NixOS · FRidh · Jan 28, 2020 · Nov 11, 2019 · Dec 30, 2019 · Jan 6, 2020
diff --git a/pkgs/applications/graphics/paraview/default.nix b/pkgs/applications/graphics/paraview/default.nix
@@ -30,7 +30,7 @@ mkDerivation rec {
   # libraries.  These reside in build/lib, and are not found by
   # default.
   preBuild = ''
-    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$PWD/lib:$PWD/VTK/ThirdParty/vtkm/vtk-m/lib
+    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH''${LD_LIBRARY_PATH:+:}$PWD/lib:$PWD/VTK/ThirdParty/vtkm/vtk-m/lib
   '';
 
   enableParallelBuilding = true;

diff --git a/pkgs/applications/misc/audio/soxr/default.nix b/pkgs/applications/misc/audio/soxr/default.nix
@@ -11,9 +11,9 @@ stdenv.mkDerivation rec {
   outputs = [ "out" "doc" ]; # headers are just two and very small
 
   preConfigure = if stdenv.isDarwin then ''
-    export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:"`pwd`/build/src
+    export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH''${DYLD_LIBRARY_PATH:+:}"`pwd`/build/src
   '' else ''
-    export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:"`pwd`/build/src
+    export LD_LIBRARY_PATH="$LD_LIBRARY_PATH''${LD_LIBRARY_PATH:+:}"`pwd`/build/src
   '';
 
   nativeBuildInputs = [ cmake ];

diff --git a/pkgs/applications/networking/ftp/filezilla/default.nix b/pkgs/applications/networking/ftp/filezilla/default.nix
@@ -18,11 +18,11 @@
 
 stdenv.mkDerivation rec {
   pname = "filezilla";
-  version = "3.46.0";
+  version = "3.46.3";
 
   src = fetchurl {
     url = "https://download.filezilla-project.org/client/FileZilla_${version}_src.tar.bz2";
-    sha256 = "0v7656p7b6w88a96wj8058b13yxbwi186l092i9whrisngnv2pnf";
+    sha256 = "15bkg9qs07h4pzkxba1gymp8f264dk0zrzd9brx48fcwm7qbzigi";
   };
 
   configureFlags = [

diff --git a/pkgs/applications/networking/ike/default.nix b/pkgs/applications/networking/ike/default.nix
@@ -28,6 +28,11 @@ stdenv.mkDerivation rec {
   nativeBuildInputs = [ cmake flex bison makeWrapper ];
   buildInputs = [ openssl libedit qt4 nettools iproute ];
 
+  postPatch = ''
+    # fix build with bison3
+    sed -i 's/define "parser_class_name"/define parser_class_name/' source/iked/conf.parse.yy
+  '';
+
   configurePhase = ''
     mkdir -p $out/{bin,sbin,lib}
     cmake -DQTGUI=YES -DETCDIR=$out/etc -DLIBDIR=$out/lib -DSBINDIR=$out/sbin -DBINDIR=$out/bin \

diff --git a/pkgs/applications/networking/mailreaders/claws-mail/default.nix b/pkgs/applications/networking/mailreaders/claws-mail/default.nix
@@ -43,7 +43,7 @@ stdenv.mkDerivation rec {
 
   preConfigure = ''
     # autotools check tries to dlopen libpython as a requirement for the python plugin
-    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${python}/lib
+    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH''${LD_LIBRARY_PATH:+:}${python}/lib
   '';
 
   postPatch = ''

diff --git a/pkgs/applications/office/gnucash/default.nix b/pkgs/applications/office/gnucash/default.nix
@@ -79,7 +79,7 @@ stdenv.mkDerivation rec {
   #   80 - test-gnc-module-scm-module (Failed)
   #   81 - test-gnc-module-scm-multi (Failed)
   preCheck = ''
-    export LD_LIBRARY_PATH=$PWD/lib:$PWD/lib/gnucash:$PWD/lib/gnucash/test:$LD_LIBRARY_PATH
+    export LD_LIBRARY_PATH=$PWD/lib:$PWD/lib/gnucash:$PWD/lib/gnucash/test''${LD_LIBRARY_PATH:+:}$LD_LIBRARY_PATH
     export NIX_CFLAGS_LINK="-lgtest -lgtest_main"
   '';
   doCheck = false;

diff --git a/pkgs/applications/radio/fldigi/default.nix b/pkgs/applications/radio/fldigi/default.nix
@@ -2,12 +2,12 @@
   libsamplerate, libpulseaudio, libXinerama, gettext, pkgconfig, alsaLib }:
 
