NixOS · Feb 29, 2020 · Mar 5, 2020 · Mar 7, 2020 · Mar 7, 2020 · Mar 8, 2020
diff --git a/nixos/modules/system/etc/etc.nix b/nixos/modules/system/etc/etc.nix
@@ -94,7 +94,7 @@ in
               default = 0;
               type = types.int;
               description = ''
-                UID of created file. Only takes affect when the file is
+                UID of created file. Only takes effect when the file is
                 copied (that is, the mode is not 'symlink').
                 '';
             };
@@ -103,7 +103,7 @@ in
               default = 0;
               type = types.int;
               description = ''
-                GID of created file. Only takes affect when the file is
+                GID of created file. Only takes effect when the file is
                 copied (that is, the mode is not 'symlink').
               '';
             };
@@ -113,7 +113,7 @@ in
               type = types.str;
               description = ''
                 User name of created file.
-                Only takes affect when the file is copied (that is, the mode is not 'symlink').
+                Only takes effect when the file is copied (that is, the mode is not 'symlink').
                 Changing this option takes precedence over <literal>uid</literal>.
               '';
             };
@@ -123,7 +123,7 @@ in
               type = types.str;
               description = ''
                 Group name of created file.
-                Only takes affect when the file is copied (that is, the mode is not 'symlink').
+                Only takes effect when the file is copied (that is, the mode is not 'symlink').
                 Changing this option takes precedence over <literal>gid</literal>.
               '';
             };

diff --git a/pkgs/applications/blockchains/polkadot/default.nix b/pkgs/applications/blockchains/polkadot/default.nix
@@ -11,24 +11,27 @@ rustPlatform.buildRustPackage rec {
 
   src = fetchFromGitHub {
     owner = "paritytech";
+    # N.B. In 2018, the thing that was "polkadot" was split off into its own
+    # repo, so if this package is ever updated it should be changed to
+    # paritytech/polkadot, as per comment here:
+    # https://github.com/paritytech/polkadot#note
     repo = "substrate";
     rev = "19f4f4d4df3bb266086b4e488739f73d3d5e588c";
     sha256 = "0v7g03rbml2afw0splmyjh9nqpjg0ldjw09hyc0jqd3qlhgxiiyj";
-  }; 
-
-  # Delete this on next update; see #79975 for details
-  legacyCargoFetcher = true;
+  };
 
-  cargoSha256 = "0gc3w0cwdyk8f7cgpp9sfawczk3n6wd7q0nhfvk87sry71b8vvwq";
+  cargoSha256 = "1h5v7c7xi2r2wzh1pj6xidrg7dx23w3rjm88mggpq7574arijk4i";
 
   buildInputs = [ pkgconfig openssl openssl.dev ];
 
   meta = with stdenv.lib; {
     description = "Polkadot Node Implementation";
-    homepage = https://polkadot.network;
+    homepage = "https://polkadot.network";
     license = licenses.gpl3;
     maintainers = [ maintainers.akru ];
     platforms = platforms.linux;
+    # Last attempt at building this was on v0.7.22
+    # https://github.com/paritytech/polkadot/releases
     broken = true;
   };
 }
diff --git a/pkgs/applications/editors/rstudio/default.nix b/pkgs/applications/editors/rstudio/default.nix
@@ -8,7 +8,7 @@ with lib;
 let
   verMajor = "1";
   verMinor = "2";
-  verPatch = "1335";
+  verPatch = "5033";
   version = "${verMajor}.${verMinor}.${verPatch}";
   ginVer = "2.1.2";
   gwtVer = "2.8.1";
@@ -26,7 +26,7 @@ mkDerivation rec {
     owner = "rstudio";
     repo = "rstudio";
     rev = "v${version}";
-    sha256 = "0jv1d4yznv2lzwp0fdf377vqpg0k2q4z9qvji4sj86fabj835lqd";
+    sha256 = "0f3p2anz9xay2859bxj3bvyj582igsp628qxsccpkgn0jifvi4np";
   };
 
