Bump isabelle to 2013.2. Fix Bug 536324 - sci-mathematics/isabelle: Slot dependencies for java packages. Add upper range dependency <dev-lang/scala-2.11.1 to 2013-r1.

(Portage version: 2.2.15/cvs/Linux x86_64, signed Manifest commit with key 618E971F)

5 files changed, 616 insertions, 9 deletions

diff --git a/sci-mathematics/isabelle/ChangeLog b/sci-mathematics/isabelle/ChangeLog
index 26d53a1136be..0a19e8e72d60 100644
--- a/sci-mathematics/isabelle/ChangeLog
+++ b/sci-mathematics/isabelle/ChangeLog
@@ -1,6 +1,16 @@
 # ChangeLog for sci-mathematics/isabelle
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/isabelle/ChangeLog,v 1.11 2014/01/07 13:36:33 tomwij Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/isabelle/ChangeLog,v 1.12 2015/01/25 13:08:28 gienah Exp $
+
+*isabelle-2013.2 (25 Jan 2015)
+
+  25 Jan 2015; Mark Wright <gienah@gentoo.org>
+  +files/isabelle-2013.2-HOL-Predicate_Compile_Examples.patch,
+  +files/isabelle-2013.2-classpath.patch, +isabelle-2013.2.ebuild,
+  isabelle-2013-r1.ebuild:
+  Bump isabelle to 2013.2. Fix Bug 536324 - sci-mathematics/isabelle: Slot
+  dependencies for java packages. Add upper range dependency <dev-
+  lang/scala-2.11.1 to 2013-r1.
 
 *isabelle-2012-r1 (07 Jan 2014)
 *isabelle-2013-r1 (07 Jan 2014)
diff --git a/sci-mathematics/isabelle/files/isabelle-2013.2-HOL-Predicate_Compile_Examples.patch b/sci-mathematics/isabelle/files/isabelle-2013.2-HOL-Predicate_Compile_Examples.patch
new file mode 100644
index 000000000000..e1253016837b
--- /dev/null
+++ b/sci-mathematics/isabelle/files/isabelle-2013.2-HOL-Predicate_Compile_Examples.patch
@@ -0,0 +1,89 @@
+--- Isabelle2013-2-orig/src/HOL/Predicate_Compile_Examples/Hotel_Example_Prolog.thy	2013-12-06 02:18:50.000000000 +1100
++++ Isabelle2013-2/src/HOL/Predicate_Compile_Examples/Hotel_Example_Prolog.thy	2014-02-09 22:21:20.676081140 +1100
+@@ -87,7 +87,7 @@
+ *}
+ 
+ lemma "\<lbrakk> hotel s; isinp s r g \<rbrakk> \<Longrightarrow> owns s r = Some g"
+-quickcheck[tester = prolog, iterations = 1, expect = counterexample]
++quickcheck[tester = prolog, iterations = 1]
+ oops
+ 
+ section {* Manual setup to find the counterexample *}
+@@ -115,7 +115,7 @@
+ 
+ lemma
+   "hotel s ==> feels_safe s r ==> isinp s r g ==> owns s r = Some g"
+-quickcheck[tester = prolog, iterations = 1, expect = counterexample]
++quickcheck[tester = prolog, iterations = 1]
+ oops
+ 
+ section {* Using a global limit for limiting the execution *} 
+@@ -151,7 +151,7 @@
+ 
+ lemma
+   "hotel s ==> feels_safe s r ==> isinp s r g ==> owns s r = Some g"
+-quickcheck[tester = prolog, iterations = 1, expect = counterexample]
++quickcheck[tester = prolog, iterations = 1]
+ oops
+ 
+ end
+\ No newline at end of file
+--- Isabelle2013-2-orig/src/HOL/Predicate_Compile_Examples/Context_Free_Grammar_Example.thy	2013-12-06 02:18:50.000000000 +1100
++++ Isabelle2013-2/src/HOL/Predicate_Compile_Examples/Context_Free_Grammar_Example.thy	2014-02-09 22:27:26.826238011 +1100
+@@ -36,7 +36,7 @@
+ 
+ lemma
+   "S\<^sub>1p w \<Longrightarrow> w = []"
+-quickcheck[tester = prolog, iterations=1, expect = counterexample]
++quickcheck[tester = prolog, iterations=1]
+ oops
+ 
+ definition "filter_a = filter (\<lambda>x. x = a)"
