From 388de5bbcbd8a0f8cb84eaf992b7a5c84e286f62 Mon Sep 17 00:00:00 2001
From: Kait Lam <39479354+katrinafyi@users.noreply.github.com>
Date: Mon, 30 Sep 2024 11:46:18 +1000
Subject: [PATCH 01/30] ci: add macos-latest

(cherry picked from commit 95fe5c1a0e2da1ea3a7f096659d6cb60aaaab9c5)
---
 .github/workflows/main.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index ee4271e..4395c05 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -36,7 +36,8 @@ jobs:
           planter,
           aslp_web, godbolt
         ]
-    runs-on: ubuntu-latest
+        os: [ubuntu-latest, macos-latest]
+    runs-on: ${{ matrix.os }}
 
     defaults:
       run: { shell: "bash -ex -o pipefail {0}" }

From ed9097e4c058d2797eaf8f7cf71ca4dae12e5d99 Mon Sep 17 00:00:00 2001
From: rina <k@rina.fyi>
Date: Mon, 30 Sep 2024 11:51:01 +1000
Subject: [PATCH 02/30] switch ordering

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 4395c05..ced5748 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -27,6 +27,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
+        os: [ubuntu-latest, macos-latest]
         # end-user packages to ci build for cache
         pkg: 
           [aslp, bap-aslp, bap-primus, basil,
@@ -36,7 +37,6 @@ jobs:
           planter,
           aslp_web, godbolt
         ]
-        os: [ubuntu-latest, macos-latest]
     runs-on: ${{ matrix.os }}
 
     defaults:

From 55d45acec479665a42ac417a4b0e2ad15912a161 Mon Sep 17 00:00:00 2001
From: rina <k@rina.fyi>
Date: Mon, 30 Sep 2024 12:06:05 +1000
Subject: [PATCH 03/30] nix build with -L

---
 .github/workflows/main.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index ced5748..20d545a 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -72,7 +72,7 @@ jobs:
         echo NIXPKGS_ALLOW_BROKEN="$("$broken" && echo 1 || echo 0)" > "$GITHUB_ENV"
       id: broken
 
-    - run: ./nix-cached.sh build --impure .#${{matrix.pkg}}
+    - run: ./nix-cached.sh build --impure -L .#${{matrix.pkg}}
       id: build
       continue-on-error: ${{ fromJSON(steps.broken.outputs.bool) }}
       
@@ -81,7 +81,7 @@ jobs:
       run: |
         for test in $(nix eval --impure .#${{matrix.pkg}}.tests --json | jq -r keys[]); do
           t=.#${{matrix.pkg}}.tests.$test 
-          ./nix-cached.sh build --impure "$t" --no-link
+          ./nix-cached.sh build --impure -L "$t" --no-link
         done
       continue-on-error: ${{ fromJSON(steps.broken.outputs.bool) }}
       if: steps.build.outcome == 'success'

From 91ae79341ccc95126349093ee498dddbf2d1c778 Mon Sep 17 00:00:00 2001
From: rina <k@rina.fyi>
Date: Mon, 30 Sep 2024 14:56:24 +1000
Subject: [PATCH 04/30] gtirb: disable clang-tidy to fix darwin build

---
 gtirb/gtirb.nix | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/gtirb/gtirb.nix b/gtirb/gtirb.nix
index e7a6db8..23162d4 100644
--- a/gtirb/gtirb.nix
+++ b/gtirb/gtirb.nix
@@ -23,7 +23,12 @@ stdenv.mkDerivation {
   buildInputs = [ cmake python3 boost doxygen ];
   propagatedBuildInputs = [ protobuf ];
 
-  cmakeFlags = [ "-DGTIRB_ENABLE_TESTS=OFF" "-DGTIRB_PY_API=ON" ];
+  cmakeFlags = [
+    "-DGTIRB_ENABLE_TESTS=OFF"
+    "-DGTIRB_PY_API=ON"
+    "-DGTIRB_RUN_CLANG_TIDY=OFF"
+    # "-DCLANG_TIDY_EXE=${lib.getExe' clang-tools "clang-tidy"}"
+  ];
 
   CXXFLAGS = "-includeset -Wno-error=unused-result -Wno-error=array-bounds";
   preConfigure = ''

From 4585b153b6396ccdc2ab17dba5e97b4f60d47b59 Mon Sep 17 00:00:00 2001
From: Nicholas Coughlin <n.coughlin@uq.edu.au>
Date: Tue, 1 Oct 2024 14:40:49 +1000
Subject: [PATCH 05/30] Fixes for macOS

---
 aslp/ocaml_z3.nix                             | 41 +++++++++++++++++
 aslp/overlay.nix                              |  3 +-
 basil/0001-basil-protoc-version.patch         | 20 +++++++++
 basil/basil.nix                               | 10 ++++-
 ...1-ddisasm-disable-concurrent-souffle.patch | 44 +++++++++++++++++++
 gtirb/0001-gtirb-link-absl.patch              | 26 +++++++++++
 gtirb/0001-gtirb_pprinter-include-map.patch   | 12 +++++
 gtirb/ddisasm.nix                             |  1 +
 gtirb/gtirb-pprinter.nix                      |  1 +
 gtirb/gtirb.nix                               |  1 +
 10 files changed, 157 insertions(+), 2 deletions(-)
 create mode 100644 aslp/ocaml_z3.nix
 create mode 100644 basil/0001-basil-protoc-version.patch
 create mode 100644 gtirb/0001-ddisasm-disable-concurrent-souffle.patch
 create mode 100644 gtirb/0001-gtirb-link-absl.patch
 create mode 100644 gtirb/0001-gtirb_pprinter-include-map.patch

diff --git a/aslp/ocaml_z3.nix b/aslp/ocaml_z3.nix
new file mode 100644
index 0000000..28bd8a8
--- /dev/null
+++ b/aslp/ocaml_z3.nix
@@ -0,0 +1,41 @@
+{ stdenv, lib, ocaml, findlib, zarith, z3 }:
+
+if lib.versionOlder ocaml.version "4.07"
+then throw "z3 is not available for OCaml ${ocaml.version}"
+else
+
+let z3-with-ocaml1 = z3.override {
+  ocamlBindings = true;
+  inherit ocaml findlib zarith;
+}; in
+
+let z3-with-ocaml = z3-with-ocaml1.overrideAttrs (p: {
+  postInstall = p.postInstall + ''
+    ln -sf $lib/lib/libz3${stdenv.hostPlatform.extensions.sharedLibrary} $OCAMLFIND_DESTDIR/stublibs/libz3${stdenv.hostPlatform.extensions.sharedLibrary} 
+  '';
+}); in
+
+stdenv.mkDerivation {
+
+  pname = "ocaml${ocaml.version}-z3";
+  inherit (z3-with-ocaml) version;
+
+  dontUnpack = true;
+
+  installPhase = ''
+    runHook preInstall
+    mkdir -p $OCAMLFIND_DESTDIR
+    cp -r ${z3-with-ocaml.ocaml}/lib/ocaml/${ocaml.version}/site-lib/stublibs $OCAMLFIND_DESTDIR
+    cp -r ${z3-with-ocaml.ocaml}/lib/ocaml/${ocaml.version}/site-lib/Z3 $OCAMLFIND_DESTDIR/z3
+    runHook postInstall
+  '';
+
+  nativeBuildInputs = [ findlib ];
+  propagatedBuildInputs = [ zarith ];
+
+  strictDeps = true;
+
+  meta = z3.meta // {
+    description = "Z3 Theorem Prover (OCaml API)";
+  };
+}
diff --git a/aslp/overlay.nix b/aslp/overlay.nix
index c871bed..3a54bc9 100644
--- a/aslp/overlay.nix
+++ b/aslp/overlay.nix
@@ -7,8 +7,9 @@ final: prev:
   inherit (final.ocamlPackages_pac_5) aslp_web;
 
   overlay_ocamlPackages = ofinal: oprev: {
+    ocaml_z3 = final.callPackage ./ocaml_z3.nix { findlib = ofinal.findlib ; zarith = ofinal.zarith ; ocaml = ofinal.ocaml ; };
 
-    asli = ofinal.callPackage ./asli.nix { inherit (final) z3; ocaml_z3 = ofinal.z3; };
+    asli = ofinal.callPackage ./asli.nix { inherit (final) z3; ocaml_z3 = ofinal.ocaml_z3; };
     aslp = ofinal.asli;
     # .overrideAttrs { src = prev.lib.cleanSource ~/progs/aslp; }
 
diff --git a/basil/0001-basil-protoc-version.patch b/basil/0001-basil-protoc-version.patch
new file mode 100644
index 0000000..db93ee6
--- /dev/null
+++ b/basil/0001-basil-protoc-version.patch
@@ -0,0 +1,20 @@
+diff --git a/build.sbt b/build.sbt
+index f1e6339f..2d9ede97 100644
+--- a/build.sbt
++++ b/build.sbt
+@@ -31,6 +31,8 @@ lazy val root = project
+ 
+ scalacOptions ++= Seq("-deprecation", "-feature")
+ 
++PB.protocExecutable := file("PROTOC_PLACEHOLDER")
++
+ Compile / PB.targets := Seq(
+   scalapb.gen() -> (Compile / sourceManaged).value / "scalapb"
+ )
+@@ -132,4 +134,4 @@ def filesContentEqual(path1: File, path2: File): Boolean = {
+   source1.close
+   source2.close
+   true
+-}
+\ No newline at end of file
++}
diff --git a/basil/basil.nix b/basil/basil.nix
index cadbff4..4eda940 100644
--- a/basil/basil.nix
+++ b/basil/basil.nix
@@ -6,6 +6,7 @@
 , jre
 , testers
 , basil
+, protobuf
 }:
 
 mkSbtDerivation {
@@ -21,7 +22,14 @@ mkSbtDerivation {
     sha256 = "sha256-juCX3X8KRGLIUqhNcGHUb/nRv09xhWs5cv/wbAs8wmM=";
   };
 
