sci-mathematics/isabelle: Bump to 2016.1. Thanks to David E. Narv?ez for

providing the isabelle 2016 patches and the 2016 ebuild. Thanks to
mgorny for reporting the get_libdir called in global scope QA bug.

Gentoo-bugs: 602958, 593380

Package-Manager: portage-2.3.3

11 files changed, 606 insertions, 0 deletions

diff --git a/sci-mathematics/isabelle/Manifest b/sci-mathematics/isabelle/Manifest
index 8e612b893f3e..613468cd97ce 100644
--- a/sci-mathematics/isabelle/Manifest
+++ b/sci-mathematics/isabelle/Manifest
@@ -1,7 +1,14 @@
 DIST Isabelle2015.tar.gz 36529154 SHA256 08723d3be6f91c57a7a69a8624c54cc1e0cd31506988bf29ed365a5aa5a5156f SHA512 052bb80316a9345368a295a7c5f3869b58d71a6879548fc6240a04fd2cf8c11406274ead8a1ed098563ef9b7573a826656da543e745044fc1d275322af5cc212 WHIRLPOOL 0be4759a1064f4759c2f227b037c448093ff36b47e16002fbb7e99d2843583e01314c4ea5c7a8cbf4d1304f8f72a383052911e483d51e4af2e68c4c36dea5121
+DIST Isabelle2016-1.tar.gz 39567637 SHA256 79831f83df4f0275fbd64caf3cd3e170354809478139907f6e25ebc8fc4a083f SHA512 c7da7900033a8c816f002b8899e398da7819dc457b3b1176dc9a19adffeb42d5524f2d14581a391487da1f36ffeabd0867bacab6462f3decfc0f7a9caf81a2d2 WHIRLPOOL 98d8cd767e04a7c46d19c91886fd7a98ca935625454b57df4f968f874340aaa5a6184004c6879ebc1c35f971b4e5ff1a52f06e33e1d14e377dbce346e201d655
+DIST bash_process-isabelle-component-1.2.1.tar.gz 33182 SHA256 50ba6bed5a8fbcf26b9e9b090af783e1288daa9b6d2e67ec65e7de8621049bf4 SHA512 d9817191af5660e38f1647401803115a93f0052291bfbbcb1cd9b41a4bab89b3ebdde22b40744a04ad3268aed8ca037ae59981c513f71b3ff6d89855d29e14c3 WHIRLPOOL f8392e4df237e758568b3edd25b83b44b916a81f9a18f6d6dd931a084de9a915930ae9e65e39b7b39b80ab9f738fd112113c4c3496ef3433fd17efff2f51068a
 DIST csdp-isabelle-component-6.x.tar.gz 493 SHA256 65dde42fa476095052ca3820df4c0e45089653d4467a53de711c8e13670a1b19 SHA512 9be28ecbf61d0f6ad23e28d44bd7ceb8f06ab22f3a05a7c823a9c5bf52ddcf5e5c300c41e14451d6b8e6a4c32b1bbd17769c731cd890fab335a866cd5e735290 WHIRLPOOL c930c531637172e4c75ec44d68f71e69e748a8b976fa3651ef4015fb6a90e30b568bd092632dc16c6389aac09bc13f3249af6c3ac261f09ad2dc5ad915282f99
 DIST exec_process-isabelle-component-1.0.3.tar.gz 814 SHA256 ee3b7b299852bcfd0bf7ffce6c8cd2279f2d71247c4a7b0042971b31c2b2a89d SHA512 7880b7f9843ff5806ab37d938a817a5b33e973772d9a6c6cf76bf04076fb532309bd22dfaa203be7c72c07f5a638f0f97e730c414ed164024fd31f1f09fc7c09 WHIRLPOOL 9d9beb7a41baac8b591ceee31bb7b69e1dd07fce66757511649977f6a85d85eef525ba0be13b0873c1aef47de0eace8bf88283b4a136397000e61cfc81da8d4d
+DIST isabelle_fonts-isabelle-component-20160830.tar.gz 249427 SHA256 1e99293f2f77f906f32c3974becd7c4a9d474050d3ab78222e3e5f40fe3d8fce SHA512 a185f79990478861832e9400ea37ffd02f582d3f916d26d901b8b0ec923027c412538bafe4a763a132adb9277a4b00a7a510762928ec49433ef550ae3fe59dbc WHIRLPOOL c15a6df44fce1d5577a7642d7b659b4b202bfd148db35c2429ec8e6c2680e7f1302b6249792150f0563a4e9cd9c92325bedc33194c0c7cf5008f2a3f4677ef02
 DIST jedit_build-isabelle-component-20150228.tar.gz 10674317 SHA256 2bee3c5242a3ce4150656f106e658096e82b6bd966e04d590e20023a956be29b SHA512 ba2d0804f21cee596fc3528a592941efc393e98b890efe054aed18fc0d31edfe459047b58ed79b42892e219b4c35a4fb5c8cca0f402b96d641ff8ce62e321339 WHIRLPOOL b2971bdef70e32d858385cb58603d6a5a7e357dbbc9810569093a31332a7838387f43a76a65048a12f259f08de86f200e962ccf2deb2bd3cd4e83dc4c1e41d8b
+DIST jedit_build-isabelle-component-20161024.tar.gz 10819946 SHA256 5b3cc4d2916a77ceef1b7aea80c3ade715795d2c2359f4f8f73b32e334c3f22e SHA512 0563b696307dd33b244e4ecc62664056a2b003c3291a5e3d7dd4f1c936dac2c3257ff90273cb2c8dc3bf9dea40fae745fabb57fc5f4ed420d0c8fd7d2b917433 WHIRLPOOL 46edf80819abef2c900a2d0dfb20530685678c25780a56946f8fa4af66abb047cfdcab17a7bb9700e60028e5465d93c227d7515084f6020546c781419d91cc03
