Merge pull request #218669 from avdv/gephi-0.10.1

gephi: 0.9.6 -> 0.10.1

pkgs/applications/science/misc/gephi/default.nix

@@ -1,20 +1,20 @@
-{ lib, stdenv, fetchFromGitHub, jdk, maven, javaPackages }:
+{ lib, stdenv, fetchFromGitHub, jdk11, maven, javaPackages }:
 
 let
-  version = "0.9.6";
+  version = "0.10.1";
 
   src = fetchFromGitHub {
     owner = "gephi";
     repo = "gephi";
     rev = "v${version}";
-    sha256 = "sha256-3+tOwcE7TUeexJCugFsx9SgsKeb7ApNqbMEIi9QaKPE=";
+    hash = "sha256-ZNSEaiD32zFfF2ISKa1CmcT9Nq6r5i2rNHooQAcVbn4=";
   };
 
   # perform fake build to make a fixed-output derivation out of the files downloaded from maven central (120MB)
   deps = stdenv.mkDerivation {
     name = "gephi-${version}-deps";
     inherit src;
-    buildInputs = [ jdk maven ];
+    buildInputs = [ jdk11 maven ];
     buildPhase = ''
       while mvn package -Dmaven.repo.local=$out/.m2 -Dmaven.wagon.rto=5000; [ $? = 1 ]; do
         echo "timeout, restart maven to continue downloading"
@@ -24,7 +24,7 @@ let
     installPhase = ''find $out/.m2 -type f -regex '.+\(\.lastUpdated\|resolver-status\.properties\|_remote\.repositories\)' -delete'';
     outputHashAlgo = "sha256";
     outputHashMode = "recursive";
-    outputHash = "sha256-kIPsZN0alRAgiMbckQnMWKOKtCZ37D/6MgT17VYcr+s=";
+    outputHash = "sha256-OdW4M5nGEkYkmHpRLM4cBQtk4SJII2uqM8TXb6y4eXk=";
   };
 in
 stdenv.mkDerivation {
@@ -33,7 +33,7 @@ stdenv.mkDerivation {
 
   inherit src;
 
-  buildInputs = [ jdk maven ];
+  buildInputs = [ jdk11 maven ];
 
   buildPhase = ''
     # 'maven.repo.local' must be writable so copy it out of nix store
@@ -49,10 +49,10 @@ stdenv.mkDerivation {
 
     # use self-compiled JOGL to avoid patchelf'ing .so inside jars
     rm $out/gephi/modules/ext/org.gephi.visualization/org-jogamp-{jogl,gluegen}/*.jar
-    cp ${javaPackages.jogl_2_3_2}/share/java/jogl*.jar $out/gephi/modules/ext/org.gephi.visualization/org-jogamp-jogl/
-    cp ${javaPackages.jogl_2_3_2}/share/java/glue*.jar $out/gephi/modules/ext/org.gephi.visualization/org-jogamp-gluegen/
+    cp ${javaPackages.jogl_2_4_0}/share/java/jogl*.jar $out/gephi/modules/ext/org.gephi.visualization/org-jogamp-jogl/
+    cp ${javaPackages.jogl_2_4_0}/share/java/glue*.jar $out/gephi/modules/ext/org.gephi.visualization/org-jogamp-gluegen/
 
-    echo "jdkhome=${jdk}" >> $out/etc/gephi.conf
+    printf "\n\njdkhome=${jdk11}\n" >> $out/etc/gephi.conf
   '';
 
   meta = with lib; {

pkgs/development/java-modules/jogl/default.nix

@@ -1,6 +1,81 @@
-{ lib, stdenv, fetchgit, ant, jdk8, git, xorg, udev, libGL, libGLU }:
+{ coreutils, lib, stdenv, fetchgit, ant, jdk8, jdk11, git, xorg, udev, libGL, libGLU, mesa, xmlstarlet }:
 