-  depsSha256 = "sha256-++gg+SKskDyaqHowNG2RPS7evuCzPYvvXMC4Rkp7b6U=";
+  patches = [ ./0001-basil-protoc-version.patch ] ;
+
+  preConfigure = ''
+    substituteInPlace build.sbt \
+      --replace 'PROTOC_PLACEHOLDER' '${protobuf}/bin/protoc'
+  '';
+
+  depsSha256 = "sha256-Cyz4kpyZ3KlUo0JmQzvgptSQMErC5G4e8Mp0dWJMaMY";
 
   buildPhase = ''
     javac -version
diff --git a/gtirb/0001-ddisasm-disable-concurrent-souffle.patch b/gtirb/0001-ddisasm-disable-concurrent-souffle.patch
new file mode 100644
index 0000000..b93dcff
--- /dev/null
+++ b/gtirb/0001-ddisasm-disable-concurrent-souffle.patch
@@ -0,0 +1,44 @@
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index 1db64e22..b1fd4848 100644
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -178,7 +178,7 @@ function(GENERATE_ARCH_CPP_SINGLE)
+     OUTPUT "${PARAM_PATH}.cpp"
+     WORKING_DIRECTORY "${SOUFFLE_DATALOG_DIR}"
+     COMMAND
+-      ${SOUFFLE} main.dl -g "${CMAKE_BINARY_DIR}/src/${PARAM_PATH}.cpp" -jauto
++      ${SOUFFLE} main.dl -g "${CMAKE_BINARY_DIR}/src/${PARAM_PATH}.cpp" 
+       -MARCH_${PARAM_MARCH} ${SOUFFLE_PREPROCESSOR_ARG} ${SOUFFLE_PROFILING_ARG}
+       -N ddisasm_${ARCH}
+     DEPENDS ${DATALOG_BASE_SOURCES} ${PARAM_DATALOG_SOURCES})
+@@ -203,7 +203,7 @@ function(GENERATE_ARCH_CPP_MANY)
+   # Generate CPP code
+   execute_process(
+     COMMAND
+-      ${SOUFFLE} main.dl -G ${STAGING_PATH} -jauto -MARCH_${PARAM_MARCH}
++      ${SOUFFLE} main.dl -G ${STAGING_PATH} -MARCH_${PARAM_MARCH}
+       ${SOUFFLE_PREPROCESSOR_ARG} ${SOUFFLE_PROFILING_ARG} -N ddisasm_${ARCH}
+     WORKING_DIRECTORY "${SOUFFLE_DATALOG_DIR}")
+ 
+diff --git a/src/passes/CMakeLists.txt b/src/passes/CMakeLists.txt
+index aa20b7d0..ad89a198 100644
+--- a/src/passes/CMakeLists.txt
++++ b/src/passes/CMakeLists.txt
+@@ -70,7 +70,7 @@ add_custom_command(
+   WORKING_DIRECTORY "${CMAKE_BINARY_DIR}/src/passes"
+   COMMAND
+     ${SOUFFLE} ${NO_RETURN_DATALOG_MAIN} -g souffle_no_return.cpp -N
+-    souffle_no_return -jauto ${SOUFFLE_PREPROCESSOR_ARG}
++    souffle_no_return ${SOUFFLE_PREPROCESSOR_ARG}
+   DEPENDS ${NO_RETURN_DATALOG_SOURCES})
+ 
+ add_library(no_return_pass STATIC NoReturnPass.cpp ${NO_RETURN_CPP})
+@@ -114,7 +114,7 @@ add_custom_command(
+   WORKING_DIRECTORY "${CMAKE_BINARY_DIR}/src/passes"
+   COMMAND
+     ${SOUFFLE} ${FUNCTION_INFERENCE_DATALOG_MAIN} -g
+-    souffle_function_inference.cpp -N souffle_function_inference -jauto
++    souffle_function_inference.cpp -N souffle_function_inference 
+     ${SOUFFLE_PREPROCESSOR_ARG}
+   DEPENDS ${FUNCTION_INFERENCE_DATALOG_SOURCES})
+ 
diff --git a/gtirb/0001-gtirb-link-absl.patch b/gtirb/0001-gtirb-link-absl.patch
new file mode 100644
index 0000000..ade3bd0
--- /dev/null
+++ b/gtirb/0001-gtirb-link-absl.patch
@@ -0,0 +1,26 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index e176b6a7..929cd452 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -432,6 +432,7 @@ if(CL_API)
+ else()
+   find_package(Protobuf 3.0.0 REQUIRED)
+ endif()
++find_package( absl REQUIRED )
+
+ if(Protobuf_VERSION VERSION_LESS 3.2)
+   add_definitions(-DPROTOBUF_SET_BYTES_LIMIT)
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index 85558737..542065cd 100644
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -140,6 +140,9 @@ target_link_libraries(
+          # Link in this static lib, but don't make it a transitive dependency of
+          # TestGTIRB, etc
+   PRIVATE gtirb_proto
++         absl::log_internal_message
++         absl::log_internal_check_op
++         absl::status
+ )
+ target_compile_definitions(
+   ${PROJECT_NAME} PRIVATE GTIRB_${PROJECT_NAME}_EXPORTS
diff --git a/gtirb/0001-gtirb_pprinter-include-map.patch b/gtirb/0001-gtirb_pprinter-include-map.patch
new file mode 100644
index 0000000..3697141
--- /dev/null
+++ b/gtirb/0001-gtirb_pprinter-include-map.patch
@@ -0,0 +1,12 @@
+diff --git a/src/gtirb_pprinter/driver/parser.hpp b/src/gtirb_pprinter/driver/parser.hpp
+index 2eca4fb..0741103 100644
+--- a/src/gtirb_pprinter/driver/parser.hpp
++++ b/src/gtirb_pprinter/driver/parser.hpp
+@@ -4,6 +4,7 @@
+ #include <optional>
+ #include <regex>
+ #include <string_view>
++#include <map>
+ 
+ namespace fs = boost::filesystem;
+
diff --git a/gtirb/ddisasm.nix b/gtirb/ddisasm.nix
index e93cdaf..5055e08 100644
--- a/gtirb/ddisasm.nix
+++ b/gtirb/ddisasm.nix
@@ -28,6 +28,7 @@ stdenv.mkDerivation {
     rev = "9edfe9fe86910ef946de1db7a7ac41ce86bc31d0";
     hash = "sha256-xFW6J3jCCMtUqT25/zVfjjy5o3MoX1HXxIlRhjM6s8A=";
   };
+  patches = if stdenv.isDarwin then [ ./0001-ddisasm-disable-concurrent-souffle.patch ] else [];
 
   buildInputs = [ cmake boost lief gtirb gtirb-pprinter libehp ];
   nativeBuildInputs = [ capstone-grammatech souffle ];
diff --git a/gtirb/gtirb-pprinter.nix b/gtirb/gtirb-pprinter.nix
index 5ca1880..808e266 100644
--- a/gtirb/gtirb-pprinter.nix
+++ b/gtirb/gtirb-pprinter.nix
@@ -21,6 +21,7 @@ stdenv.mkDerivation {
     rev = "v2.1.0";
     hash = "sha256-zgYq6FKxaJ6vLzvOTCfOU4ZUyXvMuFc3abNrqg8NADc=";
   };
+  patches = [ ./0001-gtirb_pprinter-include-map.patch ];
 
   buildInputs = [ cmake python3 gtirb boost abseil-cpp gtest ];
   nativeBuildInputs = [ capstone-grammatech ];
diff --git a/gtirb/gtirb.nix b/gtirb/gtirb.nix
index 23162d4..412ae36 100644
--- a/gtirb/gtirb.nix
+++ b/gtirb/gtirb.nix
@@ -18,6 +18,7 @@ stdenv.mkDerivation {
     rev = "v2.0.0";
     hash = "sha256-ueoqxm6iXv4JgzR/xkImT+O8xx+7bA2upx1TJ828LLA=";
   };
+  patches = if stdenv.isDarwin then [ ./0001-gtirb-link-absl.patch ] else [];
 
   nativeBuildInputs = [ ];
   buildInputs = [ cmake python3 boost doxygen ];

From 70740d861943d878c0857177caf1ce99968e45d8 Mon Sep 17 00:00:00 2001
From: Nicholas Coughlin <n.coughlin@uq.edu.au>
Date: Thu, 3 Oct 2024 09:07:18 +1000
Subject: [PATCH 06/30] Fix gtirb python package

---
 basil/0001-basil-protoc-version.patch | 7 -------
 gtirb/gtirb.nix                       | 3 +++
 gtirb/python-gtirb.nix                | 2 --
 3 files changed, 3 insertions(+), 9 deletions(-)

diff --git a/basil/0001-basil-protoc-version.patch b/basil/0001-basil-protoc-version.patch
index db93ee6..67cc3f8 100644
--- a/basil/0001-basil-protoc-version.patch
+++ b/basil/0001-basil-protoc-version.patch
@@ -11,10 +11,3 @@ index f1e6339f..2d9ede97 100644
  Compile / PB.targets := Seq(
    scalapb.gen() -> (Compile / sourceManaged).value / "scalapb"
  )
-@@ -132,4 +134,4 @@ def filesContentEqual(path1: File, path2: File): Boolean = {
-   source1.close
-   source2.close
-   true
--}
-\ No newline at end of file
-+}
diff --git a/gtirb/gtirb.nix b/gtirb/gtirb.nix
index 412ae36..4349d37 100644
--- a/gtirb/gtirb.nix
+++ b/gtirb/gtirb.nix
@@ -39,6 +39,9 @@ stdenv.mkDerivation {
     substituteInPlace src/CMakeLists.txt src/gtirb/proto/CMakeLists.txt \
       --replace 'DESTINATION lib' 'DESTINATION ''${CMAKE_INSTALL_LIBDIR}' \
       --replace 'DESTINATION include' 'DESTINATION ''${CMAKE_INSTALL_INCLUDEDIR}'
+
+    substituteInPlace python/setup.py.in \
+      --replace '@CMAKE_SOURCE_DIR@' $python
   '';
 
   postInstall = ''
diff --git a/gtirb/python-gtirb.nix b/gtirb/python-gtirb.nix
index 2214a17..af3e85a 100644
--- a/gtirb/python-gtirb.nix
+++ b/gtirb/python-gtirb.nix
@@ -12,9 +12,7 @@ python3Packages.buildPythonPackage {
   propagatedBuildInputs = with python3Packages; [ networkx typing-extensions sortedcontainers intervaltree protobuf3 ];
 
   preConfigure = ''
-    ln -s /build/gtirb* /build/source 
     cd python
-
     substituteInPlace setup.py \
       --replace 'protobuf<=3.20.1' 'protobuf'
   '';