 DIST jfreechart-isabelle-component-1.0.14-1.tar.gz 3444825 SHA256 b0eb7365c4c5877379889100f081a4afc4117afc0d332941c3dd01bef2c4aee9 SHA512 ee1d84a45e43029d5e3acee823176196da19789322e8d3c2c81d5504930ad81d50e16e5da87655e4151034901daefb4ce6b82334839e39134b3a7ce32203aa67 WHIRLPOOL e6f9caadb802ecb5b784e86e96c008e9271aa0b1c940152fb0b0358280d9c1e274bb0dee1507f8ff0fe7f43f863db538d631c76e146d1f66ab6e8a8fb27eb42d
+DIST jortho-isabelle-component-1.0-2.tar.gz 1723761 SHA256 cf004d735252dcdc00ff6d3c9b5cc400f56bc8b7eb49ed9a3227f12779639bad SHA512 8bef5e025d13b76c86a727bf93887b846cc906b2ce00299c38f69ccf33fb9dc7411e55b6fd1c56ed993c180d83a7e9ed90122f7feb6ae4fb70df93802ac21211 WHIRLPOOL 2a9aae3dcc62c52c194f17d0b5e59d710bd8efdb9e75ed6dd9fa68746a9bbc5178a218e405d7a23bf15d3957c3e1a8543ccdeb04f8556b05b8802aed47d8e537
 DIST polyml-isabelle-component-5.5.2-3.tar.gz 691 SHA256 1ba253974193efc70711b7fe32cc831d8bcc13107b0b130ddf6087bb6ff6d3e7 SHA512 45d68fa7a07ae9fc39cb21fa4c4c43a34576377fb828c8652002c56cc9ec7b3c7b5fcefb7604fc4bc90ce4868dd2fca41ddf37ce285da4902664ab21e4657b3f WHIRLPOOL 3a85c59b1bb928c5ea91f8150c6ded5309fae96bd7558b56e6c3d8f04c418b03b57fb49565af5ed919179fd9e30c957575ca7b65d938ce69c5d3131d8c55ab1e
+DIST polyml-isabelle-component-5.6-1.tar.gz 822 SHA256 158d597bb103b173ce95b40f4a5ed3bf45fce9a7185be4240e0fb69dbb74431d SHA512 403239aa48aab8c39e12cd5f82cb5e3ba7c31f9325d88f5137d3ec509bb25ab4eb8b1103a66b8ea5ad45c7c968ef092749c486217528a5db4223819106c00a59 WHIRLPOOL 6a1f766c71543748cdeab6bc1e3e1e7b8ab81b49976bebf0ec72086be8f161cd23b913d28cf0f0386b8f33a7b9637427a2c57f1bd7adf58c8c0f58054f84a9db
+DIST ssh-java-isabelle-component-20161009.tar.gz 412919 SHA256 60d9448e664a357816e64e4d21ce0db9fb27354e8c64e1199c4be839b084145e SHA512 685a9b8791046c1bc21aa77614fb1b304e7438715377e179954ebfd1603434ff66fe23e90de928a5af6f51a48ae6ea6f05f9ff8941d98f7c3a43fdda02d3b519 WHIRLPOOL 3c5c666f86e08c81d75b13442a98b6eaa51418a8a55310e87c53e68480e31ec6050c1e2b3876a0a3e06c58e5e8c9735150408e8fd120a8d83b9827b9b84b2c7c
 DIST xz-java-isabelle-component-1.5.tar.gz 315 SHA256 e7fdd433608561c87558d4d0ee39166e8396ce11242e85391417ec7fd3ce7b8e SHA512 6dfec49e12c4cafbb6b6386dd54477e86b6bb419a77c52d9606a0305aeea9cd11f087ed6bba77352c7bf9ec656052ef617e845f472e57b5cdfbccf22b2eeb4fa WHIRLPOOL 9c1fc16db0adc88557b81608902d9d69007dc90d5849f4f7501101930842ce81ded76af0e76e38df8bd0b07d137e53bafaa338bf6c7ae338e97af2a1433d5c1d
diff --git a/sci-mathematics/isabelle/files/isabelle-2016-classpath.patch b/sci-mathematics/isabelle/files/isabelle-2016-classpath.patch
new file mode 100644
index 000000000000..032b18b71f3b
--- /dev/null
+++ b/sci-mathematics/isabelle/files/isabelle-2016-classpath.patch
@@ -0,0 +1,32 @@
+Index: Isabelle2016/lib/Tools/java
+===================================================================
+--- Isabelle2016.orig/lib/Tools/java
++++ Isabelle2016/lib/Tools/java
+@@ -10,5 +10,5 @@ declare -a JAVA_ARGS; eval "JAVA_ARGS=($
+ unset CLASSPATH
+ 
+ isabelle_java java "${JAVA_ARGS[@]}" \
+-  -classpath "$(platform_path "$ISABELLE_CLASSPATH")" "$@"
++  -classpath "$(platform_path "$ISABELLE_CLASSPATH:$(java-config -p scala-2.11)")" "$@"
+ 
+Index: Isabelle2016/lib/Tools/scala
+===================================================================
+--- Isabelle2016.orig/lib/Tools/scala
++++ Isabelle2016/lib/Tools/scala
+@@ -14,4 +14,4 @@ do
+ done
+ 
+ isabelle_scala scala "${SCALA_ARGS[@]}" \
+-  -classpath "$(platform_path "$ISABELLE_CLASSPATH")" "$@"
++  -classpath "$(platform_path "$ISABELLE_CLASSPATH:$(java-config -p scala-2.11)")" "$@"
+Index: Isabelle2016/lib/Tools/scalac
+===================================================================
+--- Isabelle2016.orig/lib/Tools/scalac
++++ Isabelle2016/lib/Tools/scalac
+@@ -7,5 +7,5 @@
+ isabelle_admin_build jars || exit $?
