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/filesystems/irods/common.nix

@@ -0,0 +1,61 @@
+{ lib, stdenv, bzip2, zlib, autoconf, automake, cmake, help2man, texinfo, libtool, cppzmq, libarchive
+, avro-cpp, boost, jansson, zeromq, openssl, pam, libiodbc, libkrb5, gcc, libcxx, which, catch2, nanodbc, fmt
+, nlohmann_json, spdlog }:
+
+# Common attributes of irods packages
+
+{
+  nativeBuildInputs = [ autoconf automake cmake help2man texinfo which gcc ];
+  buildInputs = [ bzip2 zlib libtool cppzmq libarchive avro-cpp jansson zeromq openssl pam libiodbc libkrb5 boost
+                  libcxx catch2 nanodbc fmt nlohmann_json spdlog ];
+
+  cmakeFlags = [
+    "-DIRODS_EXTERNALS_FULLPATH_CLANG=${stdenv.cc}"
+    "-DIRODS_EXTERNALS_FULLPATH_CLANG_RUNTIME=${stdenv.cc}"
+    "-DIRODS_EXTERNALS_FULLPATH_ARCHIVE=${libarchive.lib}"
+    "-DIRODS_EXTERNALS_FULLPATH_AVRO=${avro-cpp}"
+    "-DIRODS_EXTERNALS_FULLPATH_BOOST=${boost}"
+    "-DIRODS_EXTERNALS_FULLPATH_JANSSON=${jansson}"
+    "-DIRODS_EXTERNALS_FULLPATH_ZMQ=${zeromq}"
+    "-DIRODS_EXTERNALS_FULLPATH_CPPZMQ=${cppzmq}"
+    "-DIRODS_EXTERNALS_FULLPATH_CATCH2=${catch2}"
+    "-DIRODS_EXTERNALS_FULLPATH_NANODBC=${nanodbc}"
+    "-DIRODS_EXTERNALS_FULLPATH_FMT=${fmt}"
+    "-DIRODS_EXTERNALS_FULLPATH_JSON=${nlohmann_json}"
+    "-DIRODS_EXTERNALS_FULLPATH_SPDLOG=${spdlog}"
+    "-DIRODS_LINUX_DISTRIBUTION_NAME=nix"
+    "-DIRODS_LINUX_DISTRIBUTION_VERSION_MAJOR=1.0"
+    "-DCPACK_GENERATOR=TGZ"
+    "-DCMAKE_CXX_FLAGS=-I${lib.getDev libcxx}/include/c++/v1"
+  ];
+
+  postPatch = ''
+    patchShebangs ./packaging ./scripts
+    substituteInPlace CMakeLists.txt \
+      --replace "DESTINATION usr/bin" "DESTINATION bin" \
+      --replace "INCLUDE_DIRS usr/include/" "INCLUDE_DIRS include/" \
+      --replace "DESTINATION usr/lib/" "DESTINATION lib/" \
+      --replace "{IRODS_EXTERNALS_FULLPATH_JSON}/include" "{IRODS_EXTERNALS_FULLPATH_JSON}/include/nlohmann"
+    export cmakeFlags="$cmakeFlags
+      -DCMAKE_INSTALL_PREFIX=$out
+    "
+  '';
+
+  meta = with lib; {
+    description = "Integrated Rule-Oriented Data System (iRODS)";
+    longDescription = ''
+      The Integrated Rule-Oriented Data System (iRODS) is open source data management
+      software used by research organizations and government agencies worldwide.
+      iRODS is released as a production-level distribution aimed at deployment in mission
+      critical environments.  It virtualizes data storage resources, so users can take
+      control of their data, regardless of where and on what device the data is stored.
+      As data volumes grow and data services become more complex, iRODS is increasingly
+      important in data management. The development infrastructure supports exhaustive
+      testing on supported platforms; plug-in support for microservices, storage resources,
+      drivers, and databases; and extensive documentation, training and support services.'';
+    homepage = "https://irods.org";
+    license = lib.licenses.bsd3;
+    maintainers = [ lib.maintainers.bzizou ];
+    platforms = lib.platforms.linux;
+  };
+}