From 302dd59b05957c8904d2123a8ec9b9ddb2bcb945 Mon Sep 17 00:00:00 2001
From: rina <k@rina.fyi>
Date: Thu, 3 Oct 2024 11:18:03 +1000
Subject: [PATCH 07/30] basil: fix protoc substitution in dependency derivation

also fixes up some nix noob mistakes
---
 basil/basil.nix | 26 +++++++++++++++++++++-----
 1 file changed, 21 insertions(+), 5 deletions(-)

diff --git a/basil/basil.nix b/basil/basil.nix
index 4eda940..8719cbd 100644
--- a/basil/basil.nix
+++ b/basil/basil.nix
@@ -9,6 +9,12 @@
 , protobuf
 }:
 
+let
+  replaceProtocPlaceholder = ''
+    substituteInPlace build.sbt \
+      --replace-fail 'PROTOC_PLACEHOLDER' '${lib.getExe protobuf}'
+  '';
+in
 mkSbtDerivation {
   pname = "basil";
   version = "0.1.2-alpha-unstable-2024-09-24";
@@ -24,19 +30,27 @@ mkSbtDerivation {
 
   patches = [ ./0001-basil-protoc-version.patch ] ;
 
-  preConfigure = ''
-    substituteInPlace build.sbt \
-      --replace 'PROTOC_PLACEHOLDER' '${protobuf}/bin/protoc'
-  '';
+  # we must run the command in both the main derivation
+  # and the dependency-generating derivation.
+  overrideDepsAttrs = depsfinal: depsprev: {
+    postPatch = replaceProtocPlaceholder;
+  };
+  postPatch = replaceProtocPlaceholder;
 
-  depsSha256 = "sha256-Cyz4kpyZ3KlUo0JmQzvgptSQMErC5G4e8Mp0dWJMaMY";
+  depsSha256 = "sha256-tDJuleKVLMPCZNJGNxokuScDOU4siLQEmM1FZff+5oM=";
 
   buildPhase = ''
+    runHook preBuild
+
     javac -version
     sbt assembly
+
+    runHook postBuild
   '';
 
   installPhase = ''
+    runHook preInstall
+
     mkdir -p $out/bin
     mkdir -p $out/share/basil
 
@@ -55,6 +69,8 @@ mkSbtDerivation {
     makeWrapper "${lib.getExe jre}" $out/bin/basil \
       --add-flags -jar \
       --add-flags "$out/share/basil/$(basename $JAR)"
+
+    runHook postInstall
   '';
 
   meta = {

From 17c485de59116124dccb56d0d87e5f630d76974d Mon Sep 17 00:00:00 2001
From: rina <k@rina.fyi>
Date: Thu, 3 Oct 2024 13:33:17 +1000
Subject: [PATCH 08/30] ddisasm: use aarch64-unknown-linux-gnu-gcc in test

---
 gtirb/ddisasm.nix | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/gtirb/ddisasm.nix b/gtirb/ddisasm.nix
index 5055e08..70bfeec 100644
--- a/gtirb/ddisasm.nix
+++ b/gtirb/ddisasm.nix
@@ -12,7 +12,7 @@
 , ddisasm
 , makeWrapper
 , runCommand
-, runCommandCC
+, gcc-aarch64
 , unrandom
 , testers
 , jq
@@ -53,13 +53,13 @@ stdenv.mkDerivation {
     version = "Disassemble";
   };
 
-  passthru.tests.ddisasm-deterministic = runCommandCC
+  passthru.tests.ddisasm-deterministic = runCommand
     "ddisasm-deterministic-test"
-    { nativeBuildInputs = [ ddisasm.deterministic jq ]; }
+    { nativeBuildInputs = [ ddisasm.deterministic jq gcc-aarch64 ]; }
     ''
       mkdir -p $out && cd $out
       echo 'int main(void) { return 0; }' > a.c
-      $CC a.c
+      aarch64-unknown-linux-gnu-gcc a.c
       ddisasm-deterministic a.out --json | jq -S > a1
       ddisasm-deterministic a.out --json | jq -S > a2
       diff -q a1 a2

From 2ae10af1860fa415e959434f72b5cf985ae90f58 Mon Sep 17 00:00:00 2001
From: rina <k@rina.fyi>
Date: Thu, 3 Oct 2024 14:37:26 +1000
Subject: [PATCH 09/30] ddisasm: use clang-aarch64 in test

---
 gtirb/ddisasm.nix | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gtirb/ddisasm.nix b/gtirb/ddisasm.nix
index 70bfeec..3173860 100644
--- a/gtirb/ddisasm.nix
+++ b/gtirb/ddisasm.nix
@@ -12,7 +12,7 @@
 , ddisasm
 , makeWrapper
 , runCommand
-, gcc-aarch64
+, clang-aarch64
 , unrandom
 , testers
 , jq
@@ -55,11 +55,11 @@ stdenv.mkDerivation {
 
   passthru.tests.ddisasm-deterministic = runCommand
     "ddisasm-deterministic-test"
-    { nativeBuildInputs = [ ddisasm.deterministic jq gcc-aarch64 ]; }
+    { nativeBuildInputs = [ ddisasm.deterministic jq clang-aarch64 ]; }
     ''
       mkdir -p $out && cd $out
       echo 'int main(void) { return 0; }' > a.c
-      aarch64-unknown-linux-gnu-gcc a.c
+      aarch64-unknown-linux-gnu-cc a.c
       ddisasm-deterministic a.out --json | jq -S > a1
       ddisasm-deterministic a.out --json | jq -S > a2
       diff -q a1 a2

From 7d6f339d4eadec6ef49afcb912ea3106463b499d Mon Sep 17 00:00:00 2001
From: Nicholas Coughlin <n.coughlin@uq.edu.au>
Date: Tue, 8 Oct 2024 20:23:04 +1000
Subject: [PATCH 10/30] More macOS fixes

gtirb: Proper fix for abseil linking
aslp-cpp: Build with clang 17 on macOS
alive2-regehr: Disable 'no-error=maybe-uninitialized' option on macOS
alive2: Build with clang 17 on macOS
llvm-custom: Fix hardcoded /build path to $NIX_BUILD_TOP
ocaml-llvm: Bump ctypes-foreign to 0.23.0 to build on macOS
---
 aslp/aslp-cpp.nix                 |  6 +++-
 gtirb/0001-gtirb-link-absl.patch  | 47 +++++++++++++++++--------------
 llvm-translator/alive2-regehr.nix |  3 +-
 llvm-translator/alive2.nix        |  6 +++-
 llvm-translator/llvm-custom.nix   |  2 +-
 overlay.nix                       | 24 ++++++++++++++--
 6 files changed, 61 insertions(+), 27 deletions(-)

diff --git a/aslp/aslp-cpp.nix b/aslp/aslp-cpp.nix
index 3b8fe6a..461491f 100644
--- a/aslp/aslp-cpp.nix
+++ b/aslp/aslp-cpp.nix
@@ -1,9 +1,13 @@
 { stdenv
 , cmake
 , asli
+, overrideCC
+, llvmPackages_17
 }:
 
-stdenv.mkDerivation {
+let buildStdenv = if stdenv.isDarwin then overrideCC stdenv llvmPackages_17.clang else stdenv; in
+
+buildStdenv.mkDerivation {
   pname = "aslp-cpp";
   version = asli.version;
 
diff --git a/gtirb/0001-gtirb-link-absl.patch b/gtirb/0001-gtirb-link-absl.patch
index ade3bd0..07aec66 100644
--- a/gtirb/0001-gtirb-link-absl.patch
+++ b/gtirb/0001-gtirb-link-absl.patch
@@ -1,26 +1,31 @@
 diff --git a/CMakeLists.txt b/CMakeLists.txt
-index e176b6a7..929cd452 100644
+index e176b6a7..1c03fe8f 100644
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
-@@ -432,6 +432,7 @@ if(CL_API)
- else()
-   find_package(Protobuf 3.0.0 REQUIRED)
- endif()
-+find_package( absl REQUIRED )
-
+@@ -427,11 +427,8 @@ endif()
+ # ---------------------------------------------------------------------------
+ # protobuf
+ # ---------------------------------------------------------------------------
+-if(CL_API)
+-  find_package(Protobuf 3.7.0 REQUIRED)
+-else()
+-  find_package(Protobuf 3.0.0 REQUIRED)
+-endif()
++set(protobuf_MODULE_COMPATIBLE TRUE CACHE BOOL "")
++find_package(Protobuf REQUIRED CONFIG)
+ 
  if(Protobuf_VERSION VERSION_LESS 3.2)
    add_definitions(-DPROTOBUF_SET_BYTES_LIMIT)
-diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
-index 85558737..542065cd 100644
---- a/src/CMakeLists.txt
-+++ b/src/CMakeLists.txt
-@@ -140,6 +140,9 @@ target_link_libraries(
-          # Link in this static lib, but don't make it a transitive dependency of
-          # TestGTIRB, etc
-   PRIVATE gtirb_proto
-+         absl::log_internal_message
-+         absl::log_internal_check_op
-+         absl::status
- )
- target_compile_definitions(
-   ${PROJECT_NAME} PRIVATE GTIRB_${PROJECT_NAME}_EXPORTS
+diff --git a/src/gtirb/proto/CMakeLists.txt b/src/gtirb/proto/CMakeLists.txt
+index 74cf20a9..d53a8bd0 100644
+--- a/src/gtirb/proto/CMakeLists.txt
++++ b/src/gtirb/proto/CMakeLists.txt
+@@ -45,7 +45,7 @@ endforeach(PROTO_H)
+ # Add proto library target
+ add_library(gtirb_proto STATIC ${PROTO_CPP_SOURCES} ${PROTO_COPIED_HEADERS})
+ 
+-target_link_libraries(gtirb_proto ${Boost_LIBRARIES} ${Protobuf_LIBRARIES})
++target_link_libraries(gtirb_proto ${Boost_LIBRARIES} protobuf::libprotobuf)
+ 
+ target_compile_definitions(gtirb_proto PRIVATE GTIRB_${PROJECT_NAME}_EXPORTS)
+ 
diff --git a/llvm-translator/alive2-regehr.nix b/llvm-translator/alive2-regehr.nix
index 0247fe4..192f477 100644
--- a/llvm-translator/alive2-regehr.nix
+++ b/llvm-translator/alive2-regehr.nix
@@ -1,4 +1,5 @@
 { alive2
+, stdenv
 , llvmPackages
 , fetchFromGitHub
 }:
@@ -15,5 +16,5 @@
   };
 
   patches = [ ];
-  CXXFLAGS = prev.CXXFLAGS or "" + " -Wno-error=maybe-uninitialized";
+  CXXFLAGS = prev.CXXFLAGS or "" + (if stdenv.isDarwin then "" else " -Wno-error=maybe-uninitialized");
 })
diff --git a/llvm-translator/alive2.nix b/llvm-translator/alive2.nix
index e1df3db..b6e4586 100644
--- a/llvm-translator/alive2.nix
+++ b/llvm-translator/alive2.nix
@@ -12,9 +12,13 @@
 , clang
 , llvmPackages
 , git-am-shim
+, overrideCC
+, llvmPackages_17
 }:
 
