Merge remote-tracking branch 'NixOS/master' into staging

24 files changed, 236 insertions, 91 deletions

diff --git a/pkgs/development/tools/ansible-lint/default.nix b/pkgs/development/tools/ansible-lint/default.nix
index 5433725b3050..12eee5f80862 100644
--- a/pkgs/development/tools/ansible-lint/default.nix
+++ b/pkgs/development/tools/ansible-lint/default.nix
@@ -2,13 +2,13 @@
 
 pythonPackages.buildPythonPackage rec {
   pname = "ansible-lint";
-  version = "3.4.23";
+  version = "3.5.1";
 
   src = fetchFromGitHub {
     owner = "willthames";
     repo = "ansible-lint";
     rev = "v${version}";
-    sha256 = "0cnfgxh5m7alzm811hc95jigbca5vc1pf8fjazmsakmhdjyfbpb7";
+    sha256 = "09qixiaqhm6dbl74s1rwxbsg31nr6jjsvr4fxfnxl9ccbxcrpzn2";
   };
 
   propagatedBuildInputs = with pythonPackages; [ pyyaml six ] ++ [ ansible ];
diff --git a/pkgs/development/tools/build-managers/alibuild/default.nix b/pkgs/development/tools/build-managers/alibuild/default.nix
index eb805dcce7a9..68f00be342c3 100644
--- a/pkgs/development/tools/build-managers/alibuild/default.nix
+++ b/pkgs/development/tools/build-managers/alibuild/default.nix
@@ -9,12 +9,9 @@ python.pkgs.buildPythonApplication rec {
     sha256 = "1mnh0h9m96p78b9ln1gbl4lw1mgl16qbyfi9fj2l13p3nxaq1sib";
   };
 
-  argparse = null;
-
   doCheck = false;
   propagatedBuildInputs = [
     python.pkgs.requests
-    python.pkgs.argparse
     python.pkgs.pyyaml
   ];
 
diff --git a/pkgs/development/tools/build-managers/bazel/bash-tools-test.nix b/pkgs/development/tools/build-managers/bazel/bash-tools-test.nix
new file mode 100644
index 000000000000..3bbab475c573
--- /dev/null
+++ b/pkgs/development/tools/build-managers/bazel/bash-tools-test.nix
@@ -0,0 +1,42 @@
+{ stdenv, writeText, runCommandCC, bazel }:
+
+# Tests that certain executables are available in bazel-executed bash shells.
+
+let
+  WORKSPACE = writeText "WORKSPACE" ''
+    workspace(name = "our_workspace")
+  '';
+
+  fileIn = writeText "input.txt" ''
+  one
+  two
+  three
+  '';
+
+  fileBUILD = writeText "BUILD" ''
+    genrule(
+      name = "tool_usage",
+      srcs = [ ":input.txt" ],
+      outs = [ "output.txt" ],
+      cmd = "cat $(location :input.txt) | gzip - | gunzip - | awk '/t/' > $@",
+    )
+  '';
+
+  runLocal = name: script: runCommandCC name { preferLocalBuild = true; } script;
+
+  workspaceDir = runLocal "our_workspace" ''
+    mkdir $out
+    cp ${WORKSPACE} $out/WORKSPACE
+    cp ${fileIn} $out/input.txt
+    cp ${fileBUILD} $out/BUILD
+  '';
+
+  testBazel = runLocal "bazel-test-bash-tools" ''
+    export HOME=$(mktemp -d)
+    cp -r ${workspaceDir} wd && chmod +w wd && cd wd
+    ${bazel}/bin/bazel build :tool_usage
+    cp bazel-genfiles/output.txt $out
+    echo "Testing content" && [ "$(cat $out | wc -l)" == "2" ] && echo "OK"
+  '';
+
+in testBazel
diff --git a/pkgs/development/tools/build-managers/bazel/default.nix b/pkgs/development/tools/build-managers/bazel/default.nix
index b1bb5708d44a..15ef2abd0946 100644
--- a/pkgs/development/tools/build-managers/bazel/default.nix
+++ b/pkgs/development/tools/build-managers/bazel/default.nix
@@ -1,6 +1,6 @@
 { stdenv, callPackage, lib, fetchurl, fetchpatch, runCommand, makeWrapper
 , jdk, zip, unzip, bash, writeCBin, coreutils
-, which, python, perl, gawk, gnused, gnugrep, findutils
+, which, python, perl, gawk, gnused, gnutar, gnugrep, gzip, findutils
 # Apple dependencies
 , cctools, clang, libcxx, CoreFoundation, CoreServices, Foundation
 # Allow to independently override the jdks used to build and run respectively
@@ -23,7 +23,35 @@ let
     for i in ${builtins.toString srcDeps}; do cp $i $out/$(stripHash $i); done
   '';
 