pkgs/tools/filesystems/irods/default.nix

@@ -0,0 +1,101 @@
+{ lib, stdenv, fetchFromGitHub, bzip2, zlib, autoconf, automake, cmake, help2man, texinfo, libtool, cppzmq
+, libarchive, avro-cpp_llvm, boost, jansson, zeromq, openssl, pam, libiodbc, libkrb5, gcc, libcxx, which, catch2
+, nanodbc_llvm, fmt, nlohmann_json, spdlog }:
+
+let
+  avro-cpp = avro-cpp_llvm;
+  nanodbc = nanodbc_llvm;
+in
+let
+  common = import ./common.nix {
+    inherit lib stdenv bzip2 zlib autoconf automake cmake
+      help2man texinfo libtool cppzmq libarchive jansson
+      zeromq openssl pam libiodbc libkrb5 gcc libcxx
+      boost avro-cpp which catch2 nanodbc fmt nlohmann_json
+      spdlog;
+  };
+in
+rec {
+
+  # irods: libs and server package
+  irods = stdenv.mkDerivation (common // rec {
+    version = "4.2.11";
+    pname = "irods";
+
+    src = fetchFromGitHub {
+      owner = "irods";
+      repo = "irods";
+      rev = version;
+      sha256 = "0prcsiddk8n3h515jjapgfz1d6hjqywhrkcf6giqd7xc7b0slz44";
+      fetchSubmodules = true;
+    };
+
+    # Patches:
+    # irods_root_path.patch : the root path is obtained by stripping 3 items of the path,
+    #                         but we don't use /usr with nix, so remove only 2 items.
+    patches = [ ./irods_root_path.patch ];
+
+    # fix build with recent llvm versions
+    NIX_CFLAGS_COMPILE = "-Wno-deprecated-register -Wno-deprecated-declarations";
+
+    postPatch = common.postPatch + ''
+      patchShebangs ./test
+      substituteInPlace plugins/database/CMakeLists.txt --replace "COMMAND cpp" "COMMAND ${gcc.cc}/bin/cpp"
+      substituteInPlace cmake/server.cmake --replace "DESTINATION usr/sbin" "DESTINATION sbin"
+      substituteInPlace cmake/server.cmake --replace "IRODS_DOC_DIR usr/share" "IRODS_DOC_DIR share"
+      substituteInPlace cmake/runtime_library.cmake --replace "DESTINATION usr/lib" "DESTINATION lib"
+      substituteInPlace cmake/development_library.cmake --replace "DESTINATION usr/lib" "DESTINATION lib"
+      substituteInPlace cmake/development_library.cmake --replace "DESTINATION usr/include" "DESTINATION include"
+      for file in unit_tests/cmake/test_config/*.cmake
+      do
+        substituteInPlace $file --replace "CATCH2}/include" "CATCH2}/include/catch2"
+      done
+      export cmakeFlags="$cmakeFlags
+        -DCMAKE_EXE_LINKER_FLAGS=-Wl,-rpath,$out/lib
+        -DCMAKE_MODULE_LINKER_FLAGS=-Wl,-rpath,$out/lib
+        -DCMAKE_SHARED_LINKER_FLAGS=-Wl,-rpath,$out/lib
+        "
+
+      substituteInPlace cmake/server.cmake --replace SETUID ""
+    '';
+
+    meta = common.meta // {
+      longDescription = common.meta.longDescription + "This package provides the servers and libraries.";
+    };
+  });
+
+
+  # icommands (CLI) package, depends on the irods package
+  irods-icommands = stdenv.mkDerivation (common // rec {
+    version = "4.2.11";
+    pname = "irods-icommands";
+
+    src = fetchFromGitHub {
+      owner = "irods";
+      repo = "irods_client_icommands";
+      rev = version;
+      sha256 = "0wgs585j2lp820py2pbizsk54xgz5id96fhxwwk9lqhbzxhfjhcg";
+    };
+
+    patches = [ ./zmqcpp-deprecated-send_recv.patch ];
+
+    buildInputs = common.buildInputs ++ [ irods ];
+
+    postPatch = common.postPatch + ''
+      patchShebangs ./bin
+    '';
+
+    cmakeFlags = common.cmakeFlags ++ [
+      "-DCMAKE_INSTALL_PREFIX=${stdenv.out}"
+      "-DIRODS_DIR=${irods}/lib/irods/cmake"
+      "-DCMAKE_EXE_LINKER_FLAGS=-Wl,-rpath,${irods}/lib"
+      "-DCMAKE_MODULE_LINKER_FLAGS=-Wl,-rpath,${irods}/lib"
+      "-DCMAKE_SHARED_LINKER_FLAGS=-Wl,-rpath,${irods}/lib"
+    ];
+
+    meta = common.meta // {
+      description = common.meta.description + " CLI clients";
+      longDescription = common.meta.longDescription + "This package provides the CLI clients, called 'icommands'.";
+    };
+  });
+}