 stdenv.mkDerivation rec {
-  version = "4.1.08";
+  version = "4.1.08.51";
   pname = "fldigi";
 
   src = fetchurl {
     url = "mirror://sourceforge/${pname}/${pname}-${version}.tar.gz";
-    sha256 = "0jbk03w0wfvd9lxh1wdazim9gwxm1lkhc5xzi3h8ag7h9zx58jq0";
+    sha256 = "0wki9d19q8rkjxcd3dz3k0a395gmbnji4fxlhw6dpcyqpfw88fcs";
   };
 
   buildInputs = [ libXinerama gettext hamlib fltk13 libjpeg libpng portaudio

diff --git a/pkgs/applications/science/math/pcalc/default.nix b/pkgs/applications/science/math/pcalc/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchgit, bison2, flex }:
+{ stdenv, fetchgit, bison, flex }:
 
 with stdenv.lib;
 
@@ -13,7 +13,7 @@ stdenv.mkDerivation rec {
   };
 
   makeFlags = [ "DESTDIR= BINDIR=$(out)/bin" ];
-  buildInputs = [ bison2 flex ];
+  buildInputs = [ bison flex ];
 
   meta = {
     homepage = http://pcalc.sourceforge.net/;

diff --git a/pkgs/applications/science/math/sage/sage-env.nix b/pkgs/applications/science/math/sage/sage-env.nix
@@ -177,7 +177,7 @@ writeTextFile rec {
     export SAGE_EXTCODE='${sagelib.src}/src/ext'
 
   # for find_library
-    export DYLD_LIBRARY_PATH="${lib.makeLibraryPath [stdenv.cc.libc singular]}:$DYLD_LIBRARY_PATH"
+    export DYLD_LIBRARY_PATH="${lib.makeLibraryPath [stdenv.cc.libc singular]}''${DYLD_LIBRARY_PATH:+:}$DYLD_LIBRARY_PATH"
   '';
 } // {
   lib = sagelib; # equivalent of `passthru`, which `writeTextFile` doesn't support

diff --git a/pkgs/applications/version-management/git-and-tools/git/default.nix b/pkgs/applications/version-management/git-and-tools/git/default.nix
@@ -21,7 +21,7 @@ assert sendEmailSupport -> perlSupport;
 assert svnSupport -> perlSupport;
 
 let
-  version = "2.24.1";
+  version = "2.25.0";
   svn = subversionClient.override { perlBindings = perlSupport; };
 
   gitwebPerlLibs = with perlPackages; [ CGI HTMLParser CGIFast FCGI FCGIProcManager HTMLTagCloud ];
@@ -33,7 +33,7 @@ stdenv.mkDerivation {
 
   src = fetchurl {
     url = "https://www.kernel.org/pub/software/scm/git/git-${version}.tar.xz";
-    sha256 = "0ql5z31vgl7b785gwrf00m129mg7zi9pa65n12ij3mpxx3f28gvj";
+    sha256 = "1l58v42aazj0x9276gk8r9mwyl9pgp9w99aakz4xfhzv7wd2jq60";
   };
 
   outputs = [ "out" ];

diff --git a/pkgs/applications/video/avidemux/default.nix b/pkgs/applications/video/avidemux/default.nix
@@ -66,7 +66,7 @@ stdenv.mkDerivation rec {
     cd "$sourceRoot"
     patchPhase
 
-    export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:${libXext}/lib"
+    export LD_LIBRARY_PATH="$LD_LIBRARY_PATH''${LD_LIBRARY_PATH:+:}${libXext}/lib"
     ${stdenv.shell} bootStrap.bash \
       --with-core \
       ${if withQT then "--with-qt" else "--without-qt"} \

diff --git a/pkgs/build-support/build-fhs-userenv/env.nix b/pkgs/build-support/build-fhs-userenv/env.nix
@@ -52,7 +52,7 @@ let
   etcProfile = writeText "profile" ''
     export PS1='${name}-chrootenv:\u@\h:\w\$ '
     export LOCALE_ARCHIVE='/usr/lib/locale/locale-archive'
-    export LD_LIBRARY_PATH="/run/opengl-driver/lib:/run/opengl-driver-32/lib:/usr/lib:/usr/lib32:$LD_LIBRARY_PATH"
+    export LD_LIBRARY_PATH="/run/opengl-driver/lib:/run/opengl-driver-32/lib:/usr/lib:/usr/lib32''${LD_LIBRARY_PATH:+:}$LD_LIBRARY_PATH"
     export PATH="/run/wrappers/bin:/usr/bin:/usr/sbin:$PATH"
     export TZDIR='/etc/zoneinfo'
 