-  defaultShellPath = lib.makeBinPath [ bash coreutils findutils gawk gnugrep gnused which unzip ];
+  defaultShellPath = lib.makeBinPath
+    # Keep this list conservative. For more exotic tools, prefer to use
+    # @rules_nixpkgs to pull in tools from the nix repository. Example:
+    #
+    # WORKSPACE:
+    #
+    #     nixpkgs_git_repository(
+    #         name = "nixpkgs",
+    #         revision = "def5124ec8367efdba95a99523dd06d918cb0ae8",
+    #     )
+    #
+    #     # This defines an external Bazel workspace.
+    #     nixpkgs_package(
+    #         name = "bison",
+    #         repositories = { "nixpkgs": "@nixpkgs//:default.nix" },
+    #     )
+    #
+    # some/BUILD.bazel:
+    #
+    #     genrule(
+    #        ...
+    #        cmd = "$(location @bison//:bin/bison) -other -args",
+    #        tools = [
+    #            ...
+    #            "@bison//:bin/bison",
+    #        ],
+    #     )
+    #
+    [ bash coreutils findutils gawk gnugrep gnutar gnused gzip which unzip ];
 
 in
 stdenv.mkDerivation rec {
@@ -38,9 +66,14 @@ stdenv.mkDerivation rec {
     platforms = platforms.linux ++ platforms.darwin;
   };
 
-  # additional tests that check bazel’s functionality
+  # Additional tests that check bazel’s functionality. Execute
+  #
+  #     nix-build . -A bazel.tests
+  #
+  # in the nixpkgs checkout root to exercise them locally.
   passthru.tests = {
-    python_bin_path = callPackage ./python-bin-path-test.nix {};
+    pythonBinPath = callPackage ./python-bin-path-test.nix {};
+    bashTools = callPackage ./bash-tools-test.nix {};
   };
 
   name = "bazel-${version}";
@@ -125,9 +158,11 @@ stdenv.mkDerivation rec {
 
     genericPatches = ''
       # Substitute python's stub shebang to plain python path. (see TODO add pr URL)
+      # See also `postFixup` where python is added to $out/nix-support
       substituteInPlace src/main/java/com/google/devtools/build/lib/bazel/rules/python/python_stub_template.txt\
           --replace "/usr/bin/env python" "${python}/bin/python" \
           --replace "NIX_STORE_PYTHON_PATH" "${python}/bin/python" \
+
       # substituteInPlace is rather slow, so prefilter the files with grep
       grep -rlZ /bin src/main/java/com/google/devtools | while IFS="" read -r -d "" path; do
         # If you add more replacements here, you must change the grep above!
@@ -262,7 +297,10 @@ stdenv.mkDerivation rec {
   # Save paths to hardcoded dependencies so Nix can detect them.
   postFixup = ''
     mkdir -p $out/nix-support
-    echo "${customBash} ${defaultShellPath}" > $out/nix-support/depends
+    echo "${customBash} ${defaultShellPath}" >> $out/nix-support/depends
+    # The templates get tar’d up into a .jar,
+    # so nix can’t detect python is needed in the runtime closure
+    echo "${python}" >> $out/nix-support/depends
   '';
 
   dontStrip = true;
diff --git a/pkgs/development/tools/build-managers/bazel/python-bin-path-test.nix b/pkgs/development/tools/build-managers/bazel/python-bin-path-test.nix
index 478ba8eaa712..54ae154a6207 100644
--- a/pkgs/development/tools/build-managers/bazel/python-bin-path-test.nix
+++ b/pkgs/development/tools/build-managers/bazel/python-bin-path-test.nix
@@ -42,8 +42,10 @@ let
 