+ 
+ isabelle_scala scalac -Dfile.encoding=UTF-8 \
+-  -classpath "$(platform_path "$ISABELLE_CLASSPATH")" "$@"
++  -classpath "$(platform_path "$ISABELLE_CLASSPATH:$(java-config -p scala-2.11)")" "$@"
+ 
diff --git a/sci-mathematics/isabelle/files/isabelle-2016-jfreechart-classpath.patch b/sci-mathematics/isabelle/files/isabelle-2016-jfreechart-classpath.patch
new file mode 100644
index 000000000000..9a88ebef26ca
--- /dev/null
+++ b/sci-mathematics/isabelle/files/isabelle-2016-jfreechart-classpath.patch
@@ -0,0 +1,16 @@
+--- Isabelle2016-orig/contrib/jfreechart-1.0.14-1/etc/settings	2013-09-12 07:46:57.000000000 +1000
++++ Isabelle2016/contrib/jfreechart-1.0.14-1/etc/settings	2016-07-07 17:22:55.716464804 +1000
+@@ -1,9 +1,8 @@
+ # -*- shell-script -*- :mode=shellscript:
+ 
+ JFREECHART_HOME="$COMPONENT"
+-JFREECHART_JAR_NAMES="iText-2.1.5.jar jcommon-1.0.18.jar jfreechart-1.0.14.jar"
+-
+-classpath "$JFREECHART_HOME/lib/iText-2.1.5.jar"
+-classpath "$JFREECHART_HOME/lib/jcommon-1.0.18.jar"
+-classpath "$JFREECHART_HOME/lib/jfreechart-1.0.14.jar"
++JFREECHART_JAR_NAMES="$(java-config --classpath itext | sed -e 's@:@ @g' -e 's@/[^ ]*/@@g') $(java-config --classpath jcommon-1.0 | sed -e 's@:@ @g' -e 's@/[^ ]*/@@g') $(java-config --classpath jfreechart-1.0 | sed -e 's@:@ @g' -e 's@/[^ ]*/@@g')"
+ 
++classpath "$(java-config --classpath itext)"
++classpath "$(java-config --classpath jcommon-1.0)"
++classpath "$(java-config --classpath jfreechart-1.0)"
diff --git a/sci-mathematics/isabelle/files/isabelle-2016-libsha1.patch b/sci-mathematics/isabelle/files/isabelle-2016-libsha1.patch
new file mode 100644
index 000000000000..04dc405823e2
--- /dev/null
+++ b/sci-mathematics/isabelle/files/isabelle-2016-libsha1.patch
@@ -0,0 +1,13 @@
+Index: work/Isabelle2016/src/Pure/General/sha1_polyml.ML
+===================================================================
+--- work.orig/Isabelle2016/src/Pure/General/sha1_polyml.ML
++++ work/Isabelle2016/src/Pure/General/sha1_polyml.ML
+@@ -18,7 +18,7 @@ fun hex_string arr i =
+   in (op ^) (apply2 hex_digit (Integer.div_mod (Char.ord c) 16)) end
+ 
+ val lib_path =
+-  ("$ML_HOME/" ^ (if ML_System.platform_is_windows then "sha1.dll" else "libsha1.so"))
++  ("$SHA1_HOME/" ^ (if ML_System.platform_is_windows then "sha1.dll" else "libsha1.so"))
+   |> Path.explode;
+ 
+ val STRING_INPUT_BYTES =
diff --git a/sci-mathematics/isabelle/files/isabelle-2016.1-bash_process-1.2.1-settings.patch b/sci-mathematics/isabelle/files/isabelle-2016.1-bash_process-1.2.1-settings.patch
new file mode 100644
index 000000000000..38d047199ce8
--- /dev/null
+++ b/sci-mathematics/isabelle/files/isabelle-2016.1-bash_process-1.2.1-settings.patch
@@ -0,0 +1,7 @@