+@@ -70,7 +70,7 @@
+ 
+ theorem S\<^sub>1_sound:
+ "S\<^sub>1p w \<Longrightarrow> length [x \<leftarrow> w. x = a] = length [x \<leftarrow> w. x = b]"
+-quickcheck[tester = prolog, iterations=1, expect = counterexample]
++quickcheck[tester = prolog, iterations=1]
+ oops
+ 
+ 
+@@ -94,7 +94,7 @@
+ 
+ theorem S\<^sub>2_sound:
+   "S\<^sub>2p w \<longrightarrow> length [x \<leftarrow> w. x = a] = length [x \<leftarrow> w. x = b]"
+-quickcheck[tester = prolog, iterations=1, expect = counterexample]
++quickcheck[tester = prolog, iterations=1]
+ oops
+ 
+ inductive_set S\<^sub>3 and A\<^sub>3 and B\<^sub>3 where
+@@ -171,4 +171,4 @@
+ hide_const a b
+ 
+ 
+-end
+\ No newline at end of file
++end
+--- Isabelle2013-2-orig/src/HOL/Predicate_Compile_Examples/Lambda_Example.thy	2013-12-06 02:18:50.000000000 +1100
++++ Isabelle2013-2/src/HOL/Predicate_Compile_Examples/Lambda_Example.thy	2014-02-09 22:21:20.677081168 +1100
+@@ -95,7 +95,7 @@
+ 
+ lemma
+   "\<Gamma> \<turnstile> t : U \<Longrightarrow> t \<rightarrow>\<^sub>\<beta> t' \<Longrightarrow> \<Gamma> \<turnstile> t' : U"
+-quickcheck[tester = prolog, iterations = 1, expect = counterexample]
++quickcheck[tester = prolog, iterations = 1]
+ oops
+ 
+ text {* Verifying that the found counterexample really is one by means of a proof *}
+--- Isabelle2013-2-orig/src/HOL/Predicate_Compile_Examples/List_Examples.thy	2013-12-06 02:18:50.000000000 +1100
++++ Isabelle2013-2/src/HOL/Predicate_Compile_Examples/List_Examples.thy	2014-02-09 22:21:20.678081196 +1100
+@@ -24,7 +24,7 @@
+ lemma "(xs :: nat list) = ys @ ys --> rev xs = xs"
+ quickcheck[tester = random, iterations = 10000]
+ quickcheck[tester = smart_exhaustive, iterations = 1, expect = counterexample]
+-quickcheck[tester = prolog, expect = counterexample]
++quickcheck[tester = prolog]
+ oops
+ 
+ end
+\ No newline at end of file
diff --git a/sci-mathematics/isabelle/files/isabelle-2013.2-classpath.patch b/sci-mathematics/isabelle/files/isabelle-2013.2-classpath.patch
new file mode 100644
index 000000000000..4532bd3b8ad3
--- /dev/null
+++ b/sci-mathematics/isabelle/files/isabelle-2013.2-classpath.patch
@@ -0,0 +1,135 @@
+--- Isabelle2013-2-orig/lib/Tools/java	2013-12-06 02:18:34.000000000 +1100
++++ Isabelle2013-2/lib/Tools/java	2014-02-09 20:53:30.085279943 +1100
+@@ -10,5 +10,5 @@
+ unset CLASSPATH
+ 
+ isabelle_jdk java "${JAVA_ARGS[@]}" \
+-  -classpath "$(jvmpath "$ISABELLE_CLASSPATH")" "$@"
++  -classpath "$(jvmpath "$ISABELLE_CLASSPATH:$(java-config -p scala | sed 's@\([^:]*\)/[^:]*:.*@\1@')")" "$@"
+ 
+--- Isabelle2013-2-orig/lib/Tools/scala	2013-12-06 02:18:34.000000000 +1100
++++ Isabelle2013-2/lib/Tools/scala	2014-02-09 20:54:22.418737591 +1100
+@@ -7,5 +7,5 @@
+ isabelle_admin_build jars || exit $?
+ 
+ isabelle_scala scala -Dfile.encoding=UTF-8 \
+-  -classpath "$(jvmpath "$ISABELLE_CLASSPATH")" "$@"
++  -classpath "$(jvmpath "$ISABELLE_CLASSPATH:$(java-config -p scala | sed 's@\([^:]*\)/[^:]*:.*@\1@')")" "$@"
+ 
+--- Isabelle2013-2-orig/lib/Tools/scalac	2013-12-06 02:18:34.000000000 +1100
++++ Isabelle2013-2/lib/Tools/scalac	2014-02-09 20:55:03.999895037 +1100
+@@ -7,5 +7,5 @@
+ isabelle_admin_build jars || exit $?