 {
+  jogl_2_4_0 =
+    let
+      version = "2.4.0";
+
+      gluegen-src = fetchgit {
+        url = "git://jogamp.org/srv/scm/gluegen.git";
+        rev = "v${version}";
+        hash = "sha256-qQzq7v2vMFeia6gXaNHS3AbOp9HhDRgISp7P++CKErA=";
+        fetchSubmodules = true;
+      };
+      jogl-src = fetchgit {
+        url = "git://jogamp.org/srv/scm/jogl.git";
+        rev = "v${version}";
+        hash = "sha256-PHDq7uFEQfJ2P0eXPUi0DGFR1ob/n5a68otgzpFnfzQ=";
+        fetchSubmodules = true;
+      };
+    in
+    stdenv.mkDerivation {
+      pname = "jogl";
+      inherit version;
+
+      srcs = [ gluegen-src jogl-src ];
+      sourceRoot = ".";
+
+      unpackCmd = "cp -r $curSrc \${curSrc##*-}";
+
+      nativeBuildInputs = [ ant jdk11 git xmlstarlet ];
+      buildInputs = [ udev xorg.libX11 xorg.libXrandr xorg.libXcursor xorg.libXi xorg.libXt xorg.libXxf86vm xorg.libXrender mesa ];
+
+      # Workaround build failure on -fno-common toolchains:
+      #   ld: ../obj/Bindingtest1p1Impl_JNI.o:(.bss+0x8): multiple definition of
+      #     `unsigned_size_t_1'; ../obj/TK_Surface_JNI.o:(.bss+0x8): first defined here
+      NIX_CFLAGS_COMPILE = "-fcommon"; # copied from 2.3.2, is this still needed?
+
+      buildPhase = ''
+        ( cd gluegen/make
+          substituteInPlace ../src/java/com/jogamp/common/util/IOUtil.java --replace '#!/bin/true' '#!${coreutils}/bin/true'
+
+          # set timestamp of files in jar to a fixed point in time
+          xmlstarlet ed --inplace \
+             --append //jar --type attr -n modificationtime --value 1980-01-01T00:00Z \
+             build.xml gluegen-cpptasks-base.xml
+
+          ant -Dtarget.sourcelevel=8 -Dtarget.targetlevel=8 -Dtarget.rt.jar='null.jar' )
+
+        ( cd jogl/make
+
+          # force way to do disfunctional "ant -Dsetup.addNativeBroadcom=false" and disable dependency on raspberrypi drivers
+          # if arm/aarch64 support will be added, this block might be commented out on those platforms
+          # on x86 compiling with default "setup.addNativeBroadcom=true" leads to unsatisfied import "vc_dispmanx_resource_delete" in libnewt.so
+          xmlstarlet ed --inplace --delete '//*[@if="setup.addNativeBroadcom"]' build-newt.xml
+
+          # set timestamp of files in jar to a fixed point in time
+          xmlstarlet ed --inplace \
+             --append //jar --type attr -n modificationtime --value 1980-01-01T00:00Z \
+             build.xml build-nativewindow.xml build-jogl.xml
+
+          ant -Dtarget.sourcelevel=8 -Dtarget.targetlevel=8 -Dtarget.rt.jar='null.jar' )
+      '';
+
+      installPhase = ''
+        mkdir -p $out/share/java
+        cp -v $NIX_BUILD_TOP/gluegen/build/gluegen-rt{,-natives-linux-amd64}.jar $out/share/java/
+        cp -v $NIX_BUILD_TOP/jogl/build/jar/jogl-all{,-natives-linux-amd64}.jar  $out/share/java/
+        cp -v $NIX_BUILD_TOP/jogl/build/nativewindow/nativewindow{,-awt,-natives-linux-amd64,-os-drm,-os-x11}.jar  $out/share/java/
+      '';
+
+      meta = with lib; {
+        description = "Java libraries for 3D Graphics, Multimedia and Processing";
+        homepage = "https://jogamp.org/";
+        license = licenses.bsd3;
+        platforms = [ "x86_64-linux" ];
+      };
+    };
+
   jogl_2_3_2 =
     let
       version = "2.3.2";

pkgs/top-level/java-packages.nix

@@ -271,7 +271,8 @@ in {
     junit_4_12;
 
   inherit (callPackage ../development/java-modules/jogl { })
-    jogl_2_3_2;
+    jogl_2_3_2
+    jogl_2_4_0;
 
   inherit (callPackage ../development/java-modules/log4j { inherit fetchMaven; })
     log4j_1_2_12;