diff --git a/pkgs/build-support/setup-hooks/make-symlinks-relative.sh b/pkgs/build-support/setup-hooks/make-symlinks-relative.sh
@@ -0,0 +1,28 @@
+fixupOutputHooks+=(_makeSymlinksRelative)
+
+# For every symlink in $output that refers to another file in $output
+# ensure that the symlink is relative. This removes references to the output
+# has from the resulting store paths and thus the NAR files.
+_makeSymlinksRelative() {
+    local symlinkTarget
+
+    if [ -n "${dontRewriteSymlinks-}" ]; then
+        return 0
+    fi
+
+    while IFS= read -r -d $'\0' f; do
+        symlinkTarget=$(readlink "$f")
+        if [[ "$symlinkTarget"/ != "$prefix"/* ]]; then
+            # skip this symlink as it doesn't point to $prefix
+            continue
+        fi
+
+        if [ ! -e "$symlinkTarget" ]; then
+            echo "the symlink $f is broken, it points to $symlinkTarget (which is missing)"
+        fi
+
+        echo "rewriting symlink $f to be relative to $prefix"
+        ln -snrf "$symlinkTarget" "$f"
+
+    done < <(find $prefix -type l -print0)
+}
diff --git a/pkgs/desktops/deepin/dde-file-manager/default.nix b/pkgs/desktops/deepin/dde-file-manager/default.nix
@@ -228,8 +228,8 @@ mkDerivation rec {
   ];
 
   preBuild = ''
-    export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:${zlib}/lib";
-    export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:${libX11}/lib";
+    export LD_LIBRARY_PATH="$LD_LIBRARY_PATH''${LD_LIBRARY_PATH:+:}${zlib}/lib";
+    export LD_LIBRARY_PATH="$LD_LIBRARY_PATH''${LD_LIBRARY_PATH:+:}${libX11}/lib";
   '';
 
   dontWrapQtApps = true;

diff --git a/pkgs/desktops/enlightenment/efl.nix b/pkgs/desktops/enlightenment/efl.nix
@@ -123,7 +123,7 @@ stdenv.mkDerivation rec {
 
   preConfigure = ''
     # allow ecore_con to find libcurl.so, which is a runtime dependency (it is dlopened)
-    export LD_LIBRARY_PATH="${curl.out}/lib:$LD_LIBRARY_PATH"
+    export LD_LIBRARY_PATH="${curl.out}/lib''${LD_LIBRARY_PATH:+:}$LD_LIBRARY_PATH"
 
     source "$setupHook"
   '';

diff --git a/pkgs/desktops/gnome-2/platform/libgnomeprint/default.nix b/pkgs/desktops/gnome-2/platform/libgnomeprint/default.nix
@@ -1,5 +1,5 @@
-{ stdenv, fetchurl, pkgconfig, gtk2, gettext, libxml2, intltool, libart_lgpl
-, libgnomecups, bison2, flex }:
+{ stdenv, fetchurl, fetchpatch, pkgconfig, gtk2, gettext, libxml2, intltool, libart_lgpl
+, libgnomecups, bison, flex }:
 
 stdenv.mkDerivation rec {
   name = "libgnomeprint-2.18.8";
@@ -9,10 +9,17 @@ stdenv.mkDerivation rec {
     sha256 = "1034ec8651051f84d2424e7a1da61c530422cc20ce5b2d9e107e1e46778d9691";
   };
 
-  patches = [ ./bug653388.patch ];
+  patches = [
+    ./bug653388.patch
+    # Fix compatibility with bison 3
+    (fetchpatch {
+      url = "https://github.com/pld-linux/libgnomeprint/raw/54c0f9c3675b86c53f6d77a5bc526ce9ef0e38cd/bison3.patch";
+      sha256 = "1sp04jbv34i1gcwf377hhmwdsmqzig70dd06rjz1isb6zwh4y01l";
+    })
+  ];
 
   nativeBuildInputs = [ pkgconfig ];
-  buildInputs = [ gtk2 gettext intltool libart_lgpl libgnomecups bison2 flex ];
+  buildInputs = [ gtk2 gettext intltool libart_lgpl libgnomecups bison flex ];
 
   propagatedBuildInputs = [ libxml2 ];
 

diff --git a/pkgs/desktops/gnome-3/core/evolution-data-server/default.nix b/pkgs/desktops/gnome-3/core/evolution-data-server/default.nix
@@ -6,13 +6,13 @@
 
 stdenv.mkDerivation rec {
   pname = "evolution-data-server";
-  version = "3.34.2";
+  version = "3.34.3";
 
   outputs = [ "out" "dev" ];
 