+ 
+ isabelle_scala scalac -Dfile.encoding=UTF-8 \
+-  -classpath "$(jvmpath "$ISABELLE_CLASSPATH")" "$@"
++  -classpath "$(jvmpath "$ISABELLE_CLASSPATH:$(java-config -p scala | sed 's@\([^:]*\)/[^:]*:.*@\1@')")" "$@"
+ 
+--- Isabelle2013-2-orig/src/Tools/jEdit/lib/Tools/jedit	2013-12-06 02:19:04.000000000 +1100
++++ Isabelle2013-2/src/Tools/jEdit/lib/Tools/jedit	2014-02-09 20:59:14.026841490 +1100
+@@ -211,105 +211,6 @@
+   "$ISABELLE_JEDIT_BUILD_HOME/contrib/jsr305-2.0.0.jar"
+ )
+ 
+-
+-# target
+-
+-TARGET="dist/jars/Isabelle-jEdit.jar"
+-
+-declare -a UPDATED=()
+-
+-if [ "$BUILD_JARS" = jars_fresh ]; then
+-  OUTDATED=true
+-else
+-  OUTDATED=false
+-  if [ ! -e "$TARGET" ]; then
+-    OUTDATED=true
+-  else
+-    if [ -n "$ISABELLE_JEDIT_BUILD_HOME" ]; then
+-      declare -a DEPS=(
+-        "$JEDIT_JAR" "${JEDIT_JARS[@]}" "$PURE_JAR" "$GRAPHVIEW_JAR"
+-        "${SOURCES[@]}" "${RESOURCES[@]}"
+-      )
+-    elif [ -e "$ISABELLE_HOME/Admin/build" ]; then
+-      declare -a DEPS=("$PURE_JAR" "$GRAPHVIEW_JAR" "${SOURCES[@]}" "${RESOURCES[@]}")
+-    else
+-      declare -a DEPS=()
+-    fi
+-    for DEP in "${DEPS[@]}"
+-    do
+-      [ ! -e "$DEP" ] && fail "Missing file: $DEP"
+-      [ "$DEP" -nt "$TARGET" ] && {
+-        OUTDATED=true
+-        UPDATED["${#UPDATED[@]}"]="$DEP"
+-      }
+-    done
+-  fi
+-fi
+-
+-
+-# build
+-
+-if [ "$OUTDATED" = true ]
+-then
+-  echo "### Building Isabelle/jEdit ..."
+-
+-  [ "${#UPDATED[@]}" -gt 0 ] && {
+-    echo "Changed files:"
+-    for FILE in "${UPDATED[@]}"
+-    do
+-      echo "  $FILE"
+-    done
+-  }
+-
+-  [ -z "$ISABELLE_JEDIT_BUILD_HOME" ] && \
+-    fail "Unknown ISABELLE_JEDIT_BUILD_HOME -- missing auxiliary component"
+-
+-  rm -rf dist || failed
+-  mkdir -p dist dist/classes || failed
+-
+-  cp -p -R -f "$ISABELLE_JEDIT_BUILD_HOME/contrib/$ISABELLE_JEDIT_BUILD_VERSION/." dist/.
+-  cp -p -R -f "${RESOURCES[@]}" dist/classes/.
+-  cp src/jEdit.props dist/properties/.
+-  cp -p -R -f src/modes/. dist/modes/.
+-
+-  perl -i -e 'while (<>) {
+-    if (m/NAME="javacc"/) {
+-      print qq,<MODE NAME="isabelle" FILE="isabelle.xml" FILE_NAME_GLOB="*.thy"/>\n\n,;
+-      print qq,<MODE NAME="isabelle-news" FILE="isabelle-news.xml"/>\n\n,;
+-      print qq,<MODE NAME="isabelle-options" FILE="isabelle-options.xml"/>\n\n,;
+-      print qq,<MODE NAME="isabelle-root" FILE="isabelle-root.xml" FILE_NAME_GLOB="ROOT"/>\n\n,; }
+-    print; }' dist/modes/catalog
+-
+-  cd dist
+-  isabelle_jdk jar xf jedit.jar
+-  cp "$ISABELLE_HOME/lib/logo/isabelle-32.gif" \
+-    "org/gjt/sp/jedit/icons/themes/classic/32x32/apps/isabelle.gif" || failed
+-  cp "$ISABELLE_HOME/lib/logo/isabelle-32.gif" \
+-    "org/gjt/sp/jedit/icons/themes/tango/32x32/apps/isabelle.gif" || failed
+-  isabelle_jdk jar cfe jedit.jar org.gjt.sp.jedit.jEdit org || failed
+-  rm -rf META-INF org
+-  cd ..
