_LDFLAGS} -o libH5Zbz2.so
++libH5Zbz2.so:
++	${CC} ${PKG_CFLAGS} ${PKG_CPICFLAGS} -shared H5Zbzip2.c \
++	   -lbz2 -o libH5Zbz2.so
+ 
+ bzip2-1.0.8/libbz2.a:
+ 	$(MAKE) -C bzip2-1.0.8
+diff --git a/src/lzf/Makefile b/src/lzf/Makefile
+index 837f80b..eeca0c8 100644
+--- a/src/lzf/Makefile
++++ b/src/lzf/Makefile
+@@ -2,7 +2,7 @@
+ all: libH5Zlzf.so
+ 
+ libH5Zlzf.so: lzf/liblzf.a
+-	${CC} ${PKG_CFLAGS} ${PKG_CPICFLAGS} -shared H5Zlzf.c $(PKG_CPPFLAGS) \
++	${CC} ${PKG_CFLAGS} ${PKG_CPICFLAGS} -shared H5Zlzf.c \
+ 	-I./lzf/ ./lzf/liblzf.a ${PKG_LDFLAGS} -o libH5Zlzf.so
+ 
+ lzf/liblzf.a:
-- 
cgit 1.4.1