-stdenv.mkDerivation {
+let buildStdenv = if stdenv.isDarwin then overrideCC stdenv llvmPackages_17.clang else stdenv; in
+
+buildStdenv.mkDerivation {
   pname = "alive2";
   version = "2022-10-26";
 
diff --git a/llvm-translator/llvm-custom.nix b/llvm-translator/llvm-custom.nix
index 894edf1..6511355 100644
--- a/llvm-translator/llvm-custom.nix
+++ b/llvm-translator/llvm-custom.nix
@@ -16,7 +16,7 @@ let
 
       # install Target .inc files from build directory for lifter project.
       postFixup = ''
-        cd /build/$sourceRoot/build/lib && file Target
+        cd $NIX_BUILD_TOP/$sourceRoot/build/lib && file Target
         find Target -name '*.inc' -print0 \
           | xargs -0 -I{} cp -v --no-clobber --parents {} $dev/include
       '';
diff --git a/overlay.nix b/overlay.nix
index 394f05e..0b53156 100644
--- a/overlay.nix
+++ b/overlay.nix
@@ -13,8 +13,28 @@ let
 
       # llvm-translator packages 
       overlay_ocamlPackages = ofinal: oprev: {
-        ocaml-llvm-14 = ofinal.callPackage ./llvm-translator/ocaml-llvm.nix { libllvm = final.llvmPackages_14.libllvm; };
-        asl-translator = ofinal.callPackage ./llvm-translator/asl-translator.nix { llvm = ofinal.ocaml-llvm-14; };
+        # ctypes and ctypes-foreign v0.22.0 do not build on macOS
+        ctypes = oprev.ctypes.overrideAttrs (old: {
+          version = "0.23.0";
+          src = prev.fetchFromGitHub {
+            owner = "ocamllabs";
+            repo = "ocaml-ctypes";
+            rev = "0.23.0";
+            hash = "sha256-fZfTsOMppHiI7BVvgICVt/9ofGFAfYjXzHSDA7L4vZk=";
+          };
+        });
+        ctypes-foreign = oprev.ctypes-foreign.override (old: {
+          ctypes = ofinal.ctypes;
+        });
+
+        ocaml-llvm-14 = ofinal.callPackage ./llvm-translator/ocaml-llvm.nix { 
+          libllvm = final.llvmPackages_14.libllvm; 
+          ctypes = ofinal.ctypes; 
+          ctypes-foreign = ofinal.ctypes-foreign ; 
+        };
+        asl-translator = ofinal.callPackage ./llvm-translator/asl-translator.nix { 
+          llvm = ofinal.ocaml-llvm-14; 
+        };
       };
       inherit (final.ocamlPackages_pac) asl-translator;
 

From 560af8a4b0689c0e80ac2b0bb9f3b24bc2f0a958 Mon Sep 17 00:00:00 2001
From: Nicholas Coughlin <n.coughlin@uq.edu.au>
Date: Tue, 8 Oct 2024 21:08:40 +1000
Subject: [PATCH 11/30] Simpler Z3 linking fix

Add additional search path to BAP wrapper
---
 aslp/ocaml_z3.nix | 41 -----------------------------------------
 aslp/overlay.nix  |  4 +---
 bap/bap.nix       | 11 +++++++++++
 bap/overlay.nix   |  3 ++-
 4 files changed, 14 insertions(+), 45 deletions(-)
 delete mode 100644 aslp/ocaml_z3.nix
 create mode 100644 bap/bap.nix

diff --git a/aslp/ocaml_z3.nix b/aslp/ocaml_z3.nix
deleted file mode 100644
index 28bd8a8..0000000
--- a/aslp/ocaml_z3.nix
+++ /dev/null
@@ -1,41 +0,0 @@
-{ stdenv, lib, ocaml, findlib, zarith, z3 }:
-
-if lib.versionOlder ocaml.version "4.07"
-then throw "z3 is not available for OCaml ${ocaml.version}"
-else
-
-let z3-with-ocaml1 = z3.override {
-  ocamlBindings = true;
-  inherit ocaml findlib zarith;
-}; in
-
-let z3-with-ocaml = z3-with-ocaml1.overrideAttrs (p: {
-  postInstall = p.postInstall + ''
-    ln -sf $lib/lib/libz3${stdenv.hostPlatform.extensions.sharedLibrary} $OCAMLFIND_DESTDIR/stublibs/libz3${stdenv.hostPlatform.extensions.sharedLibrary} 
-  '';
-}); in
-
-stdenv.mkDerivation {
-
-  pname = "ocaml${ocaml.version}-z3";
-  inherit (z3-with-ocaml) version;
-
-  dontUnpack = true;
-
-  installPhase = ''
-    runHook preInstall
-    mkdir -p $OCAMLFIND_DESTDIR
-    cp -r ${z3-with-ocaml.ocaml}/lib/ocaml/${ocaml.version}/site-lib/stublibs $OCAMLFIND_DESTDIR
-    cp -r ${z3-with-ocaml.ocaml}/lib/ocaml/${ocaml.version}/site-lib/Z3 $OCAMLFIND_DESTDIR/z3
-    runHook postInstall
-  '';
-
-  nativeBuildInputs = [ findlib ];
-  propagatedBuildInputs = [ zarith ];
-
-  strictDeps = true;
-
-  meta = z3.meta // {
-    description = "Z3 Theorem Prover (OCaml API)";
-  };
-}
diff --git a/aslp/overlay.nix b/aslp/overlay.nix
index 3a54bc9..f611151 100644
--- a/aslp/overlay.nix
+++ b/aslp/overlay.nix
@@ -7,9 +7,7 @@ final: prev:
   inherit (final.ocamlPackages_pac_5) aslp_web;
 
   overlay_ocamlPackages = ofinal: oprev: {
-    ocaml_z3 = final.callPackage ./ocaml_z3.nix { findlib = ofinal.findlib ; zarith = ofinal.zarith ; ocaml = ofinal.ocaml ; };
-
-    asli = ofinal.callPackage ./asli.nix { inherit (final) z3; ocaml_z3 = ofinal.ocaml_z3; };
+    asli = ofinal.callPackage ./asli.nix { inherit (final) z3; ocaml_z3 = ofinal.z3; };
     aslp = ofinal.asli;
     # .overrideAttrs { src = prev.lib.cleanSource ~/progs/aslp; }
 
diff --git a/bap/bap.nix b/bap/bap.nix
new file mode 100644
index 0000000..4889bf4
--- /dev/null
+++ b/bap/bap.nix
@@ -0,0 +1,11 @@
+{ stdenv, makeBinaryWrapper, symlinkJoin, orig-bap, z3 }:
+
+symlinkJoin {
+  inherit (orig-bap) version;
+  name = "bap-wrapped";
+  paths = [ orig-bap ];
+  nativeBuildInputs = [ makeBinaryWrapper ];
+  postBuild = ''
+    wrapProgram $out/bin/bap --prefix DYLD_FALLBACK_LIBRARY_PATH : ${z3.lib}/lib
+  '';
+}
diff --git a/bap/overlay.nix b/bap/overlay.nix
index dc527b7..cc554d8 100644
--- a/bap/overlay.nix
+++ b/bap/overlay.nix
@@ -1,7 +1,8 @@
 final: prev:
 {
   overlay_ocamlPackages = ofinal: oprev: {
-    bap = oprev.bap.overrideAttrs (p: {
+    bapWrapper = ofinal.callPackage ./bap.nix { orig-bap = oprev.bap ; z3 = prev.z3 ; };
+    bap = ofinal.bapWrapper.overrideAttrs (p: {
       # configurePhase = ''
       # runHook preConfigure
       # echo old "$configureFlags"

From e0c940348f2a7eec6408e6da54d886468075f2b4 Mon Sep 17 00:00:00 2001
From: Nicholas Coughlin <n.coughlin@uq.edu.au>
Date: Wed, 9 Oct 2024 07:46:06 +1000
Subject: [PATCH 12/30] Disable ddisasm-deterministic test on darwin

---
 gtirb/ddisasm.nix | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/gtirb/ddisasm.nix b/gtirb/ddisasm.nix
index 3173860..fccdeea 100644
--- a/gtirb/ddisasm.nix
+++ b/gtirb/ddisasm.nix
@@ -53,6 +53,7 @@ stdenv.mkDerivation {
     version = "Disassemble";
   };
 
+  # Deterministic fix does not work on Darwin, just test to see if ddisasm even runs
   passthru.tests.ddisasm-deterministic = runCommand
     "ddisasm-deterministic-test"
     { nativeBuildInputs = [ ddisasm.deterministic jq clang-aarch64 ]; }
@@ -62,8 +63,9 @@ stdenv.mkDerivation {
       aarch64-unknown-linux-gnu-cc a.c
       ddisasm-deterministic a.out --json | jq -S > a1
       ddisasm-deterministic a.out --json | jq -S > a2
+    '' + ( if stdenv.isDarwin then "" else ''
       diff -q a1 a2
-    '';
+    '' );
 
   meta = {
     mainProgram = "ddisasm";

From 03d38f5de2e847e958c93660f9075ff996af61a0 Mon Sep 17 00:00:00 2001
From: rina <k@rina.fyi>
Date: Thu, 10 Oct 2024 00:03:46 +1000
Subject: [PATCH 13/30] remove planter from ci & use lib.optional

---
 .github/workflows/main.yml        | 1 -
 llvm-translator/alive2-regehr.nix | 6 ++++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 20d545a..354e7bf 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -34,7 +34,6 @@ jobs:
           retdec-uq-pac, asl-translator,
           gtirb-semantics, ddisasm, 
           retdec5, remill, alive2-aslp, alive2-regehr,
-          planter,
           aslp_web, godbolt
         ]
     runs-on: ${{ matrix.os }}
diff --git a/llvm-translator/alive2-regehr.nix b/llvm-translator/alive2-regehr.nix
index 192f477..379e317 100644
--- a/llvm-translator/alive2-regehr.nix
+++ b/llvm-translator/alive2-regehr.nix
@@ -1,4 +1,5 @@
-{ alive2
+{ lib
+, alive2
 , stdenv
 , llvmPackages
 , fetchFromGitHub
@@ -16,5 +17,6 @@
   };
 
   patches = [ ];
-  CXXFLAGS = prev.CXXFLAGS or "" + (if stdenv.isDarwin then "" else " -Wno-error=maybe-uninitialized");
+  CXXFLAGS = (prev.CXXFLAGS or "")
+    + lib.optionalString (!stdenv.isDarwin) " -Wno-error=maybe-uninitialized");
 })