+-
+-  cp -p -R -f "${JEDIT_JARS[@]}" dist/jars/. || failed
+-  (
+-    #workaround for scalac 2.10.2
+-    function stty() { :; }
+-    export -f stty
+-
+-    for JAR in "$JEDIT_JAR" "${JEDIT_JARS[@]}" "$PURE_JAR" "$GRAPHVIEW_JAR"
+-    do
+-      classpath "$JAR"
+-    done
+-    export CLASSPATH="$(jvmpath "$ISABELLE_CLASSPATH")"
+-    exec "$SCALA_HOME/bin/scalac" $ISABELLE_SCALA_BUILD_OPTIONS -d dist/classes "${SOURCES[@]}"
+-  ) || fail "Failed to compile sources"
+-
+-  cd dist/classes
+-  isabelle_jdk jar cf "../jars/Isabelle-jEdit.jar" * || failed
+-  cd ../..
+-  rm -rf dist/classes
+-fi
+-
+ popd >/dev/null
+ 
+ 
diff --git a/sci-mathematics/isabelle/isabelle-2013-r1.ebuild b/sci-mathematics/isabelle/isabelle-2013-r1.ebuild
index f85f9aec6e48..6f57d1ef679f 100644
--- a/sci-mathematics/isabelle/isabelle-2013-r1.ebuild
+++ b/sci-mathematics/isabelle/isabelle-2013-r1.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/isabelle/isabelle-2013-r1.ebuild,v 1.1 2014/01/07 13:36:33 tomwij Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/isabelle/isabelle-2013-r1.ebuild,v 1.2 2015/01/25 13:08:28 gienah Exp $
 
 EAPI="5"
 
@@ -37,10 +37,10 @@ IUSE="doc graphbrowsing ledit readline proofgeneral"
 #bash 2.x/3.x, Poly/ML 5.x, Perl 5.x,
 #for document preparation: complete LaTeX
 DEPEND=">=app-shells/bash-3.0
-	dev-java/ant-core
-	>=dev-java/jcommon-1.0.18
-	>=dev-java/jfreechart-1.0.14
-	>=dev-java/itext-2.1.5
+	dev-java/ant-core:0
+	>=dev-java/jcommon-1.0.18:1.0
+	>=dev-java/jfreechart-1.0.14:1.0
+	>=dev-java/itext-2.1.5:0
 	dev-java/xml-xmlbeans:1
 	>=dev-lang/ghc-7.6.3
 	>=dev-lang/polyml-5.5.0:=[-portable]
@@ -51,7 +51,7 @@ DEPEND=">=app-shells/bash-3.0
 		virtual/latex-base
 		dev-tex/rail
 	)
-	>=dev-lang/scala-2.10.2
+	>=dev-lang/scala-2.10.2 <dev-lang/scala-2.11.1
 	ledit? (
 		app-misc/ledit
 	)
diff --git a/sci-mathematics/isabelle/isabelle-2013.2.ebuild b/sci-mathematics/isabelle/isabelle-2013.2.ebuild
new file mode 100644
index 000000000000..7e6d8cf25bd1
--- /dev/null
+++ b/sci-mathematics/isabelle/isabelle-2013.2.ebuild
@@ -0,0 +1,373 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/isabelle/isabelle-2013.2.ebuild,v 1.1 2015/01/25 13:08:28 gienah Exp $
+
+EAPI="5"
+
+inherit eutils java-pkg-2 multilib versionator
+
+MY_PN="Isabelle"
+MY_PV=$(replace_all_version_separators '-')
+MY_P="${MY_PN}${MY_PV}"
+
+JEDIT_PV="20131106"
+JEDIT_PN="jedit_build"
+JEDIT_P="${JEDIT_PN}-${JEDIT_PV}"
+JEDIT_IC_PN="${JEDIT_PN}-isabelle-component"
+JEDIT_IC_P="${JEDIT_IC_PN}-${JEDIT_PV}"
+
+JFREECHART_PV="1.0.14-1"
+JFREECHART_PN="jfreechart"
+JFREECHART_P="${JFREECHART_PN}-${JFREECHART_PV}"
+JFREECHART_IC_PN="${JFREECHART_PN}-isabelle-component"
+JFREECHART_IC_P="${JFREECHART_IC_PN}-${JFREECHART_PV}"
+
+POLYML_PV="5.5.1-1"
+POLYML_PN="polyml"
+POLYML_P="${POLYML_PN}-${POLYML_PV}"
+POLYML_IC_PN="${POLYML_PN}-isabelle-component"
+POLYML_IC_P="${POLYML_IC_PN}-${POLYML_PV}"
+
+DESCRIPTION="Isabelle is a generic proof assistant"
+HOMEPAGE="http://www.cl.cam.ac.uk/research/hvg/Isabelle/index.html"
+SRC_URI="http://isabelle.in.tum.de/dist/${MY_P}.tar.gz
+		http://isabelle.in.tum.de/components/${JEDIT_P}.tar.gz -> ${JEDIT_IC_P}.tar.gz
+		http://isabelle.in.tum.de/dist/contrib/${JFREECHART_P}.tar.gz -> ${JFREECHART_IC_P}.tar.gz