   # Hack RStudio to only use the input R and provided libclang.

diff --git a/pkgs/build-support/appimage/appimage-exec.sh b/pkgs/build-support/appimage/appimage-exec.sh
@@ -0,0 +1,142 @@
+#!@shell@
+if [ -n "$DEBUG" ] ; then
+  set -x
+fi
+
+PATH="@path@:$PATH"
+apprun_opt=true
+
+#DEBUG=0
+
+# src : AppImage
+# dest : let's unpack() create the directory
+unpack() {
+  local src=$1
+  local out=$2
+  local appimageSignature=""
+  local appimageType=0
+
+  # https://github.com/AppImage/libappimage/blob/ca8d4b53bed5cbc0f3d0398e30806e0d3adeaaab/src/libappimage/utils/MagicBytesChecker.cpp#L45-L63
+  eval "$(r2 "$src" -nn -Nqc "p8j 3 @ 8" |
+    jq -r '{appimageSignature: (.[:-1]|implode), appimageType: .[-1]}|
+      @sh "appimageSignature=\(.appimageSignature) appimageType=\(.appimageType)"')"
+
+  # check AppImage signature
+  if [[ "$appimageSignature" != "AI" ]]; then
+    echo "Not an appimage."
+    exit
+  fi
+
+  case "$appimageType" in
+    1 ) echo "Uncompress $(basename "$src") of type $appimageType."
+        mkdir "$out"
+        pv "$src" | bsdtar -x -C "$out" -f -
+        ;;
+    2)
+        # This method avoid issues with non executable appimages,
+        # non-native packer, packer patching and squashfs-root destination prefix.
+
+        # multiarch offset one-liner using same method as AppImage
+        # see https://gist.github.com/probonopd/a490ba3401b5ef7b881d5e603fa20c93
+        offset=$(r2 "$src" -nn -Nqc "pfj.elf_header @ 0" |\
+          jq 'map({(.name): .value}) | add | .shoff + (.shnum * .shentsize)')
+
+        echo "Uncompress $(basename "$src") of type $appimageType @ offset $offset."
+        unsquashfs -q -d "$out" -o "$offset" "$src"
+        chmod go-w "$out"
+        ;;
+
+    # 3) get ready, https://github.com/TheAssassin/type3-runtime
+    *)  echo Unsupported AppImage Type: "$appimageType"
+        exit
+        ;;
+  esac
+  echo "$(basename "$src") is now installed in $out"
+}
+
+apprun() {
+
+  eval "$(rahash2 "$APPIMAGE" -j | jq -r '.[] | @sh "SHA256=\(.hash)"')"
+  echo sha256 = \""$SHA256"\"\;
+  export APPDIR="${XDG_CACHE_HOME:-$HOME/.cache}/appimage-run/$SHA256"
+
+  #compatibility
+  if [ -x "$APPDIR/squashfs-root" ]; then APPDIR="$APPDIR/squashfs-root"; fi
+
+  if [ ! -x "$APPDIR" ]; then
+    mkdir -p "$(dirname "$APPDIR")"
+    unpack "$APPIMAGE" "$APPDIR"
+  else echo "$(basename "$APPIMAGE")" installed in "$APPDIR"
+  fi
+
+  export PATH="$PATH:$PWD/usr/bin"
+}
+
+wrap() {
+
+  cd "$APPDIR" || exit
+  # quite same in appimageTools
+  export APPIMAGE_SILENT_INSTALL=1
+
+  if [ -n "$APPIMAGE_DEBUG_EXEC" ]; then
+    exec "$APPIMAGE_DEBUG_EXEC"
+  fi
+
+  exec ./AppRun "$@"
+}
+
+usage() {
+  cat <<EOF
+Usage: appimage-run [appimage-run options] <AppImage> [AppImage options]
+
+-h      show this message
+-d      debug mode
+-x      <directory> : extract appimage in the directory then exit.
+-w      <directory> : run uncompressed appimage directory (used in appimageTools)
+
+[AppImage options]: Options are passed on to the appimage.
+If you want to execute a custom command in the appimage's environment, set the APPIMAGE_DEBUG_EXEC environment variable.
+
+EOF
+  exit 1
+}
+
+while getopts "x:w:dh" option; do
+    case "${option}" in
+        d)  set -x
+            ;;
+        x)  # eXtract
+            unpack_opt=true
+            APPDIR=${OPTARG}
+            ;;
+        w)  # WrapAppImage
+            export APPDIR=${OPTARG}
+            wrap_opt=true
+            ;;
+        h)  usage
+            ;;
+        *)
+            usage
+            ;;
+    esac
+done
+shift $((OPTIND-1))
+
+if [[ $wrap_opt = true ]] && [[ -d "$APPDIR" ]]; then
+  wrap "$@"
+  exit
+else
+  APPIMAGE="$(realpath "$1")" || usage
+  shift
+fi
+
+if [[ $unpack_opt = true ]] && [[ -f "$APPIMAGE" ]]; then
+  unpack "$APPIMAGE" "$APPDIR"
+  exit
+fi
+
+if [[ $apprun_opt = true ]] && [[ -f "$APPIMAGE" ]]; then
+  apprun
+  wrap "$@"
+  exit
+fi
diff --git a/pkgs/build-support/appimage/default.nix b/pkgs/build-support/appimage/default.nix
@@ -1,71 +1,39 @@
-{ stdenv, libarchive, radare2, jq, buildFHSUserEnv, squashfsTools, writeScript }:
+{ stdenv, buildFHSUserEnv, writeScript, pkgs
+, bash, radare2, jq, squashfsTools, ripgrep
+, coreutils, libarchive, file, runtimeShell, pv
+, lib, runCommand }:
 