+--- Isabelle2016-1-orig/contrib/bash_process-1.2.1/etc/settings	2016-02-14 09:48:03.000000000 +1100
++++ Isabelle2016-1/contrib/bash_process-1.2.1/etc/settings	2017-01-02 13:44:49.355549312 +1100
+@@ -1,3 +1,3 @@
+ # -*- shell-script -*- :mode=shellscript:
+ 
+-ISABELLE_BASH_PROCESS="$COMPONENT/${ISABELLE_PLATFORM64:-$ISABELLE_PLATFORM32}/bash_process"
++ISABELLE_BASH_PROCESS="$COMPONENT/bash_process"
diff --git a/sci-mathematics/isabelle/files/isabelle-2016.1-disable-jedit-build-after-install.patch b/sci-mathematics/isabelle/files/isabelle-2016.1-disable-jedit-build-after-install.patch
new file mode 100644
index 000000000000..6bac5ccbe748
--- /dev/null
+++ b/sci-mathematics/isabelle/files/isabelle-2016.1-disable-jedit-build-after-install.patch
@@ -0,0 +1,128 @@
+--- Isabelle2016-1-orig/src/Tools/jEdit/lib/Tools/jedit	2016-12-13 01:03:49.000000000 +1100
++++ Isabelle2016-1/src/Tools/jEdit/lib/Tools/jedit	2017-01-01 17:24:50.107722845 +1100
+@@ -239,125 +239,6 @@
+   "$ISABELLE_JEDIT_BUILD_HOME/contrib/jsr305-2.0.0.jar"
+ )
+ 
+-
+-# target
+-
+-TARGET="dist/jars/Isabelle-jEdit.jar"
+-
+-declare -a UPDATED=()
+-
+-if [ "$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[@]}" "$PURE_JAR"
+-        "${SOURCES[@]}" "${RESOURCES[@]}"
+-      )
+-    elif [ -e "$ISABELLE_HOME/Admin/build" ]; then
+-      declare -a DEPS=("$PURE_JAR" "${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 "${RESOURCES[@]}" dist/classes/.
+-  cp src/jEdit.props dist/properties/.
+-  cp -p -R -f src/modes/. dist/modes/.
+-
+-  perl -i -e 'while (<>) {
+-    if (m/FILE="ml.xml"/ or m/FILE_NAME_GLOB="...sml,ml."/) { }
+-    elsif (m/NAME="javacc"/) {
+-      print qq!<MODE NAME="isabelle" FILE="isabelle.xml" FILE_NAME_GLOB="{*.thy,ROOT0.ML,ROOT.ML}"/>\n\n!;
+-      print qq!<MODE NAME="isabelle-ml" FILE="isabelle-ml.xml" FILE_NAME_GLOB="*.ML"/>\n\n!;
+-      print qq!<MODE NAME="isabelle-news" FILE="isabelle-news.xml"/>\n\n!;
+-      print qq!<MODE NAME="isabelle-options" FILE="isabelle-options.xml"/>\n\n!;
+-      print qq!<MODE NAME="isabelle-root" FILE="isabelle-root.xml" FILE_NAME_GLOB="ROOT"/>\n\n!;
+-      print;
+-    }
+-    elsif (m/NAME="sqr"/) {
+-      print qq!<MODE NAME="sml" FILE="sml.xml" FILE_NAME_GLOB="*.{sml,sig}"/>\n\n!;
+-      print;
+-    }
+-    else { print; }
+-  }' dist/modes/catalog
+-
+-  cd dist
+-  isabelle_jdk jar xf jedit.jar
+-  cp "$ISABELLE_HOME/lib/logo/isabelle_transparent-32.gif" \
+-    "org/gjt/sp/jedit/icons/themes/classic/32x32/apps/isabelle.gif" || failed
+-  cp "$ISABELLE_HOME/lib/logo/isabelle_transparent-32.gif" \
+-    "org/gjt/sp/jedit/icons/themes/tango/32x32/apps/isabelle.gif" || failed
+-  isabelle_jdk jar cfe jedit.jar org.gjt.sp.jedit.jEdit org || failed
+-  rm -rf META-INF org
+-  cd ..