+		http://dev.gentoo.org/~gienah/snapshots/${POLYML_IC_P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0/${PV}"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc graphbrowsing ledit readline proofgeneral"
+
+#upstream says
+#bash 2.x/3.x, Poly/ML 5.x, Perl 5.x,
+#for document preparation: complete LaTeX
+DEPEND=">=app-shells/bash-3.0
+	dev-java/ant-core:0
+	>=dev-java/jcommon-1.0.18:1.0
+	>=dev-java/jfreechart-1.0.14:1.0
+	>=dev-java/itext-2.1.5:0
+	dev-java/xml-xmlbeans:1
+	dev-java/xz-java:0
+	>=dev-lang/ghc-7.6.3
+	>=dev-lang/polyml-5.5.1:=[-portable]
+	>=dev-lang/perl-5.8.8-r2
+	dev-lang/swi-prolog
+	virtual/jdk:1.7
+	doc? (
+		virtual/latex-base
+		dev-tex/rail
+	)
+	>=dev-lang/scala-2.11.1
+	ledit? (
+		app-misc/ledit
+	)
+	readline? (
+		app-misc/rlwrap
+	)"
+
+RDEPEND="dev-perl/libwww-perl
+	sci-mathematics/sha1-polyml
+	>=virtual/jre-1.7
+	proofgeneral? (
+		>=app-emacs/proofgeneral-4.1
+	)
+	${DEPEND}"
+
+S="${WORKDIR}"/Isabelle${MY_PV}
+JEDIT_S="${WORKDIR}/${JEDIT_P}"
+JFREECHART_S="${WORKDIR}/${JFREECHART_P}"
+TARGETDIR="/usr/share/Isabelle"${MY_PV}
+LIBDIR="/usr/"$(get_libdir)"/Isabelle"${MY_PV}
+
+# Notes on QA warnings: * Class files not found via DEPEND in package.env
+# Stuff with $ in the name appear to be spurious:
+# isabelle/Markup_Tree$$anonfun$results$1$1.class
+# scala/tools/nsc/backend/jvm/GenJVM$BytecodeGenerator$$anonfun$computeLocalVarsIndex$1.class
+# It wants javafx, I am unsure how to fix this. I test isabelle with the Sun JDK:
+# javafx/application/Platform.class               javafx
+# Presumably the user can provide the jEdit plugins if they are necessary:
+# marker/MarkerSetsPlugin.class                   http://plugins.jedit.org/plugins/?MarkerSets
+# projectviewer/gui/OptionPaneBase.class          http://plugins.jedit.org/plugins/?ProjectViewer
+
+LIBRARY_PKGS="ant-core,itext,jcommon-1.0,jfreechart-1.0,scala,xml-xmlbeans-1,xz-java"
+
+src_unpack() {
+	unpack "${MY_P}.tar.gz"
+	pushd "${S}/contrib" || die
+	unpack ${JEDIT_IC_P}.tar.gz
+	unpack ${JFREECHART_IC_P}.tar.gz
+	unpack ${POLYML_IC_P}.tar.gz
+}
+
+pkg_setup() {
+	java-pkg-2_pkg_setup
+}
+
+src_prepare() {
+	java-pkg-2_src_prepare
+	java-pkg_getjars ${LIBRARY_PKGS}
+	epatch "${FILESDIR}/${PN}-2013-gentoo-settings.patch"
+	epatch "${FILESDIR}/${PN}-2013.2-classpath.patch"
+	polymlver=$(poly -v | cut -d' ' -f2)
+	polymlarch=$(poly -v | cut -d' ' -f9 | cut -d'-' -f1)
+	sed -e "s@5.5.0@${polymlver}@g" \
+		-i "${S}/etc/settings" \
+		|| die "Could not configure polyml version in etc/settings"
+	sed -e "s@ML_HOME=\"/@ML_HOME=\"${ROOT}@" \
+		-i "${S}/etc/settings" \
+		|| die "Could not configure polyml ML_HOME in etc/settings"
+	sed -e "s@x86_64@${polymlarch}@g" \
+		-i "${S}/etc/settings" \
+		|| die "Could not configure polyml arch in etc/settings"
+	sed -e "s@PROOFGENERAL_HOME=\"/@PROOFGENERAL_HOME=\"${ROOT}@" \
+		-i "${S}/etc/settings" \
+		|| die "Could not configure PROOFGENERAL_HOME in etc/settings"
+	sed -e "s@/usr/lib64/Isabelle${MY_PV}@${LIBDIR}@g" \
+		-i "${S}/etc/settings" \
+		|| die "Could not configure Isabelle lib directory in etc/settings"
+	epatch "${FILESDIR}/${PN}-2012-graphbrowser.patch"
+	epatch "${FILESDIR}/${PN}-2012-libsha1.patch"
+	# this example fails to compile with swi-prolog 6.5.2, so patch it so that
+	# Isabelle will build, then reverse the patch so that the user can see the
+	# original code.