 rec {
-
-  extract = { name, src }: stdenv.mkDerivation {
-    name = "${name}-extracted";
-    inherit src;
-    nativeBuildInputs = [ radare2 libarchive jq squashfsTools ];
-    buildCommand = ''
-      # https://github.com/AppImage/libappimage/blob/ca8d4b53bed5cbc0f3d0398e30806e0d3adeaaab/src/libappimage/utils/MagicBytesChecker.cpp#L45-L63
-      eval $(r2 $src -nn -Nqc "p8j 3 @ 8" |
-        jq -r '{appimageSignature: (.[:-1]|implode), appimageType: .[-1]}|
-          @sh "appimageSignature=\(.appimageSignature) appimageType=\(.appimageType)"')
-
-      # check AppImage signature
-      if [[ "$appimageSignature" != "AI" ]]; then
-        echo "Not an appimage."
-        exit
-      fi
-
-      case "$appimageType" in
-        1)
-          mkdir $out
-          bsdtar -x -C $out -f $src
-          ;;
-
-        2)
-          # multiarch offset one-liner using same method as AppImage
-          # see https://gist.github.com/probonopd/a490ba3401b5ef7b881d5e603fa20c93
-          offset=$(r2 $src -nn -Nqc "pfj.elf_header @ 0" |\
-            jq 'map({(.name): .value}) | add | .shoff + (.shnum * .shentsize)')
-
-          unsquashfs -q -d $out -o $offset $src
-          chmod go-w $out
-          ;;
-
-        # 3) get ready, https://github.com/TheAssassin/type3-runtime
-        *) echo "Unsupported AppImage Type: $appimageType";;
-      esac
-    '';
+  appimage-exec = pkgs.substituteAll {
+    src = ./appimage-exec.sh;
+    isExecutable = true;
+    dir = "bin";
+    path = with pkgs; lib.makeBinPath [ pv ripgrep file radare2 libarchive jq squashfsTools coreutils bash ];
   };
 
+  extract = { name, src }: runCommand "${name}-extracted" {
+    buildInputs = [ appimage-exec ];
+  } ''
+    appimage-exec.sh -x $out ${src}
+  '';
+
+  # for compatibility, deprecated
   extractType1 = extract;
   extractType2 = extract;
+  wrapType1 = wrapType2;
 
   wrapAppImage = args@{ name, src, extraPkgs, ... }: buildFHSUserEnv (defaultFhsEnvArgs // {
     inherit name;
 