   testBazel = runLocal "bazel-test-builtin-rules" ''
     export HOME=$(mktemp -d)
-    cp -r ${workspaceDir}/* .
-    ${bazel}/bin/bazel --output_base=/tmp/bazel-tests/wd\
+    # Note https://github.com/bazelbuild/bazel/issues/5763#issuecomment-456374609
+    # about why to create a subdir for the workspace.
+    cp -r ${workspaceDir} wd && chmod u+w wd && cd wd
+    ${bazel}/bin/bazel \
       test \
         --test_output=errors \
         --host_javabase='@local_jdk//:jdk' \
diff --git a/pkgs/development/tools/build-managers/scons/default.nix b/pkgs/development/tools/build-managers/scons/default.nix
index d9bfb40b46e7..2d0bf244370f 100644
--- a/pkgs/development/tools/build-managers/scons/default.nix
+++ b/pkgs/development/tools/build-managers/scons/default.nix
@@ -7,8 +7,8 @@ in {
     version = "3.0.1";
     sha256 = "0wzid419mlwqw9llrg8gsx4nkzhqy16m4m40r0xnh6cwscw5wir4";
   };
-  scons_3_0_3 = mkScons {
-    version = "3.0.3";
-    sha256 = "1wwn0534d83ryfxjihvqk2ncj8wh5210pi3jxjd2cvjqa9mpkv6q";
+  scons_latest = mkScons {
+    version = "3.0.4";
+    sha256 = "06lv3pmdz5l23rx3kqsi1k712bdl36i942hgbjh209s94mpb7f72";
   };
 }
diff --git a/pkgs/development/tools/cargo-web/default.nix b/pkgs/development/tools/cargo-web/default.nix
index e350e475f73c..1feaf2c79a9d 100644
--- a/pkgs/development/tools/cargo-web/default.nix
+++ b/pkgs/development/tools/cargo-web/default.nix
@@ -1,21 +1,21 @@
-{ stdenv, fetchFromGitHub, openssl, pkgconfig, rustPlatform
+{ stdenv, fetchFromGitHub, openssl, perl, pkgconfig, rustPlatform
 , CoreServices, Security
 }:
 
 rustPlatform.buildRustPackage rec {
   name = "cargo-web-${version}";
-  version = "0.6.15";
+  version = "0.6.23";
 
   src = fetchFromGitHub {
     owner = "koute";
     repo = "cargo-web";
     rev = version;
-    sha256 = "076g7cd9v53vi8xvd4kfsiyzw1m2hhd1lwlwcv2dx2s5vlw4dxzh";
+    sha256 = "1qbi3z4x39il07xlhfvq5ckzjqrf0yf6p8qidf24fp92gb940zxr";
   };
 
-  cargoSha256 = "157av9zkirr00w9v11mh7yp8w36sy7rw6i80i5jmi0mgrdvcg5si";
+  cargoSha256 = "16wzgyn3k0yn70y0ciliyx1sjgppmkv9b4bn9p4x0qi6l0ah7fdp";
 
-  nativeBuildInputs = [ openssl pkgconfig ];
+  nativeBuildInputs = [ openssl perl pkgconfig ];
   buildInputs = stdenv.lib.optionals stdenv.isDarwin [ CoreServices Security ];
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/tools/jira_cli/default.nix b/pkgs/development/tools/jira_cli/default.nix
index 02ea20d8bad7..8722d49eb32e 100644
--- a/pkgs/development/tools/jira_cli/default.nix
+++ b/pkgs/development/tools/jira_cli/default.nix
@@ -19,7 +19,7 @@ in
     checkInputs = with python3Packages; [ vcrpy mock hiro ];
     buildInputs = [ libffi openssl ];
     propagatedBuildInputs = with python3Packages; [
-      argparse ordereddict requests six suds-jurko termcolor keyring
+      ordereddict requests six suds-jurko termcolor keyring
       jira  keyrings-alt
     ];
 
diff --git a/pkgs/development/tools/misc/autoconf-archive/default.nix b/pkgs/development/tools/misc/autoconf-archive/default.nix
index d051e1d57592..d7cea5c3d4ed 100644
--- a/pkgs/development/tools/misc/autoconf-archive/default.nix
+++ b/pkgs/development/tools/misc/autoconf-archive/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "autoconf-archive-${version}";
-  version = "2018.03.13";
+  version = "2019.01.06";
 
   src = fetchurl {
     url = "mirror://gnu/autoconf-archive/autoconf-archive-${version}.tar.xz";
-    sha256 = "0ng1lvpijf3kv7w7nb1shqs23vp0398yicyvkf9lsk56kw6zjxb1";
+    sha256 = "0gqya7nf4j5k98dkky0c3bnr0paciya91vkqazg7knlq621mq68p";
   };
 