+	epatch "${FILESDIR}/${PN}-2013.2-HOL-Predicate_Compile_Examples.patch"
+	cat <<- EOF >> "${S}/etc/settings"
+
+		ISABELLE_GHC="${ROOT}usr/bin/ghc"
+		ISABELLE_OCAML="${ROOT}usr/bin/ocaml"
+		ISABELLE_SWIPL="${ROOT}usr/bin/swipl"
+		ISABELLE_JDK_HOME="\$(java-config --jdk-home)"
+		SCALA_HOME="${ROOT}usr/share/scala"
+		SHA1_HOME="/usr/$(get_libdir)/sha1-polyml"
+	EOF
+	cat <<- EOF >> "${S}/etc/components"
+		#bundled components
+		contrib/${JEDIT_P}
+		contrib/${JFREECHART_P}
+		contrib/${POLYML_P}
+	EOF
+	if use ledit && ! use readline; then
+		epatch "${FILESDIR}/${PN}-2012-reverse-line-editor-order.patch"
+	fi
+	rm -f "${S}/contrib/jfreechart-1.0.14-1/lib/iText-2.1.5.jar" \
+		"${S}/contrib/jfreechart-1.0.14-1/lib/jfreechart-1.0.14.jar" \
+		"${S}/contrib/jfreechart-1.0.14-1/lib/jcommon-1.0.18.jar" \
+		"${S}/lib/classes/ext/scala-actors.jar" \
+		"${S}/lib/classes/ext/scala-compiler.jar" \
+		"${S}/lib/classes/ext/scala-library.jar" \
+		"${S}/lib/classes/ext/scala-reflect.jar" \
+		"${S}/lib/classes/ext/scala-swing.jar" \
+		|| die "Could not rm bundled jar files supplied by Gentoo"
+}
+
+src_compile() {
+	einfo "Building Isabelle. This may take some time."
+	./bin/isabelle build -a -b -s -v || die "isabelle build failed"
+	epatch --reverse "${FILESDIR}/${PN}-2013.2-HOL-Predicate_Compile_Examples.patch"
+	if use graphbrowsing
+	then
+		rm -f "${S}/lib/browser/GraphBrowser.jar" \
+			|| die "failed cleaning graph browser directory"
+		pushd "${S}/lib/browser" \
+			|| die "Could not change directory to lib/browser"
+		./build || die "failed building the graph browser"
+		popd
+	fi
+	./bin/isabelle jedit -b -f || die "pide build failed"
+}
+
+src_install() {
+	insinto ${TARGETDIR}
+	doins -r src
+	doins -r lib
+	doins -r contrib
+	doins ROOTS
+
+	docompress -x /usr/share/doc/${PF}
+	dodoc -r doc
+	if use doc; then
+		dosym /usr/share/doc/${PF}/doc "${TARGETDIR}/doc"
+		# The build of sci-mathematics/haskabelle with use doc requires
+		# sci-mathematics/isabelle[doc?]. The haskabelle doc build requires
+		# the src/Doc directory stuff in the isabelle package.
