Merge pull request #43287 from iimog/fix-rhdf5lib

rPackages.rhdf5: fix installation

pkgs/development/r-modules/default.nix

@@ -313,6 +313,7 @@ let
     Rglpk = [ pkgs.glpk ];
     RGtk2 = [ pkgs.gtk2.dev ];
     rhdf5 = [ pkgs.zlib ];
+    Rhdf5lib = [ pkgs.zlib ];
     Rhpc = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.openmpi pkgs.pcre.dev ];
     Rhtslib = [ pkgs.zlib.dev pkgs.automake pkgs.autoconf ];
     RJaCGH = [ pkgs.zlib.dev ];
@@ -744,8 +745,8 @@ let
       patches = [ ./patches/BayesXsrc.patch ];
     });
 
-    rhdf5 = old.rhdf5.overrideDerivation (attrs: {
-      patches = [ ./patches/rhdf5.patch ];
+    Rhdf5lib = old.Rhdf5lib.overrideDerivation (attrs: {
+      patches = [ ./patches/Rhdf5lib.patch ];
     });
 
     rJava = old.rJava.overrideDerivation (attrs: {

pkgs/development/r-modules/patches/Rhdf5lib.patch

@@ -0,0 +1,12 @@
+diff --git a/configure b/configure
+index e2d292e..b13c0db 100755
+--- a/configure
++++ b/configure
+@@ -2880,6 +2880,7 @@ $MAKE
+ echo "building the hdf5 library...";
+ cd ../;
+ ## we add the '-w' flag to suppress all the warnings hdf5 prints
++sed -i 's#/bin/mv#mv#' configure
+ ./configure --with-pic --enable-shared=no --enable-cxx \
+     --with-szlib \
+     CXX="${CXX}" CXFLAGS="${CXXFLAGS} -w" \

pkgs/development/r-modules/patches/rhdf5.patch

@@ -1,12 +0,0 @@
-diff --git a/configure b/configure
-index e3e21e8..3d947b6 100755
---- a/configure
-+++ b/configure
-@@ -2859,6 +2859,7 @@ fi;
- 
- echo "building the bundled hdf5 library...";
- cd ${BASEPBNAME};
-+sed -i 's#/bin/mv#mv#' configure
- ./configure  --with-pic --enable-shared=no CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" CC="${CC}" CFLAGS="${CFLAGS}" F77="${F77}"
- $MAKE lib
- cd ../../