-    targetPkgs = pkgs: defaultFhsEnvArgs.targetPkgs pkgs ++ extraPkgs pkgs;
-
-    runScript = writeScript "run" ''
-      #!${stdenv.shell}
+    targetPkgs = pkgs: [ appimage-exec ]
+      ++ defaultFhsEnvArgs.targetPkgs pkgs ++ extraPkgs pkgs;
 
-      export APPDIR=${src}
-      export APPIMAGE_SILENT_INSTALL=1
-      cd $APPDIR
-      exec ./AppRun "$@"
-    '';
+    runScript = "appimage-exec.sh -w ${src}";
   } // (removeAttrs args (builtins.attrNames (builtins.functionArgs wrapAppImage))));
 
-  wrapType1 = args@{ name, src, extraPkgs ? pkgs: [], ... }: wrapAppImage (args // {
-    inherit name extraPkgs;
-    src = extractType1 { inherit name src; };
-  });
-
   wrapType2 = args@{ name, src, extraPkgs ? pkgs: [], ... }: wrapAppImage (args // {
     inherit name extraPkgs;
-    src = extractType2 { inherit name src; };
+    src = extract { inherit name src; };
   });
 
   defaultFhsEnvArgs = {

diff --git a/pkgs/development/python-modules/acoustics/default.nix b/pkgs/development/python-modules/acoustics/default.nix
@@ -3,14 +3,14 @@
 
 buildPythonPackage rec {
   pname = "acoustics";
-  version = "0.2.3";
+  version = "0.2.4";
 
   checkInputs = [ pytest ];
   propagatedBuildInputs = [ numpy scipy matplotlib pandas tabulate ];
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "ca663059d61fbd2899aed4e3cedbc3f983aa67afd3ae1617db3c59b724206fb3";
+    sha256 = "8ccb68ac258ba81a0b9064523e85eae013f9bfce7244d01db42d7d2d21d712cc";
   };
 
   checkPhase = ''
@@ -26,6 +26,5 @@ buildPythonPackage rec {
     maintainers = with maintainers; [ fridh ];
     license = with licenses; [ bsd3 ];
     homepage = "https://github.com/python-acoustics/python-acoustics";
-    broken = true; # no longer compatible with pandas>=1
   };
 }
diff --git a/pkgs/development/python-modules/dominate/default.nix b/pkgs/development/python-modules/dominate/default.nix
@@ -2,17 +2,17 @@
 
 buildPythonPackage rec {
   pname = "dominate";
-  version = "2.4.0";
+  version = "2.5.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1775cz6lipb43hmjll77m2pxh72pikng74lpg30v9n1b66s78959";
+    sha256 = "0y4xzch6kwzddwz6pmk8cd09r3dpkxm1bh4q1byhm37a0lb4h1cv";
   };
 
   doCheck = !isPy3k;
 
   meta = with lib; {
-    homepage = https://github.com/Knio/dominate/;
+    homepage = "https://github.com/Knio/dominate/";
     description = "Dominate is a Python library for creating and manipulating HTML documents using an elegant DOM API";
     license = licenses.lgpl3;
     maintainers = with maintainers; [ ];

diff --git a/pkgs/development/python-modules/jenkins-job-builder/default.nix b/pkgs/development/python-modules/jenkins-job-builder/default.nix
@@ -10,11 +10,11 @@
 
 buildPythonPackage rec {
   pname = "jenkins-job-builder";
-  version = "3.2.0";
+  version = "3.3.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1njxww53d92cpgrqlr09w2n0pk6wamjcb0mvpns1mr2pn5hy1jhi";
+    sha256 = "0znnw1vnvnm8a6gfrk479s2b9hzlxi4qy57c9a47qphvx3mklm8x";
   };
 
   postPatch = ''