From 45cc5aa89f2a9566374dfcdac0ce82cc1933e8ee Mon Sep 17 00:00:00 2001
From: rina <k@rina.fyi>
Date: Thu, 10 Oct 2024 00:03:46 +1000
Subject: [PATCH 14/30] oops

---
 llvm-translator/alive2-regehr.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/llvm-translator/alive2-regehr.nix b/llvm-translator/alive2-regehr.nix
index 379e317..a5c0acd 100644
--- a/llvm-translator/alive2-regehr.nix
+++ b/llvm-translator/alive2-regehr.nix
@@ -18,5 +18,5 @@
 
   patches = [ ];
   CXXFLAGS = (prev.CXXFLAGS or "")
-    + lib.optionalString (!stdenv.isDarwin) " -Wno-error=maybe-uninitialized");
+    + lib.optionalString (!stdenv.isDarwin) " -Wno-error=maybe-uninitialized";
 })

From c2db3ee34cef1754ee3d41c6b5d16893ac68e157 Mon Sep 17 00:00:00 2001
From: Kait Lam <39479354+katrinafyi@users.noreply.github.com>
Date: Wed, 30 Oct 2024 15:50:44 +1000
Subject: [PATCH 15/30] ddisasm: use null in ternary to avoid rebuild

---
 gtirb/ddisasm.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gtirb/ddisasm.nix b/gtirb/ddisasm.nix
index fccdeea..4f59048 100644
--- a/gtirb/ddisasm.nix
+++ b/gtirb/ddisasm.nix
@@ -28,7 +28,7 @@ stdenv.mkDerivation {
     rev = "9edfe9fe86910ef946de1db7a7ac41ce86bc31d0";
     hash = "sha256-xFW6J3jCCMtUqT25/zVfjjy5o3MoX1HXxIlRhjM6s8A=";
   };
-  patches = if stdenv.isDarwin then [ ./0001-ddisasm-disable-concurrent-souffle.patch ] else [];
+  patches = if stdenv.isDarwin then [ ./0001-ddisasm-disable-concurrent-souffle.patch ] else null;
 
   buildInputs = [ cmake boost lief gtirb gtirb-pprinter libehp ];
   nativeBuildInputs = [ capstone-grammatech souffle ];

From 518cac620f7a7a8d90715c8d6c37af7abd9bcf4e Mon Sep 17 00:00:00 2001
From: Kait Lam <39479354+katrinafyi@users.noreply.github.com>
Date: Wed, 30 Oct 2024 17:22:17 +1000
Subject: [PATCH 16/30] try clang17Stdenv

---
 aslp/aslp-cpp.nix | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/aslp/aslp-cpp.nix b/aslp/aslp-cpp.nix
index 461491f..f667360 100644
--- a/aslp/aslp-cpp.nix
+++ b/aslp/aslp-cpp.nix
@@ -1,13 +1,12 @@
 { stdenv
+, clang17Stdenv
 , cmake
 , asli
-, overrideCC
-, llvmPackages_17
 }:
 
-let buildStdenv = if stdenv.isDarwin then overrideCC stdenv llvmPackages_17.clang else stdenv; in
+let stdenv' = if stdenv.isDarwin then clang17Stdenv else stdenv;
 
-buildStdenv.mkDerivation {
+in stdenv'.mkDerivation {
   pname = "aslp-cpp";
   version = asli.version;
 

From bcbde0ecce65e03e0f82283296da232093ea1bab Mon Sep 17 00:00:00 2001
From: rina <k@rina.fyi>
Date: Thu, 31 Oct 2024 12:11:41 +1000
Subject: [PATCH 17/30] ddisasm: use pre-built binary in test

---
 gtirb/ddisasm.nix | 32 ++++++++++++++++++++------------
 gtirb/gtirb.nix   |  2 +-
 2 files changed, 21 insertions(+), 13 deletions(-)

diff --git a/gtirb/ddisasm.nix b/gtirb/ddisasm.nix
index 4f59048..80413c1 100644
--- a/gtirb/ddisasm.nix
+++ b/gtirb/ddisasm.nix
@@ -1,6 +1,7 @@
 { lib
 , stdenv
 , fetchFromGitHub
+, fetchzip
 , cmake
 , boost
 , lief
@@ -54,18 +55,25 @@ stdenv.mkDerivation {
   };
 
   # Deterministic fix does not work on Darwin, just test to see if ddisasm even runs
-  passthru.tests.ddisasm-deterministic = runCommand
-    "ddisasm-deterministic-test"
-    { nativeBuildInputs = [ ddisasm.deterministic jq clang-aarch64 ]; }
-    ''
-      mkdir -p $out && cd $out
-      echo 'int main(void) { return 0; }' > a.c
-      aarch64-unknown-linux-gnu-cc a.c
-      ddisasm-deterministic a.out --json | jq -S > a1
-      ddisasm-deterministic a.out --json | jq -S > a2
-    '' + ( if stdenv.isDarwin then "" else ''
-      diff -q a1 a2
-    '' );
+  passthru.tests.ddisasm-deterministic =
+    let
+      test-files = fetchzip {
+        url = "https://gist.github.com/katrinafyi/8bcc7a6756b6f467a658e292181cdf8b/archive/453c9b2c5ebdca4d30816e26805b121a919dd150.tar.gz";
+        hash = "sha256-xewqpzAR+rfAMM9Hn97gwzTrhpHONjltbIjhd15PaPw=";
+      };
+    in runCommand
+      "ddisasm-deterministic-test"
+      { nativeBuildInputs = [ ddisasm.deterministic jq ]; }
+      (
+      ''
+        cp -v ${test-files}/a.out .
+        ddisasm-deterministic a.out --json | jq -S > a1
+        ddisasm-deterministic a.out --json | jq -S > a2
+        (diff -u a1 a2 || true) | tee $out
+      '' + lib.optionalString (!stdenv.isDarwin) ''
+        diff -q a1 a2
+      ''
+      );
 
   meta = {
     mainProgram = "ddisasm";
diff --git a/gtirb/gtirb.nix b/gtirb/gtirb.nix
index 4349d37..4becb60 100644
--- a/gtirb/gtirb.nix
+++ b/gtirb/gtirb.nix
@@ -18,7 +18,7 @@ stdenv.mkDerivation {
     rev = "v2.0.0";
     hash = "sha256-ueoqxm6iXv4JgzR/xkImT+O8xx+7bA2upx1TJ828LLA=";
   };
-  patches = if stdenv.isDarwin then [ ./0001-gtirb-link-absl.patch ] else [];
+  patches = if stdenv.isDarwin then [ ./0001-gtirb-link-absl.patch ] else null;
 
   nativeBuildInputs = [ ];
   buildInputs = [ cmake python3 boost doxygen ];

From 31e0759ea25f9319c99c2da951a58ec25a029694 Mon Sep 17 00:00:00 2001
From: rina <k@rina.fyi>
Date: Thu, 31 Oct 2024 16:35:25 +1000
Subject: [PATCH 18/30] touch bap.nix

---
 bap/bap.nix | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/bap/bap.nix b/bap/bap.nix
index 4889bf4..6589fc0 100644
--- a/bap/bap.nix
+++ b/bap/bap.nix
@@ -1,8 +1,10 @@
-{ stdenv, makeBinaryWrapper, symlinkJoin, orig-bap, z3 }:
+{ makeBinaryWrapper, symlinkJoin, orig-bap, z3 }:
+
+# XXX: fix in ocamlPackages.bap of upstream nixpkgs
 
 symlinkJoin {
-  inherit (orig-bap) version;
   name = "bap-wrapped";
+  inherit (orig-bap) version;
   paths = [ orig-bap ];
   nativeBuildInputs = [ makeBinaryWrapper ];
   postBuild = ''

From 24e91ebde8e1641df265cd71c57ae8439a14f0c8 Mon Sep 17 00:00:00 2001
From: rina <k@rina.fyi>
Date: Thu, 31 Oct 2024 17:45:07 +1000
Subject: [PATCH 19/30] llvm-custom: avoid NIX_BUILD_TOP

---
 llvm-translator/llvm-custom.nix | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/llvm-translator/llvm-custom.nix b/llvm-translator/llvm-custom.nix
index 6511355..aa716ff 100644
--- a/llvm-translator/llvm-custom.nix
+++ b/llvm-translator/llvm-custom.nix
@@ -15,10 +15,14 @@ let
       doCheck = false;
 
       # install Target .inc files from build directory for lifter project.
-      postFixup = ''
-        cd $NIX_BUILD_TOP/$sourceRoot/build/lib && file Target
+      # at this point, we should within the build artifact directory
+      postBuild = ''
+        mkdir -p $dev/include
+        pushd ./lib
+        file Target
         find Target -name '*.inc' -print0 \
           | xargs -0 -I{} cp -v --no-clobber --parents {} $dev/include
+        popd
       '';
     });
 

From e32b4a07d12fa0cf39f3c82b1ea4a197601fcf6c Mon Sep 17 00:00:00 2001
From: rina <k@rina.fyi>
Date: Fri, 1 Nov 2024 15:57:32 +1000
Subject: [PATCH 20/30] flake.lock: Update
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Flake lock file updates:

• Updated input 'nixpkgs':
    'github:nixos/nixpkgs/18536bf04cd71abd345f9579158841376fdd0c5a' (2024-10-25)
  → 'github:nixos/nixpkgs/e24d868aba3d21acacdcc319066ce8c4eb692605' (2024-10-31)
---
 flake.lock | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/flake.lock b/flake.lock
index 16d5981..60f8c1e 100644
--- a/flake.lock
+++ b/flake.lock
@@ -2,11 +2,11 @@
   "nodes": {
     "nixpkgs": {
       "locked": {
-        "lastModified": 1729880355,
-        "narHash": "sha256-RP+OQ6koQQLX5nw0NmcDrzvGL8HDLnyXt/jHhL1jwjM=",
+        "lastModified": 1730368100,
+        "narHash": "sha256-iRzj+H57Rd02pEhgipLLdsFRbvaSSCMuoachwmtZB2o=",
         "owner": "nixos",
         "repo": "nixpkgs",
-        "rev": "18536bf04cd71abd345f9579158841376fdd0c5a",
+        "rev": "e24d868aba3d21acacdcc319066ce8c4eb692605",
         "type": "github"
       },
       "original": {

