rPackages.Rhdf5lib: fix build
Patch is no-longer necessary; HDF5 no-longer vendored
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@ -389,7 +389,7 @@ let
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Rglpk = [ pkgs.glpk ];
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RGtk2 = [ pkgs.gtk2.dev ];
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rhdf5 = [ pkgs.zlib ];
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Rhdf5lib = [ pkgs.zlib.dev ];
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Rhdf5lib = with pkgs; [ zlib.dev hdf5.dev ];
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Rhpc = with pkgs; [ zlib bzip2.dev icu xz.dev mpi pcre.dev ];
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Rhtslib = with pkgs; [ zlib.dev automake autoconf bzip2.dev xz.dev curl.dev ];
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rjags = [ pkgs.jags ];
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@ -997,10 +997,6 @@ let
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patchPhase = "patchShebangs configure";
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});
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Rhdf5lib = old.Rhdf5lib.overrideDerivation (attrs: {
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patches = [ ./patches/Rhdf5lib.patch ];
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});
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rJava = old.rJava.overrideDerivation (attrs: {
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preConfigure = ''
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export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/
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@ -1,12 +0,0 @@
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diff --git a/configure b/configure
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index e2d292e..b13c0db 100755
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--- a/configure
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+++ b/configure
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@@ -3874,6 +3874,7 @@
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echo "building the hdf5 library...";
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cd ../;
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+sed -i 's#/bin/mv#mv#' configure
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./configure --with-pic --enable-shared=no --enable-cxx --enable-hl \
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--with-szlib=${SZIP_HOME} --with-zlib=${ZLIB_HOME} \
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${WITH_S3_VFD} \
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