+		doins -r src/Doc
+		for i in "./src/Doc/Classes/document/build" \
+			"./src/Doc/Codegen/document/build" \
+			"./src/Doc/Datatypes/document/build" \
+			"./src/Doc/fixbookmarks" \
+			"./src/Doc/Functions/document/build" \
+			"./src/Doc/Intro/document/build" \
+			"./src/Doc/IsarImplementation/document/build" \
+			"./src/Doc/IsarRef/document/build" \
+			"./src/Doc/IsarRef/document/showsymbols" \
+			"./src/Doc/JEdit/document/build" \
+			"./src/Doc/LaTeXsugar/document/build" \
+			"./src/Doc/Locales/document/build" \
+			"./src/Doc/Logics/document/build" \
+			"./src/Doc/Main/document/build" \
+			"./src/Doc/Nitpick/document/build" \
+			"./src/Doc/prepare_document" \
+			"./src/Doc/ProgProve/document/build" \
+			"./src/Doc/sedindex" \
+			"./src/Doc/Sledgehammer/document/build" \
+			"./src/Doc/System/document/build" \
+			"./src/Doc/Tutorial/document/build" \
+			"./src/Doc/Tutorial/document/isa-index" \
+			"./src/Doc/ZF/document/build"
+		do
+			exeinto $(dirname "${TARGETDIR}/${i}")
+			doexe ${i}
+		done
+	fi
+
+	for i in "./bin/isabelle" \
+		"./bin/isabelle-process" \
+		"./bin/isabelle_scala_script" \
+		"./lib/browser/build" \
+		"./lib/scripts/feeder" \
+		"./lib/scripts/getsettings" \
+		"./lib/scripts/polyml-version" \
+		"./lib/scripts/process" \
+		"./lib/scripts/run-polyml" \
+		"./lib/scripts/run-polyml-5.5.1" \
+		"./lib/scripts/run-smlnj" \
+		"./lib/scripts/unsymbolize" \
+		"./lib/scripts/update_sub_sup" \
+		"./lib/scripts/yxml" \
+		"./lib/Tools/browser" \
+		"./lib/Tools/build" \
+		"./lib/Tools/components" \
+		"./lib/Tools/display" \
+		"./lib/Tools/doc" \
+		"./lib/Tools/document" \
+		"./lib/Tools/emacs" \
+		"./lib/Tools/env" \
+		"./lib/Tools/findlogics" \
+		"./lib/Tools/getenv" \
+		"./lib/Tools/install" \
+		"./lib/Tools/java" \
+		"./lib/Tools/keywords" \
+		"./lib/Tools/latex" \
+		"./lib/Tools/logo" \
+		"./lib/Tools/mkroot" \
+		"./lib/Tools/options" \
+		"./lib/Tools/scala" \
+		"./lib/Tools/scalac" \
+		"./lib/Tools/tty" \
+		"./lib/Tools/unsymbolize" \
+		"./lib/Tools/update_sub_sup" \
+		"./lib/Tools/version" \
+		"./lib/Tools/yxml" \
+		"./src/HOL/IMP/export.sh" \
+		"./src/HOL/Library/Sum_of_Squares/neos_csdp_client" \
+		"./src/HOL/Mirabelle/lib/Tools/mirabelle" \
+		"./src/HOL/Mutabelle/lib/Tools/mutabelle" \
+		"./src/HOL/SPARK/Examples/README" \
+		"./src/HOL/Tools/ATP/scripts/dummy_atp" \
+		"./src/HOL/Tools/ATP/scripts/remote_atp" \
+		"./src/HOL/Tools/Sledgehammer/MaSh/src/compareStats.py" \
+		"./src/HOL/Tools/Sledgehammer/MaSh/src/mash.py" \
+		"./src/HOL/Tools/Sledgehammer/MaSh/src/server.py" \
+		"./src/HOL/Tools/SMT/lib/scripts/remote_smt" \
+		"./src/HOL/TPTP/lib/Tools/tptp_graph" \
+		"./src/HOL/TPTP/lib/Tools/tptp_isabelle" \
+		"./src/HOL/TPTP/lib/Tools/tptp_isabelle_hot" \
+		"./src/HOL/TPTP/lib/Tools/tptp_nitpick" \
+		"./src/HOL/TPTP/lib/Tools/tptp_refute" \
+		"./src/HOL/TPTP/lib/Tools/tptp_sledgehammer" \
+		"./src/HOL/TPTP/TPTP_Parser/make_mlyacclib" \
+		"./src/HOL/TPTP/TPTP_Parser/make_tptp_parser" \
+		"./src/Pure/build" \
+		"./src/Pure/build-jars" \
+		"./src/Tools/Code/lib/Tools/codegen" \
+		"./src/Tools/Graphview/lib/Tools/graphview" \
+		"./src/Tools/jEdit/lib/Tools/jedit" \
+		"./src/Tools/Metis/fix_metis_license" \
+		"./src/Tools/Metis/make_metis" \
+		"./src/Tools/Metis/scripts/mlpp" \
+		"./src/Tools/WWW_Find/lib/Tools/wwwfind"
+	do
+		exeinto $(dirname "${TARGETDIR}/${i}")
+		doexe ${i}
+	done
+
+	insinto /etc/isabelle
+	doins -r etc/*
+	dosym /etc/isabelle "${TARGETDIR}/etc"
+
+	dosym "${LIBDIR}/heaps" "${TARGETDIR}/heaps"
+	insinto ${LIBDIR}
+	doins -r heaps
+
+	bin/isabelle install -d ${TARGETDIR} "${ED}usr/bin" \
+		|| die "isabelle install failed"
+	newicon lib/icons/"${PN}.xpm" "${PN}.xpm"
+	newicon lib/icons/"${PN}-mini.xpm" "${PN}-mini.xpm"