From 8f0378dfa8d7978558ee4fe1d7e7c63ed37f2c47 Mon Sep 17 00:00:00 2001
From: rina <k@rina.fyi>
Date: Thu, 28 Nov 2024 10:47:00 +1000
Subject: [PATCH 21/30] ddisasm: use pre-built aarch64 elf binaries for testing

[skip ci] for now.
---
 gtirb/ddisasm.nix | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/gtirb/ddisasm.nix b/gtirb/ddisasm.nix
index 7723edd..ed26c9c 100644
--- a/gtirb/ddisasm.nix
+++ b/gtirb/ddisasm.nix
@@ -12,12 +12,17 @@
 , capstone-grammatech
 , souffle
 , ddisasm
-, runCommandCC
+, runCommand
 , testers
 , jq
 }:
 
-stdenv.mkDerivation {
+let
+  elf-test-files = fetchzip {
+    url = "https://gist.github.com/katrinafyi/8bcc7a6756b6f467a658e292181cdf8b/archive/453c9b2c5ebdca4d30816e26805b121a919dd150.tar.gz";
+    hash = "sha256-xewqpzAR+rfAMM9Hn97gwzTrhpHONjltbIjhd15PaPw=";
+  };
+in stdenv.mkDerivation {
   pname = "ddisasm";
   version = "0-unstable-2024-10-31";
 
@@ -50,17 +55,12 @@ stdenv.mkDerivation {
     version = "Disassemble";
   };
 
-  # test-files = fetchzip {
-  #   url = "https://gist.github.com/katrinafyi/8bcc7a6756b6f467a658e292181cdf8b/archive/453c9b2c5ebdca4d30816e26805b121a919dd150.tar.gz";
-  #   hash = "sha256-xewqpzAR+rfAMM9Hn97gwzTrhpHONjltbIjhd15PaPw=";
-  # };
-  passthru.tests.ddisasm-deterministic = runCommandCC
+  passthru.tests.ddisasm-deterministic = runCommand
     "ddisasm-deterministic-test"
     { nativeBuildInputs = [ ddisasm.deterministic jq ]; }
     ''
       mkdir -p $out && cd $out
-      echo 'int main(void) { return 0; }' > a.c
-      $CC a.c
+      cp -v ${elf-test-files}/a.out .
       ddisasm a.out --json | jq -S > a1
       ddisasm a.out --json | jq -S > a2
       diff -u a1 a2

From 92957348fa1f0b1f6f5a37b05007fd7a729579de Mon Sep 17 00:00:00 2001
From: rina <k@rina.fyi>
Date: Fri, 29 Nov 2024 20:27:54 +1000
Subject: [PATCH 22/30] mirage-crypto-rng: disable tests ;-;

until they fix aarch64 things
---
 aslp/overlay.nix | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/aslp/overlay.nix b/aslp/overlay.nix
index f611151..01a7d11 100644
--- a/aslp/overlay.nix
+++ b/aslp/overlay.nix
@@ -46,6 +46,8 @@ final: prev:
       }
       oprev.ocaml_pcre;
 
+
+    mirage-crypto-rng = oprev.mirage-crypto-rng.overrideAttrs { doCheck = false; };
   };
 }
 

From c1682bfc9684e1ed5cce914654a9f057c6ac17ac Mon Sep 17 00:00:00 2001
From: rina <k@rina.fyi>
Date: Fri, 29 Nov 2024 20:28:29 +1000
Subject: [PATCH 23/30] flake.lock: Update
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Flake lock file updates:

• Updated input 'nixpkgs':
    'github:nixos/nixpkgs/e24d868aba3d21acacdcc319066ce8c4eb692605' (2024-10-31)
  → 'github:nixos/nixpkgs/4633a7c72337ea8fd23a4f2ba3972865e3ec685d' (2024-11-25)
---
 flake.lock | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/flake.lock b/flake.lock
index 60f8c1e..9a06f64 100644
--- a/flake.lock
+++ b/flake.lock
@@ -2,11 +2,11 @@
   "nodes": {
     "nixpkgs": {
       "locked": {
-        "lastModified": 1730368100,
-        "narHash": "sha256-iRzj+H57Rd02pEhgipLLdsFRbvaSSCMuoachwmtZB2o=",
+        "lastModified": 1732521221,
+        "narHash": "sha256-2ThgXBUXAE1oFsVATK1ZX9IjPcS4nKFOAjhPNKuiMn0=",
         "owner": "nixos",
         "repo": "nixpkgs",
-        "rev": "e24d868aba3d21acacdcc319066ce8c4eb692605",
+        "rev": "4633a7c72337ea8fd23a4f2ba3972865e3ec685d",
         "type": "github"
       },
       "original": {

From 0e21f14af2331647d2323a0221ca9fc595608f37 Mon Sep 17 00:00:00 2001
From: rina <k@rina.fyi>
Date: Fri, 29 Nov 2024 22:38:34 +1000
Subject: [PATCH 24/30] retdec5: copy derivation from new pr and fix yaramod
 version

https://www.github.com/NixOS/nixpkgs/pull/293962
---
 llvm-translator/retdec5.nix | 217 ++++++++++++++++++++++++++----------
 1 file changed, 156 insertions(+), 61 deletions(-)

diff --git a/llvm-translator/retdec5.nix b/llvm-translator/retdec5.nix
index 70972fa..7e736d2 100644
--- a/llvm-translator/retdec5.nix
+++ b/llvm-translator/retdec5.nix
@@ -1,9 +1,12 @@
 { stdenv
 , fetchFromGitHub
+, fetchpatch
 , fetchzip
+, writeText
 , lib
 , openssl
 , cmake
+, ninja
 , autoconf
 , automake
 , libtool
@@ -14,11 +17,16 @@
 , perl
 , python3
 , ncurses
+, time
+, upx
 , gtest
 , libffi
 , libxml2
 , zlib
+, buildEnv
 , enableTests ? true
+, buildDevTools ? true
+, compileYaraPatterns ? false
 }:
 
 let
@@ -28,25 +36,36 @@ let
     owner = "capstone-engine";
     repo = "capstone";
     rev = "5.0-rc2";
-    sha256 = "sha256-nB7FcgisBa8rRDS3k31BbkYB+tdqA6Qyj9hqCnFW+ME=";
+    hash = "sha256-nB7FcgisBa8rRDS3k31BbkYB+tdqA6Qyj9hqCnFW+ME=";
   };
   llvm = fetchFromGitHub {
     owner = "avast-tl";
     repo = "llvm";
     rev = "2a1f3d8a97241c6e91710be8f84cf3cf80c03390";
-    sha256 = "sha256-+v1T0VI9R92ed9ViqsfYZMJtPCjPHCr4FenoYdLuFOU=";
+    hash = "sha256-+v1T0VI9R92ed9ViqsfYZMJtPCjPHCr4FenoYdLuFOU=";
   };
   yaracpp = fetchFromGitHub {
     owner = "VirusTotal";
     repo = "yara";
     rev = "v4.2.0-rc1";
-    sha256 = "sha256-WcN6ClYO2d+/MdG06RHx3kN0o0WVAY876dJiG7CwJ8w=";
+    hash = "sha256-WcN6ClYO2d+/MdG06RHx3kN0o0WVAY876dJiG7CwJ8w=";
   };
   yaramod = fetchFromGitHub {
     owner = "avast";
     repo = "yaramod";
-    rev = "a367d910ae79698e64e99d8414695281723cd34b";
-    sha256 = "sha256-mnjYQOn/Z37XAtW8YsfPewM9t1WYsyjivTnmRwYWSQ0=";
+    rev = "aa06dd408c492a8f4488774caf2ee105ccc23ab5";
+    hash = "sha256-wiD4A+6Jsd7bzGo8mmWnkb7l2XcjEgLCK/A4iW9Zt/A=";
+
+    # yaramod builds yet more dependencies. these need to be installed to "lib"
+    postFetch = ''
+      (
+      cd $out
+      shopt -s globstar
+      substituteInPlace src/CMakeLists.txt deps/**/CMakeLists.txt \
+        --replace-quiet CMAKE_ARGS 'CMAKE_ARGS -DCMAKE_INSTALL_LIBDIR=lib' \
+        --replace-quiet '$'{CMAKE_INSTALL_LIBDIR} lib
+      )
+    '';
   };
   keystone = fetchFromGitHub {
     # only for tests
@@ -55,14 +74,14 @@ let
     rev = "d7ba8e378e5284e6384fc9ecd660ed5f6532e922";
     sha256 = "1yzw3v8xvxh1rysh97y0i8y9svzbglx2zbsqjhrfx18vngh0x58f";
   };
-  # googletest imported from nixpkgs
 
   retdec-support-version = "2019-03-08";
   retdec-support =
     { rev = retdec-support-version; } // # for checking the version against the expected version
     fetchzip {
       url = "https://github.com/avast-tl/retdec-support/releases/download/${retdec-support-version}/retdec-support_${retdec-support-version}.tar.xz";
-      hash = "sha256-paeNrxXTE7swuKjP+sN42xnCYS7x5Y5CcUe7tyzsLxs=";
+      hash = "sha256-t1tx4MfLW/lwtbO5JQ1nrFBIOeMclq+0dENuXW+ahIM=";
+      stripRoot = false;
     };
 
   check-dep = name: dep:
@@ -82,20 +101,41 @@ let
     CAPSTONE = capstone;
     LLVM = llvm;
     YARA = yaracpp;
-    YARAMOD = yaramod;
+    YARAMOD = yaramod // { rev = ""; };
     SUPPORT_PKG = retdec-support;
   } // lib.optionalAttrs enableTests {
     KEYSTONE = keystone;
+    GOOGLETEST = gtest.src // { rev = ""; };  # empty rev bypasses dep version checking
   };
+
+  # overwrite install-share.py to copy instead of download.
+  # we use this so the copy happens at the right time in the build,
+  # otherwise, the build process cleans the directory.
+  install-share =
+    writeText
+      "install-share.py"
+      ''
+        import os, sys, shutil, subprocess
+
+        install_path, arch_url, sha256hash_ref, version = sys.argv[1:]
+        support_dir = os.path.join(install_path, 'share', 'retdec', 'support')
+
+        assert os.path.isdir(arch_url), "nix install-share.py expects a path for support url"
+
+        os.makedirs(support_dir, exist_ok=True)
+        shutil.copytree(arch_url, support_dir, dirs_exist_ok=True)
+        subprocess.check_call(['chmod', '-R', 'u+w', support_dir])
+      '';
 in
 stdenv.mkDerivation (self: {
   pname = "retdec";
 