+-
+-  cp -p -R -f "${JEDIT_JARS[@]}" dist/jars/. || failed
+-  (
+-    #FIXME workarounds for scalac 2.11.0
+-    export CYGWIN="nodosfilewarning"
+-    function stty() { :; }
+-    export -f stty
+-
+-    for JAR in "$JEDIT_JAR" "${JEDIT_JARS[@]}" "$PURE_JAR"
+-    do
+-      classpath "$JAR"
+-    done
+-    export CLASSPATH="$(platform_path "$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
+-
+-  cp "$ISABELLE_JEDIT_BUILD_HOME/doc/jedit5.3.0manual-a4.pdf" dist/doc/jedit-manual.pdf
+-  cp dist/doc/CHANGES.txt dist/doc/jedit-changes
+-  cat > dist/doc/Contents <<EOF
+-Original jEdit Documentation
+-  jedit-manual    jEdit 5.3 User's Guide
+-  jedit-changes   jEdit 5.3 Version History
+-
+-EOF
+-
+-fi
+-
+ popd >/dev/null
+ 
+ 
diff --git a/sci-mathematics/isabelle/files/isabelle-2016.1-jortho-1.0-2-classpath.patch b/sci-mathematics/isabelle/files/isabelle-2016.1-jortho-1.0-2-classpath.patch
new file mode 100644
index 000000000000..a34cae3fcf45
--- /dev/null
+++ b/sci-mathematics/isabelle/files/isabelle-2016.1-jortho-1.0-2-classpath.patch
@@ -0,0 +1,8 @@
+--- Isabelle2016-1-orig/contrib/jortho-1.0-2/etc/settings	2014-04-16 06:03:34.000000000 +1000
++++ Isabelle2016-1/contrib/jortho-1.0-2/etc/settings	2017-01-02 00:13:01.619790577 +1100
+@@ -3,4 +3,4 @@
+ JORTHO_HOME="$COMPONENT"
+ JORTHO_DICTIONARIES="$JORTHO_HOME/dictionaries/en.gz:$JORTHO_HOME/dictionaries/en_US.gz:$JORTHO_HOME/dictionaries/en_GB-ise.gz:$JORTHO_HOME/dictionaries/en_GB-ize.gz:$JORTHO_HOME/dictionaries/en_CA.gz"
+ 
+-classpath "$JORTHO_HOME/jortho.jar"
++classpath "$(java-config -p jortho)"
diff --git a/sci-mathematics/isabelle/files/isabelle-2016.1-libsha1.patch b/sci-mathematics/isabelle/files/isabelle-2016.1-libsha1.patch
new file mode 100644
index 000000000000..f19436acd1c3
--- /dev/null
+++ b/sci-mathematics/isabelle/files/isabelle-2016.1-libsha1.patch
@@ -0,0 +1,11 @@
+--- Isabelle2016-1-orig/src/Pure/General/sha1.ML	2016-12-13 01:03:45.000000000 +1100
++++ Isabelle2016-1/src/Pure/General/sha1.ML	2016-12-28 20:50:36.814706587 +1100
+@@ -146,7 +146,7 @@
+ (* C library and memory *)
+ 
+ val library_path =
+-  Path.explode ("$ML_HOME/" ^ (if ML_System.platform_is_windows then "sha1.dll" else "libsha1.so"));
++  Path.explode ("$SHA1_HOME/" ^ (if ML_System.platform_is_windows then "sha1.dll" else "libsha1.so"));
+ 
+ fun with_memory n =
+   Thread_Attributes.uninterruptible (fn restore_attributes => fn f =>
diff --git a/sci-mathematics/isabelle/files/isabelle-2016.1-smt_read_only_certificates.patch b/sci-mathematics/isabelle/files/isabelle-2016.1-smt_read_only_certificates.patch
new file mode 100644
index 000000000000..d766a957021d
--- /dev/null
+++ b/sci-mathematics/isabelle/files/isabelle-2016.1-smt_read_only_certificates.patch
@@ -0,0 +1,33 @@
+--- Isabelle2016-1-orig/src/HOL/SMT_Examples/Boogie.thy	2016-12-13 01:03:38.000000000 +1100
++++ Isabelle2016-1/src/HOL/SMT_Examples/Boogie.thy	2016-12-30 23:46:11.947737290 +1100
+@@ -52,7 +52,7 @@
+ section \<open>Verification condition proofs\<close>
+ 
+ declare [[smt_oracle = false]]
+-declare [[smt_read_only_certificates = true]]
++declare [[smt_read_only_certificates = false]]
+ 
+ 
+ declare [[smt_certificates = "Boogie_Max.certs"]]
+--- Isabelle2016-1-orig/src/HOL/SMT_Examples/SMT_Examples.thy	2016-12-13 01:03:38.000000000 +1100
++++ Isabelle2016-1/src/HOL/SMT_Examples/SMT_Examples.thy	2016-12-30 23:46:11.953737338 +1100
+@@ -9,7 +9,7 @@
+ begin
+ 
+ declare [[smt_certificates = "SMT_Examples.certs"]]
+-declare [[smt_read_only_certificates = true]]
++declare [[smt_read_only_certificates = false]]
+ 
+ 
+ section \<open>Propositional and first-order logic\<close>
+--- Isabelle2016-1-orig/src/HOL/SMT_Examples/SMT_Word_Examples.thy	2016-12-13 01:03:38.000000000 +1100
++++ Isabelle2016-1/src/HOL/SMT_Examples/SMT_Word_Examples.thy	2016-12-30 23:46:11.967737450 +1100
+@@ -11,7 +11,7 @@
+ declare [[smt_oracle = true]]
+ declare [[z3_extensions = true]]
+ declare [[smt_certificates = "SMT_Word_Examples.certs"]]
+-declare [[smt_read_only_certificates = true]]
++declare [[smt_read_only_certificates = false]]
+ 
+ text \<open>
+ Currently, there is no proof reconstruction for words.
diff --git a/sci-mathematics/isabelle/files/isabelle-2016.1-smt_timeout.patch b/sci-mathematics/isabelle/files/isabelle-2016.1-smt_timeout.patch
new file mode 100644
index 000000000000..249c94bd2583
--- /dev/null
+++ b/sci-mathematics/isabelle/files/isabelle-2016.1-smt_timeout.patch
@@ -0,0 +1,22 @@
+--- Isabelle2016-1-orig/src/HOL/SMT.thy	2016-12-13 01:03:38.000000000 +1100
++++ Isabelle2016-1/src/HOL/SMT.thy	2016-12-30 14:11:09.379863215 +1100
+@@ -201,7 +201,7 @@
+ (given in seconds) to restrict their runtime.
