Revert "Introduce patchShebangsPhase ran in preConfigurePhases"

This reverts commit 512fbb280f72980e84230b72b631258df1755919.

See #5368

33 files changed, 72 insertions, 4 deletions

diff --git a/pkgs/development/compilers/go/1.1-darwin.nix b/pkgs/development/compilers/go/1.1-darwin.nix
index 411c3e029a6..5b17f56ac37 100644
--- a/pkgs/development/compilers/go/1.1-darwin.nix
+++ b/pkgs/development/compilers/go/1.1-darwin.nix
@@ -22,6 +22,7 @@ stdenv.mkDerivation {
     fi
     cd go
 
+    patchShebangs ./ # replace /bin/bash
     rm src/pkg/net/{multicast_test.go,parse_test.go,port_test.go}
     # The os test wants to read files in an existing path. Just it don't be /usr/bin.
     sed -i 's,/usr/bin,'"`pwd`", src/pkg/os/os_test.go
diff --git a/pkgs/development/compilers/go/1.1.nix b/pkgs/development/compilers/go/1.1.nix
index 1a6bfcad399..11640f2393d 100644
--- a/pkgs/development/compilers/go/1.1.nix
+++ b/pkgs/development/compilers/go/1.1.nix
@@ -33,6 +33,7 @@ stdenv.mkDerivation {
     fi
     cd go
 
+    patchShebangs ./ # replace /bin/bash
     # !!! substituteInPlace does not seems to be effective.
     sed -i 's,/lib/ld-linux.so.2,${loader386},' src/cmd/8l/asm.c
     sed -i 's,/lib64/ld-linux-x86-64.so.2,${loaderAmd64},' src/cmd/6l/asm.c
diff --git a/pkgs/development/compilers/go/1.2.nix b/pkgs/development/compilers/go/1.2.nix
index c091312c2a9..a00fe734670 100644
--- a/pkgs/development/compilers/go/1.2.nix
+++ b/pkgs/development/compilers/go/1.2.nix
@@ -32,6 +32,7 @@ stdenv.mkDerivation {
     fi
     cd go
 
+    patchShebangs ./ # replace /bin/bash
     # !!! substituteInPlace does not seems to be effective.
     sed -i 's,/lib/ld-linux.so.2,${loader386},' src/cmd/8l/asm.c
     sed -i 's,/lib64/ld-linux-x86-64.so.2,${loaderAmd64},' src/cmd/6l/asm.c
diff --git a/pkgs/development/compilers/go/default.nix b/pkgs/development/compilers/go/default.nix
index 8756aaa6629..b35159c10e7 100644
--- a/pkgs/development/compilers/go/default.nix
+++ b/pkgs/development/compilers/go/default.nix
@@ -30,6 +30,7 @@ stdenv.mkDerivation {
     fi
     cd go
 
+    patchShebangs ./ # replace /bin/bash
     # !!! substituteInPlace does not seems to be effective.
     sed -i 's,/lib/ld-linux.so.2,${loader386},' src/cmd/8l/asm.c
     sed -i 's,/lib64/ld-linux-x86-64.so.2,${loaderAmd64},' src/cmd/6l/asm.c
diff --git a/pkgs/development/compilers/julia/0.3.3.nix b/pkgs/development/compilers/julia/0.3.3.nix
index 89297995c4e..a8ad9d00aec 100644
--- a/pkgs/development/compilers/julia/0.3.3.nix
+++ b/pkgs/development/compilers/julia/0.3.3.nix
@@ -106,6 +106,8 @@ stdenv.mkDerivation rec {
 
     export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$PWD/usr/lib:$PWD/usr/lib/julia"
 
+    patchShebangs . contrib
+
     export PATH="$PATH:${stdenv.cc.libc}/sbin"
 
