Merge pull request #125556 from ivan-tkatchev/rhdf5

rhdf5: fix build (#125101)

pkgs/development/r-modules/default.nix

@@ -309,7 +309,7 @@ let
     Rglpk = [ pkgs.glpk ];
     RGtk2 = [ pkgs.gtk2.dev ];
     rhdf5 = [ pkgs.zlib ];
-    Rhdf5lib = [ pkgs.zlib ];
+    Rhdf5lib = [ pkgs.zlib.dev ];
     Rhpc = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.xz.dev pkgs.mpi pkgs.pcre.dev ];
     Rhtslib = [ pkgs.zlib.dev pkgs.automake pkgs.autoconf pkgs.bzip2.dev pkgs.xz.dev pkgs.curl.dev ];
     rjags = [ pkgs.jags ];

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

@@ -2,11 +2,11 @@ diff --git a/configure b/configure
 index e2d292e..b13c0db 100755
 --- a/configure
 +++ b/configure
-@@ -2880,6 +2880,7 @@ $MAKE
+@@ -3874,6 +3874,7 @@
+ 
  echo "building the hdf5 library...";
  cd ../;
- ## we add the '-w' flag to suppress all the warnings hdf5 prints
 +sed -i 's#/bin/mv#mv#' configure
- ./configure --with-pic --enable-shared=no --enable-cxx \
-     --with-szlib \
-     CXX="${CXX}" CXFLAGS="${CXXFLAGS} -w" \
+ ./configure --with-pic --enable-shared=no --enable-cxx --enable-hl \
+     --with-szlib=${SZIP_HOME} --with-zlib=${ZLIB_HOME} \
+     ${WITH_S3_VFD} \