+ \<close>
+ 
+-declare [[smt_timeout = 20]]
++declare [[smt_timeout = 300]]
+ 
+ text \<open>
+ SMT solvers apply randomized heuristics. In case a problem is not
+--- Isabelle2016-1-orig/src/HOL/Tools/SMT/smt_config.ML	2016-12-13 01:03:42.000000000 +1100
++++ Isabelle2016-1/src/HOL/Tools/SMT/smt_config.ML	2016-12-30 14:11:27.186904132 +1100
+@@ -170,7 +170,7 @@
+ (* options *)
+ 
+ val oracle = Attrib.setup_config_bool @{binding smt_oracle} (K true)
+-val timeout = Attrib.setup_config_real @{binding smt_timeout} (K 30.0)
++val timeout = Attrib.setup_config_real @{binding smt_timeout} (K 300.0)
+ val reconstruction_step_timeout = Attrib.setup_config_real @{binding smt_reconstruction_step_timeout} (K 10.0)
+ val random_seed = Attrib.setup_config_int @{binding smt_random_seed} (K 1)
+ val read_only_certificates = Attrib.setup_config_bool @{binding smt_read_only_certificates} (K false)
diff --git a/sci-mathematics/isabelle/isabelle-2016.1.ebuild b/sci-mathematics/isabelle/isabelle-2016.1.ebuild
new file mode 100644
index 000000000000..8d18ecba582d
--- /dev/null
+++ b/sci-mathematics/isabelle/isabelle-2016.1.ebuild
@@ -0,0 +1,329 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="6"
+
+inherit eutils check-reqs java-pkg-2 versionator
+
+MY_PN="Isabelle"
+MY_PV=$(replace_all_version_separators '-')
+MY_P="${MY_PN}${MY_PV}"
+
+BP_PV="1.2.1"
+BP_PN="bash_process"
+BP_P="${BP_PN}-${BP_PV}"
+BP_IC_PN="${BP_PN}-isabelle-component"
+BP_IC_P="${BP_IC_PN}-${BP_PV}"
+
+# csdp is used in the compile of HOL_ex in
+# Library/Sum_of_Squares/sos_wrapper.ML where it execs $ISABELLE_CSDP
+CSDP_PV="6.x"
+CSDP_PN="csdp"
+CSDP_P="${CSDP_PN}-${CSDP_PV}"
+CSDP_IC_PN="${CSDP_PN}-isabelle-component"
+CSDP_IC_P="${CSDP_IC_PN}-${CSDP_PV}"
+
+ISABELLE_FONTS_PV="20160830"
+ISABELLE_FONTS_PN="isabelle_fonts"
+ISABELLE_FONTS_P="${ISABELLE_FONTS_PN}-${ISABELLE_FONTS_PV}"
+ISABELLE_FONTS_IC_PN="${ISABELLE_FONTS_PN}-isabelle-component"
+ISABELLE_FONTS_IC_P="${ISABELLE_FONTS_IC_PN}-${ISABELLE_FONTS_PV}"
+
+JEDIT_PV="20161024"
+JEDIT_PN="jedit_build"
+JEDIT_P="${JEDIT_PN}-${JEDIT_PV}"
+JEDIT_IC_PN="${JEDIT_PN}-isabelle-component"
+JEDIT_IC_P="${JEDIT_IC_PN}-${JEDIT_PV}"
+
+JORTHO_PV="1.0-2"
+JORTHO_PN="jortho"
+JORTHO_P="${JORTHO_PN}-${JORTHO_PV}"
+JORTHO_IC_PN="${JORTHO_PN}-isabelle-component"
+JORTHO_IC_P="${JORTHO_IC_PN}-${JORTHO_PV}"
+
+JFREECHART_PV="1.0.14-1"
+JFREECHART_PN="jfreechart"
+JFREECHART_P="${JFREECHART_PN}-${JFREECHART_PV}"
+JFREECHART_IC_PN="${JFREECHART_PN}-isabelle-component"
+JFREECHART_IC_P="${JFREECHART_IC_PN}-${JFREECHART_PV}"
+
+POLYML_PV="5.6-1"
+POLYML_PN="polyml"
+POLYML_P="${POLYML_PN}-${POLYML_PV}"
+POLYML_IC_PN="${POLYML_PN}-isabelle-component"
+POLYML_IC_P="${POLYML_IC_PN}-${POLYML_PV}"
+
+SSH_JAVA_PV="20161009"
+SSH_JAVA_PN="ssh-java"
+SSH_JAVA_P="${SSH_JAVA_PN}-${SSH_JAVA_PV}"
+SSH_JAVA_IC_PN="${SSH_JAVA_PN}-isabelle-component"
+SSH_JAVA_IC_P="${SSH_JAVA_IC_PN}-${SSH_JAVA_PV}"
+
+XZ_JAVA_PV="1.5"
+XZ_JAVA_PN="xz-java"
+XZ_JAVA_P="${XZ_JAVA_PN}-${XZ_JAVA_PV}"
+XZ_JAVA_IC_PN="${XZ_JAVA_PN}-isabelle-component"
+XZ_JAVA_IC_P="${XZ_JAVA_IC_PN}-${XZ_JAVA_PV}"
+
+SS="2.11"
+
+DESCRIPTION="Isabelle is a generic proof assistant"
+HOMEPAGE="http://www.cl.cam.ac.uk/research/hvg/Isabelle/index.html"
+SRC_URI="http://isabelle.in.tum.de/website-${MY_P}/dist/${MY_P}.tar.gz
+		http://isabelle.in.tum.de/dist/contrib/${BP_P}.tar.gz -> ${BP_IC_P}.tar.gz
+		http://dev.gentoo.org/~gienah/snapshots/${CSDP_IC_P}.tar.gz