   src = fetchurl {
     url = "mirror://gnome/sources/evolution-data-server/${stdenv.lib.versions.majorMinor version}/${pname}-${version}.tar.xz";
-    sha256 = "16z85y6hhazcrp5ngw47w4x9r0j8zrj7awv5im58hhp0xs19zf1y";
+    sha256 = "1af3f218i5h3df81xkjdij0n9knsw355fsmhzdrfh1bflxfarpyj";
   };
 
   patches = [

diff --git a/pkgs/development/compilers/halide/default.nix b/pkgs/development/compilers/halide/default.nix
@@ -29,7 +29,7 @@ in llvmPackages.stdenv.mkDerivation {
   # To handle the lack of 'local' RPATH; required, as they call one of
   # their built binaries requiring their libs, in the build process.
   preBuild = ''
-    export LD_LIBRARY_PATH="$(pwd)/lib:$LD_LIBRARY_PATH"
+    export LD_LIBRARY_PATH="$(pwd)/lib''${LD_LIBRARY_PATH:+:}$LD_LIBRARY_PATH"
   '';
 
   enableParallelBuilding = true;

diff --git a/pkgs/development/compilers/llvm/4/clang/default.nix b/pkgs/development/compilers/llvm/4/clang/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetch, cmake, libxml2, llvm, version, release_version, clang-tools-extra_src, python
+{ stdenv, fetch, cmake, libxml2, llvm, version, release_version, clang-tools-extra_src, python3
 , fixDarwinDylibNames
 , enableManpages ? false
 }:
@@ -19,8 +19,8 @@ let
       mv clang-tools-extra-* $sourceRoot/tools/extra
     '';
 
-    nativeBuildInputs = [ cmake python ]
-      ++ stdenv.lib.optional enableManpages python.pkgs.sphinx;
+    nativeBuildInputs = [ cmake python3 ]
+      ++ stdenv.lib.optional enableManpages python3.pkgs.sphinx;
 
     buildInputs = [ libxml2 llvm ]
       ++ stdenv.lib.optional stdenv.isDarwin fixDarwinDylibNames;

diff --git a/pkgs/development/compilers/llvm/4/default.nix b/pkgs/development/compilers/llvm/4/default.nix
@@ -1,5 +1,5 @@
 { lowPrio, newScope, pkgs, stdenv, cmake, libstdcxxHook
-, libxml2, python, isl, fetchurl, overrideCC, wrapCCWith
+, libxml2, python3, isl, fetchurl, overrideCC, wrapCCWith
 , buildLlvmTools # tools, but from the previous stage, for cross
 , targetLlvmLibraries # libraries, but from the next stage, for cross
 }:
@@ -17,7 +17,7 @@ let
   clang-tools-extra_src = fetch "clang-tools-extra" "1dhmp7ccfpr42bmvk3kp37ngjpf3a9m5d4kkpsn7d00hzi7fdl9m";
 
   tools = stdenv.lib.makeExtensible (tools: let
-    callPackage = newScope (tools // { inherit stdenv cmake libxml2 python isl release_version version fetch; });
+    callPackage = newScope (tools // { inherit stdenv cmake libxml2 python3 isl release_version version fetch; });
   in {
 
     llvm = callPackage ./llvm.nix {
@@ -29,12 +29,12 @@ let
 
     llvm-manpages = lowPrio (tools.llvm.override {
       enableManpages = true;
-      python = pkgs.python;  # don't use python-boot
+      python3 = pkgs.python3;  # don't use python-boot
     });
 
     clang-manpages = lowPrio (tools.clang-unwrapped.override {
       enableManpages = true;
-      python = pkgs.python;  # don't use python-boot
+      python3 = pkgs.python3;  # don't use python-boot
     });
 
     libclang = tools.clang-unwrapped.lib;
@@ -57,7 +57,7 @@ let
   });
 
   libraries = stdenv.lib.makeExtensible (libraries: let
-    callPackage = newScope (libraries // buildLlvmTools // { inherit stdenv cmake libxml2 python isl release_version version fetch; });
+    callPackage = newScope (libraries // buildLlvmTools // { inherit stdenv cmake libxml2 python3 isl release_version version fetch; });
   in {
 
     stdenv = overrideCC stdenv buildLlvmTools.clang;

diff --git a/pkgs/development/compilers/llvm/4/libc++/default.nix b/pkgs/development/compilers/llvm/4/libc++/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetch, cmake, python, libcxxabi, fixDarwinDylibNames, version }:
+{ lib, stdenv, fetch, cmake, python3, libcxxabi, fixDarwinDylibNames, version }:
 