-  # If you update this you will also need to adjust the versions of the updated dependencies. You can do this by first just updating retdec
-  # itself and trying to build it. The build should fail and tell you which dependencies you have to upgrade to which versions.
+  # If you update this you will also need to adjust the versions of the updated dependencies.
   # I've notified upstream about this problem here:
   # https://github.com/avast-tl/retdec/issues/412
-  # gcc is pinned to gcc8 in all-packages.nix. That should probably be re-evaluated on update.
+  #
+  # The dependencies and their sources are listed in this file:
+  # https://github.com/avast/retdec/blob/master/cmake/deps.cmake
   version = "5.0";
 
   src = fetchFromGitHub {
@@ -105,8 +145,22 @@ stdenv.mkDerivation (self: {
     sha256 = "sha256-H4e+aSgdBBbG6X6DzHGiDEIASPwBVNVsfHyeBTQLAKI=";
   };
 
+  patches = [
+    # gcc 13 compatibility: https://github.com/avast/retdec/pull/1153
+    (fetchpatch {
+      url = "https://github.com/avast/retdec/commit/dbaab2c3d17b1eae22c581e8ab6bfefadf4ef6ae.patch";
+      hash = "sha256-YqHYPGAGWT4x6C+CpsOSsOIZ+NPM2FBQtGQFs74OUIQ=";
+    })
+    # aarch64 compatibility: https://github.com/avast/retdec/pull/1195
+    (fetchpatch {
+      url = "https://github.com/avast/retdec/commit/93233e79a0b14e6aeeee6b117a1c93feba88577b.patch";
+      hash = "sha256-0VT7J9mcrneUo80BSi+unqCGdNNp4HaRx615M6hm0n8=";
+    })
+  ];
+
   nativeBuildInputs = [
     cmake
+    ninja
     autoconf
     automake
     libtool
@@ -127,70 +181,111 @@ stdenv.mkDerivation (self: {
   ] ++ lib.optional self.doInstallCheck gtest;
 
   cmakeFlags = [
-    "-DRETDEC_TESTS=${if self.doInstallCheck then "ON" else "OFF"}" # build tests
-  ] ++ lib.mapAttrsToList (k: v: "-D${k}_URL=${v}") deps;
-
-  patches = [ ];
-
-  # fix for a gcc13 change.
-  env.CXXFLAGS = "-include cstdint";
+    (lib.cmakeBool "RETDEC_TESTS" self.doInstallCheck) # build tests
+    (lib.cmakeBool "RETDEC_DEV_TOOLS" buildDevTools) # build tools e.g. capstone2llvmir, retdectool
+    (lib.cmakeBool "RETDEC_COMPILE_YARA" compileYaraPatterns) # build and install compiled patterns
+  ] ++ lib.mapAttrsToList (k: v: lib.cmakeFeature "${k}_URL" "${v}") deps;
 
   preConfigure =
-    lib.concatStringsSep "\n" (lib.mapAttrsToList check-dep deps)
+    lib.concatLines (lib.mapAttrsToList check-dep deps)
     +
     ''
-            mkdir -p "$out/share/retdec"
-            cp --no-preserve=mode -r ${retdec-support} "$out/share/retdec/support" # write permission needed during install
-
-            # the CMakeLists assume CMAKE_INSTALL_BINDIR, etc are path components but in Nix, they are absolute.
-            # therefore, we need to remove the unnecessary CMAKE_INSTALL_PREFIX prepend.
-            substituteInPlace ./CMakeLists.txt \
-              --replace "''$"{CMAKE_INSTALL_PREFIX}/"''$"{RETDEC_INSTALL_BIN_DIR} "''$"{CMAKE_INSTALL_FULL_BINDIR} \
-              --replace "''$"{CMAKE_INSTALL_PREFIX}/"''$"{RETDEC_INSTALL_LIB_DIR} "''$"{CMAKE_INSTALL_FULL_LIBDIR} \
-              --replace "''$"{CMAKE_INSTALL_PREFIX}/"''$"{RETDEC_INSTALL_SUPPORT_DIR} "''$"{RETDEC_INSTALL_SUPPORT_DIR} \
-
-            # similarly for yaramod. here, we fix the LIBDIR to lib64. for whatever reason, only "lib64" works.
-            substituteInPlace deps/yaramod/CMakeLists.txt \
-              --replace "''$"{YARAMOD_INSTALL_DIR}/"''$"{CMAKE_INSTALL_LIBDIR} "''$"{YARAMOD_INSTALL_DIR}/lib64 \
-              --replace CMAKE_ARGS 'CMAKE_ARGS -DCMAKE_INSTALL_LIBDIR=lib64'
-
-            # yara needs write permissions in the generated source directory.
-            echo ${lib.escapeShellArg ''
-              ExternalProject_Add_Step(
-                yara chmod WORKING_DIRECTORY ''${YARA_DIR}
-      	        DEPENDEES download COMMAND chmod -R u+rw .
-              )
-            ''} >> deps/yara/CMakeLists.txt
-
-            # patch gtest to use the system package
-            gtest=deps/googletest/CMakeLists.txt
-            old="$(cat $gtest)"
-            (echo 'find_package(GTest REQUIRED)'; echo "$old") > $gtest
-            sed -i 's/ExternalProject_[^(]\+[(]/ set(IGNORED /g' $gtest
-
-            substituteInPlace $gtest \
-              --replace '$'{GTEST_LIB} "GTest::gtest"\
-              --replace '$'{GMOCK_LIB} "GTest::gmock"\
-              --replace '$'{GTEST_MAIN_LIB} "GTest::gtest_main"\
-              --replace '$'{GMOCK_MAIN_LIB} "GTest::gmock_main"
-
-            # without git history, there's no chance of these tests passing.
-            substituteInPlace tests/utils/version_tests.cpp \
-              --replace VersionTests DISABLED_VersionTests
+      cp -v ${install-share} ./support/install-share.py
+
+      # the CMakeLists assume CMAKE_INSTALL_BINDIR, etc are path components but in Nix, they are absolute.
+      # therefore, we need to remove the unnecessary CMAKE_INSTALL_PREFIX prepend.
+      substituteInPlace ./CMakeLists.txt \
+        --replace-fail "''$"{CMAKE_INSTALL_PREFIX}/"''$"{RETDEC_INSTALL_BIN_DIR} "''$"{CMAKE_INSTALL_FULL_BINDIR} \
+        --replace-fail "''$"{CMAKE_INSTALL_PREFIX}/"''$"{RETDEC_INSTALL_LIB_DIR} "''$"{CMAKE_INSTALL_FULL_LIBDIR} \
+
+      # --replace "''$"{CMAKE_INSTALL_PREFIX}/"''$"{RETDEC_INSTALL_SUPPORT_DIR} "''$"{RETDEC_INSTALL_SUPPORT_DIR}
+      # note! Nix does not set CMAKE_INSTALL_DATADIR to an absolute path, so this replacement would be incorrect
+
+      # similarly for yaramod.
+      substituteInPlace deps/yaramod/CMakeLists.txt \
+        --replace-fail "''$"{YARAMOD_INSTALL_DIR}/"''$"{CMAKE_INSTALL_LIBDIR} "''$"{YARAMOD_INSTALL_DIR}/lib
+
+      # yara needs write permissions in the generated source directory.
+      echo '
+        ExternalProject_Add_Step(
+          yara chmod WORKING_DIRECTORY ''${YARA_DIR}
+          DEPENDEES download COMMAND chmod -R u+w .
+        )
+      ' >> deps/yara/CMakeLists.txt
+
+      # yara: to support building retdec with ninja
+      substituteInPlace deps/yara/CMakeLists.txt \
+        --replace-fail '$'{YARA_CONFIGURE_ARGS} ' ''${YARA_CONFIGURE_ARGS} --disable-dependency-tracking' \
+        --replace-fail '$'{YARA_MAKE_PROGRAM} $(command -v make)
+
+      # all vendored dependencies must build their libs into the "lib" subdirectory.
+      # retdec's install phase will copy these into the correct Nix output.
+      substituteInPlace deps/*/CMakeLists.txt \
+        --replace-quiet CMAKE_ARGS 'CMAKE_ARGS -DCMAKE_INSTALL_LIBDIR=lib'
+
+      substituteInPlace src/utils/CMakeLists.txt \
+        --replace-warn '$'{RETDEC_GIT_VERSION_TAG} ${self.version} \
+        --replace-warn '$'{RETDEC_GIT_COMMIT_HASH} ${self.src.rev}
+
+
+      # tests: without git history, there is no chance these tests will pass.
+      substituteInPlace tests/utils/version_tests.cpp \
+        --replace-warn VersionTests DISABLED_VersionTests
+
+
+      # scripts: patch paths
+      substituteInPlace scripts/retdec-utils.py \
+        --replace-fail /usr/bin/time ${time} \
+        --replace-fail /usr/local/bin/gtime ${time}
+      substituteInPlace scripts/retdec-unpacker.py \
+        --replace-fail "'upx'" "'${upx}'"
     '';
 
   doInstallCheck = enableTests;
   installCheckPhase = ''
-    ${python3.interpreter} "$out/bin/retdec-tests-runner.py"
+    ${python3.interpreter} "''${!outputBin}/bin/retdec-tests-runner.py"
 
     rm -rf $out/bin/__pycache__
   '';
 