   buildInputs = [ xz ];
diff --git a/pkgs/development/tools/misc/dejagnu/default.nix b/pkgs/development/tools/misc/dejagnu/default.nix
index 9464ad463f66..693c791875be 100644
--- a/pkgs/development/tools/misc/dejagnu/default.nix
+++ b/pkgs/development/tools/misc/dejagnu/default.nix
@@ -48,6 +48,6 @@ stdenv.mkDerivation rec {
     license = licenses.gpl2Plus;
 
     platforms = platforms.unix;
-    maintainers = with maintainers; [ wkennington vrthra ];
+    maintainers = with maintainers; [ vrthra ];
   };
 }
diff --git a/pkgs/development/tools/misc/mdl/.bundle/config b/pkgs/development/tools/misc/mdl/.bundle/config
new file mode 100644
index 000000000000..d28c8337bc45
--- /dev/null
+++ b/pkgs/development/tools/misc/mdl/.bundle/config
@@ -0,0 +1,3 @@
+---
+BUNDLE_PATH: "vendor/bundle"
+BUNDLE_CACHE_ALL: "true"
diff --git a/pkgs/development/tools/misc/mdl/Gemfile b/pkgs/development/tools/misc/mdl/Gemfile
new file mode 100644
index 000000000000..15b33c53a653
--- /dev/null
+++ b/pkgs/development/tools/misc/mdl/Gemfile
@@ -0,0 +1,3 @@
+source "https://rubygems.org"
+
+gem "mdl"
diff --git a/pkgs/development/tools/misc/mdl/Gemfile.lock b/pkgs/development/tools/misc/mdl/Gemfile.lock
new file mode 100644
index 000000000000..aabcd784d867
--- /dev/null
+++ b/pkgs/development/tools/misc/mdl/Gemfile.lock
@@ -0,0 +1,21 @@
+GEM
+  remote: https://rubygems.org/
+  specs:
+    kramdown (1.17.0)
+    mdl (0.5.0)
+      kramdown (~> 1.12, >= 1.12.0)
+      mixlib-cli (~> 1.7, >= 1.7.0)
+      mixlib-config (~> 2.2, >= 2.2.1)
+    mixlib-cli (1.7.0)
+    mixlib-config (2.2.18)
+      tomlrb
+    tomlrb (1.2.8)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  mdl
+
+BUNDLED WITH
+   1.16.3
diff --git a/pkgs/development/tools/misc/mdl/default.nix b/pkgs/development/tools/misc/mdl/default.nix
new file mode 100644
index 000000000000..a3c361efc9d5
--- /dev/null
+++ b/pkgs/development/tools/misc/mdl/default.nix
@@ -0,0 +1,15 @@
+{ lib, bundlerEnv, ruby }:
+
+bundlerEnv {
+  inherit ruby;
+  pname = "mdl";
+  gemdir = ./.;
+
+  meta = with lib; {
+    description = "A tool to check markdown files and flag style issues";
+    homepage = https://github.com/markdownlint/markdownlint;
+    license = licenses.mit;
+    maintainers = with maintainers; [ gerschtli ];
+    platforms = platforms.all;
+  };
+}
diff --git a/pkgs/development/tools/misc/mdl/gemset.nix b/pkgs/development/tools/misc/mdl/gemset.nix
new file mode 100644
index 000000000000..54994f3da6ab
--- /dev/null
+++ b/pkgs/development/tools/misc/mdl/gemset.nix
@@ -0,0 +1,44 @@
+{
+  kramdown = {
+    source = {
+      remotes = ["https://rubygems.org"];
+      sha256 = "1n1c4jmrh5ig8iv1rw81s4mw4xsp4v97hvf8zkigv4hn5h542qjq";
+      type = "gem";
+    };
+    version = "1.17.0";
+  };
+  mdl = {
+    dependencies = ["kramdown" "mixlib-cli" "mixlib-config"];
+    source = {
+      remotes = ["https://rubygems.org"];
+      sha256 = "047hp8z1ma630wp38bm1giklkf385rp6wly8aidn825q831w2g4i";
+      type = "gem";
+    };
+    version = "0.5.0";
+  };
+  mixlib-cli = {
+    source = {
+      remotes = ["https://rubygems.org"];
+      sha256 = "0647msh7kp7lzyf6m72g6snpirvhimjm22qb8xgv9pdhbcrmcccp";
+      type = "gem";
+    };
+    version = "1.7.0";
+  };
+  mixlib-config = {
+    dependencies = ["tomlrb"];
+    source = {
+      remotes = ["https://rubygems.org"];
+      sha256 = "1gm6yj9cbbgsl9x4xqxga0vz5w0ksq2jnq1wj8hvgm5c4wfcrswb";
+      type = "gem";
+    };
+    version = "2.2.18";
+  };
+  tomlrb = {
+    source = {
+      remotes = ["https://rubygems.org"];
+      sha256 = "0g28ssfal6vry3cmhy509ba3vi5d5aggz1gnffnvvmc8ml8vkpiv";
+      type = "gem";
+    };
+    version = "1.2.8";
+  };
+}
\ No newline at end of file
diff --git a/pkgs/development/tools/misc/swig/3.x.nix b/pkgs/development/tools/misc/swig/3.x.nix
index 136ea9c9062f..903693b92808 100644