pkgs/tools/filesystems/irods/irods_root_path.patch

@@ -0,0 +1,49 @@
+diff -r -u irods-4.2.0.orig/scripts/irods/paths.py irods-4.2.0/scripts/irods/paths.py
+--- irods-4.2.0.orig/scripts/irods/paths.py	2016-11-15 06:23:55.000000000 +0000
++++ irods-4.2.0/scripts/irods/paths.py	2016-12-21 15:17:07.437864606 +0000
+@@ -10,7 +10,7 @@
+     return os.path.join(root_directory(), 'var', 'lib', 'irods')
+ 
+ def config_directory():
+-    return os.path.join(root_directory(), 'etc', 'irods')
++    return os.path.join(os.path.abspath('/'), 'etc', 'irods')
+ 
+ def plugins_directory():
+     return os.path.join(root_directory(), 'usr', 'lib', 'irods', 'plugins')
+@@ -37,7 +37,7 @@
+ 
+ def version_path():
+     return os.path.join(
+-        irods_directory(),
++        home_directory(),
+         'VERSION.json')
+ 
+ def hosts_config_path():
+@@ -64,7 +64,7 @@
+ 
+ def log_directory():
+     return os.path.join(
+-        irods_directory(),
++        home_directory(),
+         'log')
+ 
+ def control_log_path():
+@@ -110,8 +110,7 @@
+ def server_bin_directory():
+     return os.path.join(
+         root_directory(),
+-        'usr',
+-        'sbin')
++        'bin')
+ 
+ def server_executable():
+     return os.path.join(
+@@ -132,7 +131,7 @@
+     return os.path.join(config_directory(), 'service_account.config')
+ 
+ def genosauth_path():
+-    return os.path.join(irods_directory(), 'clients', 'bin', 'genOSAuth')
++    return os.path.join(home_directory(), 'clients', 'bin', 'genOSAuth')
+ 
+ def irods_user_and_group_entries():
+     try:

pkgs/tools/filesystems/irods/zmqcpp-deprecated-send_recv.patch

@@ -0,0 +1,21 @@
+diff -r -u source/src/irods-grid.cpp source.new/src/irods-grid.cpp
+--- source/src/irods-grid.cpp	1970-01-01 01:00:01.000000000 +0100
++++ source.new/src/irods-grid.cpp	2020-05-05 16:34:35.566464346 +0200
+@@ -412,7 +412,7 @@
+             data_to_send.data(),
+             data_to_send.size() );
+         try {
+-            if (!zmq_skt.send(req)) {
++            if (!zmq_skt.send( req, zmq::send_flags::dontwait )) {
+                 std::cerr << "ZeroMQ encountered an error sending a message.\n";
+                 return errno;
+             }
+@@ -426,7 +426,7 @@
+         zmq::message_t rep;
+         // wait for the server reponse
+         try {
+-            if (!zmq_skt.recv( &rep )) {
++            if (!zmq_skt.recv( rep, zmq::recv_flags::dontwait )) {
+                 std::cerr << "ZeroMQ encountered an error receiving a message.\n";
+                 return errno;
+             }