     # ldconfig doesn't seem to ever work on NixOS; system-wide ldconfig cache
diff --git a/pkgs/development/compilers/mono/default.nix b/pkgs/development/compilers/mono/default.nix
index c715a684395..e098f48a24c 100644
--- a/pkgs/development/compilers/mono/default.nix
+++ b/pkgs/development/compilers/mono/default.nix
@@ -35,6 +35,7 @@ stdenv.mkDerivation rec {
   # LLVM path to point into the Mono LLVM build, since it's private anyway.
   preBuild = ''
     makeFlagsArray=(INSTALL=`type -tp install`)
+    patchShebangs ./
   '' + stdenv.lib.optionalString withLLVM ''
     substituteInPlace mono/mini/aot-compiler.c --replace "llvm_path = g_strdup (\"\")" "llvm_path = g_strdup (\"${llvm}/bin/\")"
   '';
diff --git a/pkgs/development/compilers/opa/default.nix b/pkgs/development/compilers/opa/default.nix
index f60b9029632..f0b503bd0be 100644
--- a/pkgs/development/compilers/opa/default.nix
+++ b/pkgs/development/compilers/opa/default.nix
@@ -19,6 +19,7 @@ stdenv.mkDerivation rec {
   codeGeneratorPaths = "${ocamlPackages.ocaml}/bin:${gcc}/bin:${binutils}/bin:${gnumake}/bin:${nodejs}/bin";
 
   preConfigure = ''
+    patchShebangs .
     (
     cat ./compiler/buildinfos/buildInfos.ml.pre
     ./compiler/buildinfos/generate_buildinfos.sh . --release --version ./compiler/buildinfos/version_major.txt 
diff --git a/pkgs/development/libraries/agda/agda-iowa-stdlib/default.nix b/pkgs/development/libraries/agda/agda-iowa-stdlib/default.nix
index 446bfdf9ca7..2c76c2f4350 100644
--- a/pkgs/development/libraries/agda/agda-iowa-stdlib/default.nix
+++ b/pkgs/development/libraries/agda/agda-iowa-stdlib/default.nix
@@ -12,6 +12,7 @@ agda.mkDerivation (self: rec {
 
   sourceDirectories = [ "./." ];
   buildPhase = ''
+    patchShebangs find-deps.sh
     make
   '';
 
diff --git a/pkgs/development/libraries/dbus/default.nix b/pkgs/development/libraries/dbus/default.nix
index 145462b38d0..d332321a22a 100644
--- a/pkgs/development/libraries/dbus/default.nix
+++ b/pkgs/development/libraries/dbus/default.nix
@@ -47,6 +47,7 @@ let
     buildInputs = [ autoconf automake libtool ]; # ToDo: optional selinux?
 
     preConfigure = ''
+      patchShebangs .
       substituteInPlace tools/Makefile.am --replace 'install-localstatelibDATA:' 'disabled:'
       autoreconf -fi
     '';
diff --git a/pkgs/development/libraries/folly/default.nix b/pkgs/development/libraries/folly/default.nix
index dced097a05a..66d4f73096b 100644
--- a/pkgs/development/libraries/folly/default.nix
+++ b/pkgs/development/libraries/folly/default.nix
@@ -17,6 +17,9 @@ stdenv.mkDerivation rec {
   nativeBuildInputs = [ autoreconfHook python boost ];
 
   postUnpack = "sourceRoot=\${sourceRoot}/folly";
+  preBuild = ''
+    patchShebangs build
+  '';
 
   configureFlags = [ "--with-boost-libdir=${boost.lib}/lib" ];
 
diff --git a/pkgs/development/libraries/hspell/default.nix b/pkgs/development/libraries/hspell/default.nix
index 9cd071f6cbe..9b44d12c293 100644
--- a/pkgs/development/libraries/hspell/default.nix
+++ b/pkgs/development/libraries/hspell/default.nix
@@ -13,6 +13,7 @@ stdenv.mkDerivation rec {
     sha256 = "08x7rigq5pa1pfpl30qp353hbdkpadr1zc49slpczhsn0sg36pd6";
   };
 