--- a/pkgs/development/tools/misc/swig/3.x.nix
+++ b/pkgs/development/tools/misc/swig/3.x.nix
@@ -32,6 +32,5 @@ stdenv.mkDerivation rec {
     # Different types of licenses available: http://www.swig.org/Release/LICENSE .
     license = licenses.gpl3Plus;
     platforms = with platforms; linux ++ darwin;
-    maintainers = with maintainers; [ wkennington ];
   };
 }
diff --git a/pkgs/development/tools/ocaml/opam/default.nix b/pkgs/development/tools/ocaml/opam/default.nix
index 8e89dd3fadd2..b3e9e71ebc05 100644
--- a/pkgs/development/tools/ocaml/opam/default.nix
+++ b/pkgs/development/tools/ocaml/opam/default.nix
@@ -11,8 +11,8 @@ let
       sha256 = "18jqphjiifljlh9jg8zpl6310p3iwyaqphdkmf89acyaix0s4kj1";
     };
     cppo = fetchurl {
-      url = "https://github.com/mjambon/cppo/archive/v1.6.4.tar.gz";
-      sha256 = "0jdb7d21lfa3ck4k59mrqs5pljzq5rb504jq57nnrc6klljm42j7";
+      url = "https://github.com/mjambon/cppo/archive/v1.6.5.tar.gz";
+      sha256 = "1dkm3d5h6h56y937gcdk2wixlpzl59vv5pmiafglr89p20kf7gqf";
     };
     cudf = fetchurl {
       url = "https://gforge.inria.fr/frs/download.php/36602/cudf-0.9.tar.gz";
@@ -22,42 +22,46 @@ let
       url = "https://gforge.inria.fr/frs/download.php/file/36063/dose3-5.0.1.tar.gz";
       sha256 = "00yvyfm4j423zqndvgc1ycnmiffaa2l9ab40cyg23pf51qmzk2jm";
     };
+    dune-local = fetchurl {
+      url = "https://github.com/ocaml/dune/releases/download/1.2.1/dune-1.2.1.tbz";
+      sha256 = "00c5dbm4hkdapc2i7pg07b2lj8sv6ly38qr7zid58cdmbmzq21z9";
+    };
     extlib = fetchurl {
       url = "http://ygrek.org.ua/p/release/ocaml-extlib/extlib-1.7.5.tar.gz";
       sha256 = "19slqf5bdj0rrph2w41giwmn6df2qm07942jn058pjkjrnk30d4s";
     };
-    jbuilder = fetchurl {
-      url = "https://github.com/ocaml/dune/releases/download/1.0+beta20/jbuilder-1.0.beta20.tbz";
-      sha256 = "07hl9as5llffgd6hbw41rs76i1ibgn3n9r0dba5h0mdlkapcwb10";
-    };
     mccs = fetchurl {
-      url = "https://github.com/AltGr/ocaml-mccs/archive/1.1+8.tar.gz";
-      sha256 = "0xavfvxfrcf3lmry8ymma1yzy0hw3ijbx94c9zq3pzlwnylrapa4";
+      url = "https://github.com/AltGr/ocaml-mccs/archive/1.1+9.tar.gz";
+      sha256 = "0gf86c65jdxxcwd96kcmrqxrmnnzc0570gb9ad6c57rl3fyy8yhv";
     };
     ocamlgraph = fetchurl {
       url = "http://ocamlgraph.lri.fr/download/ocamlgraph-1.8.8.tar.gz";
       sha256 = "0m9g16wrrr86gw4fz2fazrh8nkqms0n863w7ndcvrmyafgxvxsnr";
     };
     opam-file-format = fetchurl {
-      url = "https://github.com/ocaml/opam-file-format/archive/2.0.0-rc2.tar.gz";
-      sha256 = "1mgk08msp7hxn0hs0m82vky3yv6hcq4pw5402b3vhx4c49431jsb";
+      url = "https://github.com/ocaml/opam-file-format/archive/2.0.0.tar.gz";
+      sha256 = "0cjw69r7iilidi7b6arr92kjnjspchvwnmwr1b1gyaxqxpr2s98m";
     };
     re = fetchurl {
-      url = "https://github.com/ocaml/ocaml-re/releases/download/1.7.3/re-1.7.3.tbz";
-      sha256 = "0nv933qfl8y9i19cqvhsalwzif3dkm28vg478rpnr4hgfqjlfryr";
+      url = "https://github.com/ocaml/ocaml-re/releases/download/1.8.0/re-1.8.0.tbz";
+      sha256 = "0qkv42a4hpqpxvqa4kdkkcbhbg7aym9kv4mqgm3m51vxbd0pq0lv";
     };
     result = fetchurl {
       url = "https://github.com/janestreet/result/releases/download/1.3/result-1.3.tbz";
       sha256 = "1lrnbxdq80gbhnp85mqp1kfk0bkh6q1c93sfz2qgnq2qyz60w4sk";
     };
+    seq = fetchurl {
+      url = "https://github.com/c-cube/seq/archive/0.1.tar.gz";
+      sha256 = "02lb2d9i12bxrz2ba5wygk2bycan316skqlyri0597q7j9210g8r";
+    };
     opam = fetchurl {
-      url = "https://github.com/ocaml/opam/archive/2.0.0.zip";
-      sha256 = "0m4ilsldrfkkn0vlvl119bk76j2pwvqvdi8mpg957z4kqflfbfp8";
+      url = "https://github.com/ocaml/opam/archive/2.0.2.zip";
+      sha256 = "0hxf0ns3si03rl7dxix7i30limbl50ffyvdyk9bqqms4ir8dcza6";
     };
   };
 in stdenv.mkDerivation rec {
   name = "opam-${version}";
-  version = "2.0.0";
+  version = "2.0.2";
 
