rPackages.rhdf5filters: fix build
- use hdf5-blosc from nixpkgs to fix failing vendored build - add missing build dependencies
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ccfbc19630
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@ -582,7 +582,7 @@ let
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podkat = [ pkgs.zlib.dev ];
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qrqc = [ pkgs.zlib.dev ];
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rJPSGCS = [ pkgs.zlib.dev ];
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rhdf5filters = [ pkgs.zlib.dev ];
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rhdf5filters = with pkgs; [ zlib.dev bzip2.dev ];
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rtk = [ pkgs.zlib.dev ];
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scPipe = [ pkgs.zlib.dev ];
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seqTools = [ pkgs.zlib.dev ];
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@ -1323,6 +1323,11 @@ let
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propagatedBuildInputs = attrs.propagatedBuildInputs ++ [ pkgs.hdf5_1_10.dev pkgs.libaec ];
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patches = [ ./patches/Rhdf5lib.patch ];
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});
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rhdf5filters = old.rhdf5filters.overrideAttrs (attrs: {
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propagatedBuildInputs = with pkgs; attrs.propagatedBuildInputs ++ [ (hdf5-blosc.override {hdf5 = hdf5_1_10;}) ];
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patches = [ ./patches/rhdf5filters.patch ];
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});
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});
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};
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in
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46
pkgs/development/r-modules/patches/rhdf5filters.patch
Normal file
46
pkgs/development/r-modules/patches/rhdf5filters.patch
Normal file
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@ -0,0 +1,46 @@
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diff --git a/src/Makevars.in b/src/Makevars.in
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index 4441634..665a2dd 100644
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--- a/src/Makevars.in
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+++ b/src/Makevars.in
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@@ -20,10 +20,9 @@ export PKG_LDFLAGS=@LDFLAGS@
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all: copying $(SHLIB)
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#copy hdf5 library headers to package include
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-copying: blosc/libH5Zblosc.so bzip2/libH5Zbz2.so lzf/libH5Zlzf.so
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+copying: bzip2/libH5Zbz2.so lzf/libH5Zlzf.so
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mkdir -p "${USER_LIB_DIR}"
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cp ${BZIP2_LIB} "${USER_LIB_DIR}"
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- cp ${BLOSC_LIB} "${USER_LIB_DIR}"
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cp ${LZF_LIB} "${USER_LIB_DIR}"
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blosc/libH5Zblosc.so:
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diff --git a/src/bzip2/Makefile b/src/bzip2/Makefile
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index 449bbe7..154354e 100644
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--- a/src/bzip2/Makefile
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+++ b/src/bzip2/Makefile
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@@ -1,9 +1,9 @@
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all: libH5Zbz2.so
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-libH5Zbz2.so: bzip2-1.0.8/libbz2.a
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- ${CC} ${PKG_CFLAGS} ${PKG_CPICFLAGS} -shared H5Zbzip2.c $(PKG_CPPFLAGS) \
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- -I./bzip2-1.0.8/ ./bzip2-1.0.8/libbz2.a ${PKG_LDFLAGS} -o libH5Zbz2.so
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+libH5Zbz2.so:
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+ ${CC} ${PKG_CFLAGS} ${PKG_CPICFLAGS} -shared H5Zbzip2.c \
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+ -lbz2 -o libH5Zbz2.so
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bzip2-1.0.8/libbz2.a:
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$(MAKE) -C bzip2-1.0.8
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diff --git a/src/lzf/Makefile b/src/lzf/Makefile
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index 837f80b..eeca0c8 100644
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--- a/src/lzf/Makefile
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+++ b/src/lzf/Makefile
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@@ -2,7 +2,7 @@
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all: libH5Zlzf.so
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libH5Zlzf.so: lzf/liblzf.a
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- ${CC} ${PKG_CFLAGS} ${PKG_CPICFLAGS} -shared H5Zlzf.c $(PKG_CPPFLAGS) \
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+ ${CC} ${PKG_CFLAGS} ${PKG_CPICFLAGS} -shared H5Zlzf.c \
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-I./lzf/ ./lzf/liblzf.a ${PKG_LDFLAGS} -o libH5Zlzf.so
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lzf/liblzf.a:
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