+
+  # static-code patterns are split out since they are rarely needed by end users.
+  # from retdec's wiki:
+  #   However, these are mainly for older compilers used for testing purposes.
+  #   If you want to remove code from newer compilers or some custom libraries,
+  #   you have to create your own signature files.
+  # see: https://github.com/avast/retdec/wiki/Removing-Statically-Linked-Code
+  postFixup = ''
+    mkdir -p $dev/lib/retdec
+    mv -v $out/share/retdec/cmake $dev/lib/retdec
+
+    yara_dir=share/retdec/support/generic/yara_patterns
+    mkdir -p $patterns/$yara_dir
+    mv -v $out/$yara_dir/static-code $patterns/$yara_dir
+  '';
+
+  outputs = [ "out" "lib" "dev" "patterns" ];
+
+  passthru.full = buildEnv {
+    name = "${self.pname}-full-${self.version}";
+    inherit (self.finalPackage) meta;
+    paths = [ self.finalPackage.out self.finalPackage.patterns ];
+    postBuild = ''
+      config=$out/share/retdec/decompiler-config.json
+      cp -v --remove-destination $(readlink -f $config) $config
+
+      static_code=support/generic/yara_patterns/static-code/
+      substituteInPlace $config \
+        --replace-fail ./$static_code $out/share/retdec/$static_code
+    '';
+  };
+
+  passthru.deps = deps;
+
   meta = with lib; {
-    description = "A retargetable machine-code decompiler based on LLVM";
+    description = "Retargetable machine-code decompiler based on LLVM";
     homepage = "https://retdec.com";
     license = licenses.mit;
-    maintainers = with maintainers; [ dtzWill timokau ];
-    platforms = [ "x86_64-linux" "i686-linux" ];
+    maintainers = with maintainers; [ katrinafyi ];
   };
 })

From b05e05d8d44ff4428fdcec2e629824ccfe7ae6cb Mon Sep 17 00:00:00 2001
From: rina <k@rina.fyi>
Date: Fri, 29 Nov 2024 23:20:04 +1000
Subject: [PATCH 25/30] remill: mark broken on aarch64-darwin

---
 llvm-translator/remill.nix | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/llvm-translator/remill.nix b/llvm-translator/remill.nix
index e46f9e4..efec31e 100644
--- a/llvm-translator/remill.nix
+++ b/llvm-translator/remill.nix
@@ -64,7 +64,7 @@ stdenv.mkDerivation (self:
   sleigh = sleigh' self;
 
   nativeBuildInputs = [ cmake ];
-  buildInputs = [ self.sleigh llvm xed glog gtest abseil-cpp glibc_multi ];
+  buildInputs = [ self.sleigh llvm glog gtest abseil-cpp xed glibc_multi ];
 
   outputs = [ "out" "dev" "lib" ];
 
@@ -140,4 +140,12 @@ stdenv.mkDerivation (self:
 
   hardeningDisable = [ "zerocallusedregs" ];
 
+  meta = with lib; {
+    description = "Library for lifting machine code to LLVM bitcode";
+    homepage = "https://github.com/lifting-bits/remill";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ katrinafyi ];
+    broken = stdenv.isAarch64; # XXX: problems with xed (fixable) and libcxx (unsolved) 
+  };
+
 })

From e3a3f2a07770a8a2a92a029b0b589153a04d67bf Mon Sep 17 00:00:00 2001
From: rina <k@rina.fyi>
Date: Sat, 30 Nov 2024 00:13:33 +1000
Subject: [PATCH 26/30] alive2-aslp: disable run-arm-tv.pl test

problems on macos and it didnt do much anyway

[skip ci]
---
 llvm-translator/alive2-aslp.nix | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/llvm-translator/alive2-aslp.nix b/llvm-translator/alive2-aslp.nix
index d388f45..78850f8 100644
--- a/llvm-translator/alive2-aslp.nix
+++ b/llvm-translator/alive2-aslp.nix
@@ -62,11 +62,11 @@
     '';
   };
 
-  passthru.tests.run-arm-tv = runCommand "test-run-arm-tv" {} ''
-    rm -rfv logs logs-aslp
-    set +o pipefail
-    ${alive2-aslp.arm-tv-scripts}/bin/run-arm-tv.pl 2>&1 | tee /dev/stderr | grep 'please specify'
-    touch $out
-  '';
+  # passthru.tests.run-arm-tv = runCommand "test-run-arm-tv" {} ''
+  #   rm -rfv logs logs-aslp
+  #   set +o pipefail
+  #   ${alive2-aslp.arm-tv-scripts}/bin/run-arm-tv.pl 2>&1 | tee /dev/stderr | grep 'please specify'
+  #   touch $out
+  # '';
 
 })

From 94863b11afdcc8fb6fba96fc1749a29b3275b948 Mon Sep 17 00:00:00 2001
From: rina <k@rina.fyi>
Date: Sat, 30 Nov 2024 21:43:16 +1000
Subject: [PATCH 27/30] working on more determinism... [skip ci]

---
 gtirb/ddisasm.nix | 7 ++++++-
 gtirb/gtirb.nix   | 7 +++++++
 2 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/gtirb/ddisasm.nix b/gtirb/ddisasm.nix
index ed26c9c..1df8660 100644
--- a/gtirb/ddisasm.nix
+++ b/gtirb/ddisasm.nix
@@ -45,7 +45,12 @@ in stdenv.mkDerivation {
 
   cmakeFlags = [ "-DDDISASM_ENABLE_TESTS=OFF" "-DDDISASM_GENERATE_MANY=ON" ];
 
-  CXXFLAGS = [ "-includeset" ];
+  postPatch = ''
+    (
+    shopt -u globstar
+    substituteInPlace **/*.h --replace-warn unordered_map map --replace-warn unordered_set set
+    )
+  '';
 
   passthru.deterministic = ddisasm;
 
diff --git a/gtirb/gtirb.nix b/gtirb/gtirb.nix
index 4e0722b..8c4855b 100644
--- a/gtirb/gtirb.nix
+++ b/gtirb/gtirb.nix
@@ -27,6 +27,13 @@ stdenv.mkDerivation {
     })
   ] ++ lib.optional stdenv.isDarwin ./0001-gtirb-link-absl.patch;
 
+  postPatch = ''
+    (
+    shopt -u globstar
+    substituteInPlace include/gtirb/{CFG,Module}.hpp --replace-warn unordered_map map --replace-warn unordered_set set
+    )
+  '';
+
   nativeBuildInputs = [ ];
   buildInputs = [ cmake python3 boost doxygen ];
   propagatedBuildInputs = [ protobuf ];

From e1a299e657d1d9a3a0b489d3afbf205fb3a02319 Mon Sep 17 00:00:00 2001
From: rina <k@rina.fyi>
Date: Sun, 1 Dec 2024 20:05:55 +1000
Subject: [PATCH 28/30] more complete determinism

---
 gtirb/ddisasm.nix        | 8 ++++++--
 gtirb/gtirb-pprinter.nix | 8 ++++++++
 2 files changed, 14 insertions(+), 2 deletions(-)

diff --git a/gtirb/ddisasm.nix b/gtirb/ddisasm.nix
index 1df8660..f66e22a 100644
--- a/gtirb/ddisasm.nix
+++ b/gtirb/ddisasm.nix
@@ -47,8 +47,12 @@ in stdenv.mkDerivation {
 
   postPatch = ''
     (
-    shopt -u globstar
-    substituteInPlace **/*.h --replace-warn unordered_map map --replace-warn unordered_set set
+    shopt -s globstar
+    substituteInPlace **/*.cpp **/*.h --replace-warn unordered_map map --replace-warn unordered_set set
+    substituteInPlace src/passes/Disassembler.cpp \
+      --replace-fail \
+      'gtirb::UUID Uuid;' \
+      'gtirb::UUID Uuid{gtirb::Node::UUIDGenerator()};'
     )
   '';
 
diff --git a/gtirb/gtirb-pprinter.nix b/gtirb/gtirb-pprinter.nix
index 789444c..a58744a 100644
--- a/gtirb/gtirb-pprinter.nix
+++ b/gtirb/gtirb-pprinter.nix
@@ -21,8 +21,16 @@ stdenv.mkDerivation {
     rev = "762a287f3d12c6aac3d3d000cdc8bf20f5ee34f2";
     hash = "sha256-9CZ+ndHX5f4rKbGXvCrqEg55Ep9JEkS/u//grdqTpTc=";
   };
+
   patches = [ ./0001-gtirb_pprinter-include-map.patch ];
 
+  postPatch = ''
+    (
+    shopt -s globstar
+    substituteInPlace **/*.cpp **/*.hpp --replace-warn unordered_map map --replace-warn unordered_set set
+    )
+  '';
+
   buildInputs = [ cmake python3 gtirb boost abseil-cpp gtest ];
   nativeBuildInputs = [ capstone-grammatech ];
 

From 2fd8e15db0b4e5f01b5e2041c28b649d04b35df0 Mon Sep 17 00:00:00 2001
From: rina <k@rina.fyi>
Date: Mon, 2 Dec 2024 14:36:38 +1000
Subject: [PATCH 29/30] fix?

sporadic failure
---
 llvm-translator/retdec5.nix | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/llvm-translator/retdec5.nix b/llvm-translator/retdec5.nix
index 7e736d2..63c5ee6 100644
--- a/llvm-translator/retdec5.nix
+++ b/llvm-translator/retdec5.nix
@@ -241,6 +241,11 @@ stdenv.mkDerivation (self: {
         --replace-fail "'upx'" "'${upx}'"
     '';
 
+  # build first to make sure YARA_DIR has u+w permissions?
+  preBuild = ''
+    ninja yara
+  '';
+
   doInstallCheck = enableTests;
   installCheckPhase = ''
     ${python3.interpreter} "''${!outputBin}/bin/retdec-tests-runner.py"

From 8607c9dd47ee85080dfc11f98100ce0cffe332bb Mon Sep 17 00:00:00 2001
From: rina <k@rina.fyi>
Date: Mon, 2 Dec 2024 14:45:35 +1000
Subject: [PATCH 30/30] retdec-uq-pac: append patches

---
 llvm-translator/retdec-uq-pac.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/llvm-translator/retdec-uq-pac.nix b/llvm-translator/retdec-uq-pac.nix
index 47c221d..1b1093f 100644
--- a/llvm-translator/retdec-uq-pac.nix
+++ b/llvm-translator/retdec-uq-pac.nix
@@ -2,7 +2,7 @@
 
 retdec.overrideAttrs (final: prev: {
   cmakeFlags = prev.cmakeFlags ++ [ "-DRETDEC_DEV_TOOLS=1" ];
-  patches = [
+  patches = prev.patches ++ [
     (fetchurl {
       url = "https://gist.githubusercontent.com/katrinafyi/c33f6f9ccaad4420f76f84e6cb219fe0/raw/0001-emit-names-for-capstone-intrinsics.patch";
       hash = "sha256-LJjzLw2R8ckB10jL92RH/kHggX2oQrAZNQUsonM6ciQ=";