   buildInputs = [ unzip curl ncurses ocaml makeWrapper getconf ] ++ lib.optional stdenv.isLinux bubblewrap;
 
@@ -68,16 +72,17 @@ in stdenv.mkDerivation rec {
     ln -sv ${srcs.cppo} $sourceRoot/src_ext/cppo.tar.gz
     ln -sv ${srcs.cudf} $sourceRoot/src_ext/cudf.tar.gz
     ln -sv ${srcs.dose3} $sourceRoot/src_ext/dose3.tar.gz
+    ln -sv ${srcs.dune-local} $sourceRoot/src_ext/dune-local.tbz
     ln -sv ${srcs.extlib} $sourceRoot/src_ext/extlib.tar.gz
-    ln -sv ${srcs.jbuilder} $sourceRoot/src_ext/jbuilder.tbz
     ln -sv ${srcs.mccs} $sourceRoot/src_ext/mccs.tar.gz
     ln -sv ${srcs.ocamlgraph} $sourceRoot/src_ext/ocamlgraph.tar.gz
     ln -sv ${srcs.opam-file-format} $sourceRoot/src_ext/opam-file-format.tar.gz
     ln -sv ${srcs.re} $sourceRoot/src_ext/re.tbz
     ln -sv ${srcs.result} $sourceRoot/src_ext/result.tbz
+    ln -sv ${srcs.seq} $sourceRoot/src_ext/seq.tar.gz
   '';
 