 stdenv.mkDerivation {
   pname = "libc++";
@@ -31,7 +31,7 @@ stdenv.mkDerivation {
   '' + lib.optionalString stdenv.hostPlatform.isMusl ''
     patchShebangs utils/cat_files.py
   '';
-  nativeBuildInputs = [ cmake ] ++ stdenv.lib.optional stdenv.hostPlatform.isMusl python;
+  nativeBuildInputs = [ cmake ] ++ stdenv.lib.optional stdenv.hostPlatform.isMusl python3;
 
   buildInputs = [ libcxxabi ] ++ lib.optional stdenv.isDarwin fixDarwinDylibNames;
 

diff --git a/pkgs/development/compilers/llvm/4/lldb.nix b/pkgs/development/compilers/llvm/4/lldb.nix
@@ -9,7 +9,7 @@
 , libxml2
 , llvm
 , clang-unwrapped
-, python
+, python3
 , version
 , darwin
 }:
@@ -31,7 +31,7 @@ stdenv.mkDerivation {
       cmake/modules/LLDBStandalone.cmake
   '';
 
-  nativeBuildInputs = [ cmake python which swig ];
+  nativeBuildInputs = [ cmake python3 which swig ];
   buildInputs = [ ncurses zlib libedit libxml2 llvm ]
     ++ stdenv.lib.optionals stdenv.isDarwin [ darwin.libobjc darwin.apple_sdk.libs.xpc darwin.apple_sdk.frameworks.Foundation darwin.bootstrap_cmds darwin.apple_sdk.frameworks.Carbon darwin.apple_sdk.frameworks.Cocoa ];
 

diff --git a/pkgs/development/compilers/llvm/4/llvm.nix b/pkgs/development/compilers/llvm/4/llvm.nix
@@ -2,7 +2,7 @@
 , fetch
 , fetchpatch
 , cmake
-, python
+, python3
 , libffi
 , libbfd
 , libxml2
@@ -40,8 +40,8 @@ stdenv.mkDerivation ({
   outputs = [ "out" ]
     ++ stdenv.lib.optional enableSharedLibraries "lib";
 
-  nativeBuildInputs = [ cmake python ]
-    ++ stdenv.lib.optional enableManpages python.pkgs.sphinx;
+  nativeBuildInputs = [ cmake python3 ]
+    ++ stdenv.lib.optional enableManpages python3.pkgs.sphinx;
 
   buildInputs = [ libxml2 libffi ];
 
@@ -143,7 +143,7 @@ stdenv.mkDerivation ({
   '';
 
   preCheck = ''
-    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$PWD/lib
+    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH''${LD_LIBRARY_PATH:+:}$PWD/lib
   '';
 
   postInstall = stdenv.lib.optionalString enableSharedLibraries ''

diff --git a/pkgs/development/compilers/llvm/5/clang/default.nix b/pkgs/development/compilers/llvm/5/clang/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetch, cmake, libxml2, llvm, version, clang-tools-extra_src, python
+{ stdenv, fetch, cmake, libxml2, llvm, version, clang-tools-extra_src, python3
 , fixDarwinDylibNames
 , enableManpages ? false
 }:
@@ -19,8 +19,8 @@ let
       mv clang-tools-extra-* $sourceRoot/tools/extra
     '';
 
-    nativeBuildInputs = [ cmake python ]
-      ++ stdenv.lib.optional enableManpages python.pkgs.sphinx;
+    nativeBuildInputs = [ cmake python3 ]
+      ++ stdenv.lib.optional enableManpages python3.pkgs.sphinx;
 
     buildInputs = [ libxml2 llvm ]
       ++ stdenv.lib.optional stdenv.isDarwin fixDarwinDylibNames;

diff --git a/pkgs/development/compilers/llvm/5/compiler-rt.nix b/pkgs/development/compilers/llvm/5/compiler-rt.nix
@@ -1,11 +1,11 @@
-{ stdenv, version, fetch, cmake, python, llvm, libcxxabi }:
+{ stdenv, version, fetch, cmake, python3, llvm, libcxxabi }:
 with stdenv.lib;
 stdenv.mkDerivation {
   pname = "compiler-rt";
   inherit version;
   src = fetch "compiler-rt" "0ipd4jdxpczgr2w6lzrabymz6dhzj69ywmyybjjc1q397zgrvziy";
 
-  nativeBuildInputs = [ cmake python llvm ];
+  nativeBuildInputs = [ cmake python3 llvm ];
   buildInputs = stdenv.lib.optional stdenv.hostPlatform.isDarwin libcxxabi;
 
   configureFlags = [