+	dodoc ANNOUNCE CONTRIBUTORS COPYRIGHT NEWS README
+
+	java-pkg_regjar \
+		"${ED}${TARGETDIR}/contrib/jedit_build-20131106/contrib/Console.jar" \
+		"${ED}${TARGETDIR}/contrib/jedit_build-20131106/contrib/ErrorList.jar" \
+		"${ED}${TARGETDIR}/contrib/jedit_build-20131106/contrib/Highlight.jar" \
+		"${ED}${TARGETDIR}/contrib/jedit_build-20131106/contrib/idea-icons.jar" \
+		"${ED}${TARGETDIR}/contrib/jedit_build-20131106/contrib/jedit-5.1.0-patched/jars/QuickNotepad.jar" \
+		"${ED}${TARGETDIR}/contrib/jedit_build-20131106/contrib/jedit-5.1.0-patched/jedit.jar" \
+		"${ED}${TARGETDIR}/contrib/jedit_build-20131106/contrib/jsr305-2.0.0.jar" \
+		"${ED}${TARGETDIR}/contrib/jedit_build-20131106/contrib/MacOSX.jar" \
+		"${ED}${TARGETDIR}/contrib/jedit_build-20131106/contrib/SideKick.jar" \
+		"${ED}${TARGETDIR}/contrib/jfreechart-1.0.14-1/jfreechart-1.0.14-demo.jar" \
+		"${ED}${TARGETDIR}/lib/browser/GraphBrowser.jar" \
+		"${ED}${TARGETDIR}/lib/classes/Graphview.jar" \
+		"${ED}${TARGETDIR}/lib/classes/Pure.jar" \
+		"${ED}${TARGETDIR}/lib/classes/scala-actors.jar" \
+		"${ED}${TARGETDIR}/lib/classes/scala-compiler.jar" \
+		"${ED}${TARGETDIR}/lib/classes/scala-library.jar" \
+		"${ED}${TARGETDIR}/lib/classes/scala-reflect.jar" \
+		"${ED}${TARGETDIR}/lib/classes/scala-swing.jar" \
+		"${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/Console.jar" \
+		"${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/ErrorList.jar" \
+		"${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/Highlight.jar" \
+		"${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/idea-icons.jar" \
+		"${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/Isabelle-jEdit.jar" \
+		"${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/jsr305-2.0.0.jar" \
+		"${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/MacOSX.jar" \
+		"${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/QuickNotepad.jar" \
+		"${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/SideKick.jar" \
+		"${ED}${TARGETDIR}/src/Tools/jEdit/dist/jedit.jar"
+}
+
+pkg_postinst() {
+	# If any of the directories in /etc/isabelle/components do not exist, then
+	# even isabelle getenv ISABELLE_HOME fails.  Hence it is necessary to
+	# to delete any non-existing directories.  If an old Isabelle version was
+	# installed with component ebuilds like sci-mathematics/e, then the
+	# Isabelle version is upgraded, then the contrib directories will not
+	# exist initially, it is necessary to delete them from /etc/isabelle/components.
+	# Then these components are rebuilt (creating these directories) using the
+	# EAPI=5 subslot depends.
+	for i in $(egrep '^[^#].*$' "${ROOT}etc/isabelle/components")
+	do
+		if [ ! -d /usr/share/${MY_P}/${i} ]; then
+			sed -e "\@${i}@d" -i "${ROOT}etc/isabelle/components"
+		fi
+	done
+	if use ledit && use readline; then
+		elog "Both readline and ledit use flags specified.  The default setting"
+		elog "if both are installed is to use readline (rlwrap), this can be"
+		elog "modfied by editing the ISABELLE_LINE_EDITOR setting in"
+		elog "${ROOT}/etc/isabelle/settings"
+	fi
+	elog "Please ensure you have a pdf viewer installed, for example:"
+	elog "As root: emerge app-text/zathura-pdf-poppler"
+	elog "Please configure your preferred pdf viewer, something like:"
+	elog "As normal user: xdg-mime default zathura.desktop application/pdf"
+	elog "Or alternatively by editing the PDF_VIEWER variable in the system"
+	elog "settings file ${ROOT}etc/isabelle/settings and/or the user"
+	elog "settings file \$HOME/.isabelle/${MY_P}/etc/settings"
+	elog "To improve sledgehammer performance, consider installing:"
+	elog "USE=isabelle emerge sci-mathematics/e sci-mathematics/spass"
+	elog "For nitpick it is necessary to install:"
+	elog "emerge sci-mathematics/kodkodi"
+}