-  patches = [ ./opam-pull-3487.patch ./opam-shebangs.patch ./opam-mccs-darwin.patch ];
+  patches = [ ./opam-shebangs.patch ];
 
   preConfigure = ''
     substituteInPlace ./src_ext/Makefile --replace "%.stamp: %.download" "%.stamp:"
@@ -98,7 +103,8 @@ in stdenv.mkDerivation rec {
     mv $out/bin/opam $out/bin/.opam-wrapped
     makeWrapper $out/bin/.opam-wrapped $out/bin/opam \
       --argv0 "opam" \
-      --suffix PATH : ${aspcud}/bin:${unzip}/bin:${curl}/bin:${lib.optionalString stdenv.isLinux "${bubblewrap}/bin:"}${getconf}/bin
+      --suffix PATH : ${aspcud}/bin:${unzip}/bin:${curl}/bin:${lib.optionalString stdenv.isLinux "${bubblewrap}/bin:"}${getconf}/bin \
+      --set OPAM_USER_PATH_RO /run/current-system/sw/bin:/nix/store
     $out/bin/opam-installer --prefix=$installer opam-installer.install
   '';
 
@@ -111,4 +117,4 @@ in stdenv.mkDerivation rec {
     platforms = platforms.all;
   };
 }
-# Generated by: ./opam.nix.pl -v 2.0.0 -p opam-pull-3487.patch,opam-shebangs.patch,opam-mccs-darwin.patch
+# Generated by: ./opam.nix.pl -v 2.0.2 -p opam-shebangs.patch
diff --git a/pkgs/development/tools/ocaml/opam/opam-mccs-darwin.patch b/pkgs/development/tools/ocaml/opam/opam-mccs-darwin.patch
deleted file mode 100644
index 501242c40a01..000000000000
--- a/pkgs/development/tools/ocaml/opam/opam-mccs-darwin.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-diff --git a/src_ext/patches/mccs/build-on-darwin.patch b/src_ext/patches/mccs/build-on-darwin.patch
-new file mode 100644
-index 00000000..157e2094
---- /dev/null
-+++ b/src_ext/patches/mccs/build-on-darwin.patch
-@@ -0,0 +1,12 @@
-+diff --git a/src/context_flags.ml b/src/context_flags.ml
-+index 7470030..6e07370 100644
-+--- a/src/context_flags.ml
-++++ b/src/context_flags.ml
-+@@ -24,6 +24,7 @@ let ifc c x = if c then x else []
-+ 
-+ let cxxflags =
-+   let flags =
-++    (ifc (Config.system = "macosx") ["-x"; "c++"]) @
-+     (ifc (Sys.win32 && Config.ccomp_type = "msvc") ["/EHsc"]) @
-+     (ifc useGLPK ["-DUSEGLPK"]) @
-+     (ifc useCOIN ["-DUSECOIN"]) @
diff --git a/pkgs/development/tools/ocaml/opam/opam-pull-3487.patch b/pkgs/development/tools/ocaml/opam/opam-pull-3487.patch
deleted file mode 100644
index e047c8298bc3..000000000000
--- a/pkgs/development/tools/ocaml/opam/opam-pull-3487.patch
+++ /dev/null
@@ -1,23 +0,0 @@
-diff --git a/src/state/shellscripts/bwrap.sh b/src/state/shellscripts/bwrap.sh
-index 6f5d7dbea..3e1a3e1b4 100755
---- a/src/state/shellscripts/bwrap.sh
-+++ b/src/state/shellscripts/bwrap.sh
-@@ -1,4 +1,6 @@
--#!/bin/bash -ue
-+#!/usr/bin/env bash
-+
-+set -ue
- 
- if ! command -v bwrap >/dev/null; then
-     echo "The 'bwrap' command was not found. Install 'bubblewrap' on your system, or" >&2
-@@ -11,7 +13,9 @@ fi
- 
- ARGS=(--unshare-net --new-session)
- ARGS=("${ARGS[@]}" --proc /proc --dev /dev)
--ARGS=("${ARGS[@]}" --bind /tmp /tmp --tmpfs /run --tmpfs /var)
-+ARGS=("${ARGS[@]}" --bind "${TMPDIR:-/tmp}" /tmp)
-+ARGS=("${ARGS[@]}" --setenv TMPDIR /tmp --setenv TMP /tmp --setenv TEMPDIR /tmp --setenv TEMP /tmp)
-+ARGS=("${ARGS[@]}" --tmpfs /run --tmpfs /var)
- 
- add_mounts() {
-     case "$1" in
diff --git a/pkgs/development/tools/ocaml/opam/opam.nix.pl b/pkgs/development/tools/ocaml/opam/opam.nix.pl
index 1862add452d6..537997eb8a45 100755
--- a/pkgs/development/tools/ocaml/opam/opam.nix.pl
+++ b/pkgs/development/tools/ocaml/opam/opam.nix.pl
@@ -113,7 +113,8 @@ print <<'EOF';
     mv $out/bin/opam $out/bin/.opam-wrapped
     makeWrapper $out/bin/.opam-wrapped $out/bin/opam \
       --argv0 "opam" \
-      --suffix PATH : ${aspcud}/bin:${unzip}/bin:${curl}/bin:${lib.optionalString stdenv.isLinux "${bubblewrap}/bin:"}${getconf}/bin
+      --suffix PATH : ${aspcud}/bin:${unzip}/bin:${curl}/bin:${lib.optionalString stdenv.isLinux "${bubblewrap}/bin:"}${getconf}/bin \
+      --set OPAM_USER_PATH_RO /run/current-system/sw/bin:/nix/store
     $out/bin/opam-installer --prefix=$installer opam-installer.install
   '';
 
