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rPackages.rhdf5filters: fix build

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- use hdf5-blosc from nixpkgs to fix failing vendored build
- add missing build dependencies
This commit is contained in:
Justin Bedo 2023-03-22 09:43:03 +11:00
parent ccfbc19630
commit 442e1b87d1
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GPG key ID: 2C18202C56C182BD
2 changed files with 52 additions and 1 deletions
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7
pkgs/development/r-modules/default.nix
View file

@ -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

46
pkgs/development/r-modules/patches/rhdf5filters.patch Normal file
View file

@ -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: