uboot: (firmwareOdroidC2/C4) don't invoke patch tool, use patches = [] instead

https://github.com/NixOS/nixpkgs/blob/master/pkgs/stdenv/generic/setup.sh#L948
this can do it nicely.

Signed-off-by: Anton Arapov <anton@deadbeef.mx>

pkgs/tools/misc/hdf5/1.10.nix

@@ -0,0 +1,58 @@
+{ lib
+, stdenv
+, fetchurl
+, removeReferencesTo
+, zlibSupport ? true
+, zlib
+, enableShared ? !stdenv.hostPlatform.isStatic
+, javaSupport ? false
+, jdk
+}:
+
+let inherit (lib) optional optionals; in
+
+stdenv.mkDerivation rec {
+  # pinned to 1.10.6 for pythonPackages.tables v3.6.1. tables has test errors for hdf5 > 1.10.6. https://github.com/PyTables/PyTables/issues/845
+  version = "1.10.6";
+  pname = "hdf5";
+  src = fetchurl {
+    url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${lib.versions.majorMinor version}/${pname}-${version}/src/${pname}-${version}.tar.bz2";
+    sha256 = "1gf38x51128hn00744358w27xgzjk0ff4wra4yxh2lk804ck1mh9";
+  };
+
+  outputs = [ "out" "dev" ];
+
+  buildInputs = optional javaSupport jdk;
+
+  nativeBuildInputs = [ removeReferencesTo ];
+
+  propagatedBuildInputs = optional zlibSupport zlib;
+
+  configureFlags = optional enableShared "--enable-shared"
+    ++ optional javaSupport "--enable-java";
+
+  patches = [
+    ./bin-mv.patch
+  ];
+
+  postInstall = ''
+    find "$out" -type f -exec remove-references-to -t ${stdenv.cc} '{}' +
+    moveToOutput 'bin/h5cc' "''${!outputDev}"
+    moveToOutput 'bin/h5c++' "''${!outputDev}"
+    moveToOutput 'bin/h5fc' "''${!outputDev}"
+    moveToOutput 'bin/h5pcc' "''${!outputDev}"
+  '';
+
+  meta = {
+    description = "Data model, library, and file format for storing and managing data";
+    longDescription = ''
+      HDF5 supports an unlimited variety of datatypes, and is designed for flexible and efficient
+      I/O and for high volume and complex data. HDF5 is portable and is extensible, allowing
+      applications to evolve in their use of HDF5. The HDF5 Technology suite includes tools and
+      applications for managing, manipulating, viewing, and analyzing data in the HDF5 format.
+    '';
+    license = lib.licenses.bsd3; # Lawrence Berkeley National Labs BSD 3-Clause variant
+    homepage = "https://www.hdfgroup.org/HDF5/";
+    platforms = lib.platforms.unix;
+  };
+}

pkgs/tools/misc/hdf5/bin-mv.patch

@@ -0,0 +1,30 @@
+diff -rc hdf5-1.8.5/configure hdf5-1.8.5-new/configure
+*** hdf5-1.8.5/configure	2010-06-04 20:26:04.000000000 +0200
+--- hdf5-1.8.5-new/configure	2010-08-02 10:30:26.000000000 +0200
+***************
+*** 30587,30598 ****
+    sed 's/#define /#define H5_/' <src/H5config.h |\
+      sed 's/#undef /#undef H5_/' >pubconf
+    if test ! -f src/H5pubconf.h; then
+!     /bin/mv -f pubconf src/H5pubconf.h
+    elif (diff pubconf src/H5pubconf.h >/dev/null); then
+      rm -f pubconf
+      echo "src/H5pubconf.h is unchanged"
+    else
+!     /bin/mv -f pubconf src/H5pubconf.h
+    fi
+    echo "Post process src/libhdf5.settings"
+    sed '/^#/d' < src/libhdf5.settings > libhdf5.settings.TMP
+--- 30587,30598 ----
+    sed 's/#define /#define H5_/' <src/H5config.h |\
+      sed 's/#undef /#undef H5_/' >pubconf
+    if test ! -f src/H5pubconf.h; then
+!     mv -f pubconf src/H5pubconf.h
+    elif (diff pubconf src/H5pubconf.h >/dev/null); then
+      rm -f pubconf
+      echo "src/H5pubconf.h is unchanged"
+    else
+!     mv -f pubconf src/H5pubconf.h
+    fi
+    echo "Post process src/libhdf5.settings"
+    sed '/^#/d' < src/libhdf5.settings > libhdf5.settings.TMP

pkgs/tools/misc/hdf5/default.nix

@@ -0,0 +1,107 @@
+{ lib
+, stdenv
+, fetchurl
+, removeReferencesTo
+, cppSupport ? false
+, fortranSupport ? false
+, fortran
+, zlibSupport ? true
+, zlib
+, szipSupport ? false
+, szip
+, mpiSupport ? false
+, mpi
+, enableShared ? !stdenv.hostPlatform.isStatic
+, javaSupport ? false
+, jdk
+, usev110Api ? false
+, threadsafe ? false
+}:
+
+# cpp and mpi options are mutually exclusive
+# (--enable-unsupported could be used to force the build)
+assert !cppSupport || !mpiSupport;
+
+let inherit (lib) optional optionals; in
+
+stdenv.mkDerivation rec {
+  version = "1.12.1";
+  pname = "hdf5"
+    + lib.optionalString cppSupport "-cpp"
+    + lib.optionalString fortranSupport "-fortran"
+    + lib.optionalString mpiSupport "-mpi"
+    + lib.optionalString threadsafe "-threadsafe";
+
+  src = fetchurl {
+    url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${lib.versions.majorMinor version}/hdf5-${version}/src/hdf5-${version}.tar.bz2";
+    sha256 = "sha256-qvn1MrPtqD09Otyfi0Cpt2MVIhj6RTScO8d1Asofjxw=";
+  };
+
+  passthru = {
+    inherit
+      cppSupport
+      fortranSupport
+      fortran
+      zlibSupport
+      zlib
+      szipSupport
+      szip
+      mpiSupport
+      mpi
+      ;
+  };
+
+  outputs = [ "out" "dev" ];
+
+  nativeBuildInputs = [ removeReferencesTo ]
+    ++ optional fortranSupport fortran;
+
+  buildInputs = optional fortranSupport fortran
+    ++ optional szipSupport szip
+    ++ optional javaSupport jdk;
+
+  propagatedBuildInputs = optional zlibSupport zlib
+    ++ optional mpiSupport mpi;
+
+  configureFlags = optional cppSupport "--enable-cxx"
+    ++ optional fortranSupport "--enable-fortran"
+    ++ optional szipSupport "--with-szlib=${szip}"
+    ++ optionals mpiSupport [ "--enable-parallel" "CC=${mpi}/bin/mpicc" ]
+    ++ optional enableShared "--enable-shared"
+    ++ optional javaSupport "--enable-java"
+    ++ optional usev110Api "--with-default-api-version=v110"
+    # hdf5 hl (High Level) library is not considered stable with thread safety and should be disabled.
+    ++ optionals threadsafe [ "--enable-threadsafe" "--disable-hl" ];
+
+  patches = [
+    ./bin-mv.patch
+
+    # Avoid non-determinism in autoconf build system:
+    # - build time
+    # - build user
+    # - uname -a (kernel version)
+    # Can be dropped once/if we switch to cmake.
+    ./hdf5-more-determinism.patch
+  ];
+
+  postInstall = ''
+    find "$out" -type f -exec remove-references-to -t ${stdenv.cc} '{}' +
+    moveToOutput 'bin/h5cc' "''${!outputDev}"
+    moveToOutput 'bin/h5c++' "''${!outputDev}"
+    moveToOutput 'bin/h5fc' "''${!outputDev}"
+    moveToOutput 'bin/h5pcc' "''${!outputDev}"
+  '';
+
+  meta = {
+    description = "Data model, library, and file format for storing and managing data";
+    longDescription = ''
+      HDF5 supports an unlimited variety of datatypes, and is designed for flexible and efficient
+      I/O and for high volume and complex data. HDF5 is portable and is extensible, allowing
+      applications to evolve in their use of HDF5. The HDF5 Technology suite includes tools and
+      applications for managing, manipulating, viewing, and analyzing data in the HDF5 format.
+    '';
+    license = lib.licenses.bsd3; # Lawrence Berkeley National Labs BSD 3-Clause variant
+    homepage = "https://www.hdfgroup.org/HDF5/";
+    platforms = lib.platforms.unix;
+  };
+}

pkgs/tools/misc/hdf5/hdf5-more-determinism.patch

@@ -0,0 +1,15 @@
+diff --git a/src/libhdf5.settings.in b/src/libhdf5.settings.in
+index a4d4af6..70f1909 100644
+--- a/src/libhdf5.settings.in
++++ b/src/libhdf5.settings.in
+@@ -4,10 +4,7 @@
+ General Information:
+ -------------------
+                    HDF5 Version: @H5_VERSION@
+-                  Configured on: @CONFIG_DATE@
+-                  Configured by: @CONFIG_USER@
+                     Host system: @host_cpu@-@host_vendor@-@host_os@
+-              Uname information: @UNAME_INFO@
+                        Byte sex: @BYTESEX@
+              Installation point: @prefix@
+