+		http://isabelle.in.tum.de/dist/contrib/${ISABELLE_FONTS_P}.tar.gz -> ${ISABELLE_FONTS_IC_P}.tar.gz
+		http://isabelle.in.tum.de/components/${JORTHO_P}.tar.gz -> ${JORTHO_IC_P}.tar.gz
+		http://isabelle.in.tum.de/components/${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
+		http://isabelle.in.tum.de/dist/contrib/${SSH_JAVA_P}.tar.gz -> ${SSH_JAVA_IC_P}.tar.gz
+		http://dev.gentoo.org/~gienah/snapshots/${XZ_JAVA_IC_P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0/${PV}"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc graphbrowsing ledit readline"
+
+#upstream says
+#bash 2.x/3.x, Poly/ML 5.x, Perl 5.x,
+#for document preparation: complete LaTeX
+DEPEND=">=app-shells/bash-3.0:*
+	>=dev-java/jcommon-1.0.18:1.0
+	dev-java/jortho:0
+	>=dev-java/jfreechart-1.0.14:1.0
+	>=dev-java/itext-2.1.5:0
+	dev-java/xz-java:0
+	>=dev-lang/ghc-7.6.3
+	>=dev-lang/polyml-5.6:=[-portable]
+	>=dev-lang/perl-5.8.8-r2
+	>=dev-lang/swi-prolog-6.6.6
+	sci-libs/coinor-csdp
+	=sci-mathematics/z3-4.4*[isabelle]
+	>=virtual/jdk-1.8
+	doc? (
+		virtual/latex-base
+		dev-tex/rail
+	)
+	>=dev-lang/scala-2.11.8:${SS}
+	ledit? (
+		app-misc/ledit
+	)
+	readline? (
+		app-misc/rlwrap
+	)"
+
+RDEPEND="dev-perl/libwww-perl
+	sci-mathematics/sha1-polyml
+	>=virtual/jre-1.8
+	${DEPEND}"
+
+S="${WORKDIR}"/Isabelle${MY_PV}
+TARGETDIR="/usr/share/Isabelle"
+
+# 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$1.class
+# It wants javafx, I am unsure how to fix this. I test isabelle with the Sun JDK:
+# javafx/application/Platform.class               javafx
+# Presumably the user can provide the jEdit plugins if they are necessary:
+# marker/MarkerSetsPlugin.class                   http://plugins.jedit.org/plugins/?MarkerSets
+# projectviewer/gui/OptionPaneBase.class          http://plugins.jedit.org/plugins/?ProjectViewer
+
+JAVA_GENTOO_CLASSPATH="itext,jcommon-1.0,jortho,jfreechart-1.0,scala-${SS},xz-java"
+
+CHECKREQS_MEMORY="8192M"
+CHECKREQS_DISK_BUILD="17G"
+CHECKREQS_DISK_USR="8G"
+
+src_unpack() {
+	unpack "${MY_P}.tar.gz"
+	cd "${S}/contrib" || die
+	unpack ${BP_IC_P}.tar.gz
+	unpack ${CSDP_IC_P}.tar.gz
+	unpack ${ISABELLE_FONTS_IC_P}.tar.gz
+	unpack ${JEDIT_IC_P}.tar.gz
+	unpack ${JORTHO_IC_P}.tar.gz
+	unpack ${JFREECHART_IC_P}.tar.gz
+	unpack ${POLYML_IC_P}.tar.gz
+	unpack ${SSH_JAVA_IC_P}.tar.gz
+	unpack ${XZ_JAVA_IC_P}.tar.gz
+}
+
+pkg_setup() {
+	java-pkg-2_pkg_setup
+	check-reqs_pkg_setup
+}
+
+src_prepare() {
+	java-pkg-2_src_prepare
+	java-pkg_getjars ${JAVA_GENTOO_CLASSPATH}
+	rm -rf "${S}/contrib/${BP_P}/{x86-cygwin,x86-darwin,x86_64-darwin,x86-linux,x86_64-linux}" \
+		|| die "Could not remove bash_process binaries"
+	rm -f "${S}/contrib/${JORTHI_P}/${JORTHO_PN}.jar" \
+		|| die "Could not remove  contrib/${JORTHI_P}/${JORTHO_PN}.jar"
+	eapply "${FILESDIR}/${PN}-2016-classpath.patch"
+	eapply "${FILESDIR}/${PN}-2016-jfreechart-classpath.patch"
+	eapply "${FILESDIR}/${PN}-2016.1-bash_process-1.2.1-settings.patch"
+	eapply "${FILESDIR}/${PN}-2012-graphbrowser.patch"
+	eapply "${FILESDIR}/${PN}-2016.1-libsha1.patch"
+	eapply "${FILESDIR}/${PN}-2016.1-smt_timeout.patch"
+	eapply "${FILESDIR}/${PN}-2016.1-smt_read_only_certificates.patch"
+	eapply "${FILESDIR}/${PN}-2016.1-disable-jedit-build-after-install.patch"
+	eapply "${FILESDIR}/${PN}-2016.1-jortho-1.0-2-classpath.patch"
+	local polymlver=$(poly -v | cut -d' ' -f2)
+	local polymlarch=$(poly -v | cut -d' ' -f9 | cut -d'-' -f1)