diff --git a/pkgs/development/tools/packer/default.nix b/pkgs/development/tools/packer/default.nix
index 25ec443be42b..5e54a8b37058 100644
--- a/pkgs/development/tools/packer/default.nix
+++ b/pkgs/development/tools/packer/default.nix
@@ -1,7 +1,7 @@
 { stdenv, buildGoPackage, fetchFromGitHub }:
 buildGoPackage rec {
   name = "packer-${version}";
-  version = "1.3.1";
+  version = "1.3.3";
 
   goPackagePath = "github.com/hashicorp/packer";
 
@@ -11,7 +11,7 @@ buildGoPackage rec {
     owner = "hashicorp";
     repo = "packer";
     rev = "v${version}";
-    sha256 = "0aif4ilzfv8qyqk4mn525r38xw2w34ryknzd2vrg6mcjcarm8myq";
+    sha256 = "1b1yp5k2apccyqw9zb2xclnm16gfnnkaiwh2s0p79prsy6gjkp7y";
   };
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/tools/toluapp/default.nix b/pkgs/development/tools/toluapp/default.nix
index 5ad9a7c58efb..90d36c71caa9 100644
--- a/pkgs/development/tools/toluapp/default.nix
+++ b/pkgs/development/tools/toluapp/default.nix
@@ -14,7 +14,7 @@ stdenv.mkDerivation rec {
   nativeBuildInputs = [ sconsPackages.scons_3_0_1 ];
   buildInputs = [ lua ];
 
-  patches = [ ./environ-and-linux-is-kinda-posix.patch ];
+  patches = [ ./environ-and-linux-is-kinda-posix.patch ./headers.patch ];
 
   preConfigure = ''
     substituteInPlace config_posix.py \
diff --git a/pkgs/development/tools/toluapp/headers.patch b/pkgs/development/tools/toluapp/headers.patch
new file mode 100644
index 000000000000..59a47bb989a9
--- /dev/null
+++ b/pkgs/development/tools/toluapp/headers.patch
@@ -0,0 +1,15 @@
+diff --git a/include/tolua++.h b/include/tolua++.h
+index ed53449..f57d56d 100644
+--- a/include/tolua++.h
++++ b/include/tolua++.h
+@@ -43,8 +43,8 @@ extern "C" {
+
+ typedef int lua_Object;
+
+-#include "lua.h"
+-#include "lauxlib.h"
++#include <lua.h>
++#include <lauxlib.h>
+
+ struct tolua_Error
+ {
diff --git a/pkgs/development/tools/uftrace/default.nix b/pkgs/development/tools/uftrace/default.nix
index 7d5569b4376b..cb10a252d121 100644
--- a/pkgs/development/tools/uftrace/default.nix
+++ b/pkgs/development/tools/uftrace/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   name = "uftrace-${version}";
-  version = "0.9.1";
+  version = "0.9.2";
 
   src = fetchFromGitHub {
     owner = "namhyung";
     repo = "uftrace";
     rev = "v${version}";
-    sha256 = "1jb4dp6crvfzxzmi5iflc7p13b7p2v1djyj6smbf9ns4wr515y6b";
+    sha256 = "0s7yfnf7kcqlfw3zzv4y8akkd12f8di69c4sranympnl7z5srfam";
   };
 
   postUnpack = ''