+	cat <<- EOF >> "${S}/etc/settings"
+		# Poly/ML Gentoo (${polymlarch,,})
+		ML_PLATFORM=${polymlarch,,}-linux
+		ML_HOME="${ROOT}usr/bin"
+		ML_SYSTEM=polyml-${polymlver}
+		ML_OPTIONS="-H 1000"
+		ML_SOURCES="${ROOT}usr/src/debug/dev-lang/polyml-${polymlver}"
+
+		ISABELLE_GHC="${ROOT}usr/bin/ghc"
+		ISABELLE_OCAML="${ROOT}usr/bin/ocaml"
+		ISABELLE_SWIPL="${ROOT}usr/bin/swipl"
+		ISABELLE_JDK_HOME="\$(java-config --jdk-home)"
+		ISABELLE_BUILD_JAVA_OPTIONS="-Djava.awt.headless=true"
+		SCALA_HOME="${ROOT}usr/share/scala-${SS}"
+		SHA1_HOME="${ROOT}usr/$(get_libdir)/sha1-polyml"
+	EOF
+	local Z3_P="$(best_version sci-mathematics/z3 | sed 's:sci-mathematics/::')"
+	cat <<- EOF >> "${S}/etc/components"
+		#bundled components
+		contrib/${BP_P}
+		contrib/${CSDP_P}
+		contrib/${ISABELLE_FONTS_P}
+		contrib/${JEDIT_P}
+		contrib/${JORTHO_P}
+		contrib/${JFREECHART_P}
+		contrib/${POLYML_P}
+		contrib/${SSH_JAVA_P}
+		contrib/${XZ_JAVA_P}
+		contrib/${Z3_P}
+	EOF
+	local Z3_RC="${ROOT}usr/share/Isabelle/contrib/${Z3_P}"
+	[ -d "${Z3_RC}" ] \
+		|| die "z3 isabelle component directory ${Z3_RC} does not exist"
+	ln -s "${Z3_RC}" \
+	   "${S}/contrib/${Z3_P}" \
+		|| die "Failed to create z3 isabelle component symbolic link"
+	if use ledit && ! use readline; then
+		eapply "${FILESDIR}/${PN}-2012-reverse-line-editor-order.patch"
+	fi
+	rm -f "${S}/contrib/${JFREECHART_P}/lib"/*.jar \
+		|| die "Could not rm bundled jar files supplied by Gentoo"
+}
+
+src_compile() {
+	unset DISPLAY
+	einfo "Building Isabelle. This may take some time."
+	pushd contrib/${BP_P} || die "Could not cd to contrib/${BP_P}"
+	$(tc-getCC) ${CFLAGS} ${LDFLAGS} -o ${BP_PN} ${BP_PN}.c \
+		|| die "Could not build ${BP_PN}"
+	popd || die
+	if use graphbrowsing
+	then
+		rm -f "${S}/lib/browser/GraphBrowser.jar" \
+			|| die "failed cleaning graph browser directory"
+		pushd "${S}/lib/browser" \
+			|| die "Could not change directory to lib/browser"
+		./build || die "failed building the graph browser"
+		popd
+	fi
+	./bin/isabelle jedit -b -f || die "pide build failed"
+	pushd "${S}"/src/Pure || die "Could not change directory to src/Pure"
+	../../bin/isabelle env ./build-jars -f || die "build-jars failed"
+	popd || die
+	./bin/isabelle build -a -b -s -v || die "isabelle build failed"
+}
+
+src_install() {
+	local Z3_P="$(best_version sci-mathematics/z3 | sed 's:sci-mathematics/::')"
+	rm "${S}/contrib/${Z3_P}" \
+		|| die "Failed to remove z3 isabelle component symbolic link"
+
+	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 $(find ./src/Doc -type f -executable -print)
+		do
+			exeinto $(dirname "${TARGETDIR}/${i}")
+			doexe ${i}
+		done
+	fi
+
+	for i in $(find \
+		./{bin,lib,"contrib/${BP_P}/${BP_PN}",src/HOL,src/Pure,src/Tools} \
+		-type f -executable -print)
+	do
+		exeinto $(dirname "${TARGETDIR}/${i}")
+		doexe ${i}
+	done
+
+	insinto /etc/isabelle
+	doins -r etc/*
+	dosym /etc/isabelle "${TARGETDIR}/etc"
+
+	local LIBDIR="/usr/"$(get_libdir)"/Isabelle"${MY_PV}
+	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"
+
+	java-pkg_regjar \
+		$(find . -type f -name \*.jar -print | sed -e "s@^\.@${ED}${TARGETDIR}@g")
+
+	local DOCS=( "ANNOUNCE" "CONTRIBUTORS" "COPYRIGHT" "NEWS" "README" )
+	einstalldocs
+}
+
+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 ${TARGETDIR}/${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 "For nitpick it is necessary to install:"
+	elog "emerge sci-mathematics/kodkodi"
+}