+  patchPhase = ''patchShebangs .'';
   buildInputs = [ perl zlib ];
 
   makeFlags = "CFLAGS=-fPIC";
diff --git a/pkgs/development/libraries/ibus/default.nix b/pkgs/development/libraries/ibus/default.nix
index ef794b45279..6b426169a70 100644
--- a/pkgs/development/libraries/ibus/default.nix
+++ b/pkgs/development/libraries/ibus/default.nix
@@ -20,6 +20,7 @@ stdenv.mkDerivation rec {
   ];
 
   preBuild = ''
+    patchShebangs ./scripts
     substituteInPlace data/dconf/Makefile --replace "dconf update" "echo"
   '';
 
diff --git a/pkgs/development/libraries/libcouchbase/default.nix b/pkgs/development/libraries/libcouchbase/default.nix
index 3e125121579..841edd3dff6 100644
--- a/pkgs/development/libraries/libcouchbase/default.nix
+++ b/pkgs/development/libraries/libcouchbase/default.nix
@@ -11,6 +11,7 @@ stdenv.mkDerivation {
   };
 
   preConfigure = ''
+    patchShebangs ./config/
     ./config/autorun.sh
   '';
 
@@ -24,4 +25,4 @@ stdenv.mkDerivation {
     license = stdenv.lib.licenses.asl20;
     platforms = stdenv.lib.platforms.unix;
   };
-}
+}
\ No newline at end of file
diff --git a/pkgs/development/libraries/libctemplate/default.nix b/pkgs/development/libraries/libctemplate/default.nix
index 578ccffd094..142025c1e51 100644
--- a/pkgs/development/libraries/libctemplate/default.nix
+++ b/pkgs/development/libraries/libctemplate/default.nix
@@ -12,6 +12,10 @@ stdenv.mkDerivation rec {
 
   buildInputs = [ python ];
 
+  postPatch = ''
+    patchShebangs .
+  '';
+
   meta = {
     description = "A simple but powerful template language for C++";
     longDescription = ''
diff --git a/pkgs/development/libraries/libqmi/default.nix b/pkgs/development/libraries/libqmi/default.nix
index 9a934befde9..a0292067dbb 100644
--- a/pkgs/development/libraries/libqmi/default.nix
+++ b/pkgs/development/libraries/libqmi/default.nix
@@ -8,6 +8,10 @@ stdenv.mkDerivation rec {
     sha256 = "03gf221yjcdzvnl4v2adwpc6cyg5mlbccn20s00fp5bgvmq81pgs";
   };
 
+  preBuild = ''
+    patchShebangs .
+  '';
+
   buildInputs = [ pkgconfig glib python ];
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/libraries/libsoup/default.nix b/pkgs/development/libraries/libsoup/default.nix
index 517eed606e6..cd2a15ffc66 100644
--- a/pkgs/development/libraries/libsoup/default.nix
+++ b/pkgs/development/libraries/libsoup/default.nix
@@ -14,6 +14,10 @@ stdenv.mkDerivation {
     sha256 = "ea34dd64fe44343445daf6dd690d0691e9d973468de44878da97371c16d89784";
   };
 
+  patchPhase = ''
+    patchShebangs libsoup/
+  '';
+
   buildInputs = libintlOrEmpty ++ [ intltool python ];
   nativeBuildInputs = [ pkgconfig ];
   propagatedBuildInputs = [ glib libxml2 gobjectIntrospection ]
diff --git a/pkgs/development/libraries/libvirt/default.nix b/pkgs/development/libraries/libvirt/default.nix
index b6b82a12ed6..8bd4866cb21 100644
--- a/pkgs/development/libraries/libvirt/default.nix
+++ b/pkgs/development/libraries/libvirt/default.nix
@@ -25,6 +25,7 @@ stdenv.mkDerivation rec {
 
   preConfigure = ''
     PATH=${iproute}/sbin:${iptables}/sbin:${ebtables}/sbin:${lvm2}/sbin:${udev}/sbin:${dnsmasq}/bin:$PATH
+    patchShebangs . # fixes /usr/bin/python references
   '';
 
   configureFlags = [
diff --git a/pkgs/development/libraries/lirc/default.nix b/pkgs/development/libraries/lirc/default.nix
index 755bb48af1c..278eb8e9e52 100644
--- a/pkgs/development/libraries/lirc/default.nix
+++ b/pkgs/development/libraries/lirc/default.nix
@@ -15,6 +15,8 @@ stdenv.mkDerivation rec {
     })
   ];
 
+  preBuild = "patchShebangs .";
+
   buildInputs = [ alsaLib help2man ];
 
   configureFlags = [
diff --git a/pkgs/development/libraries/mesa-darwin/default.nix b/pkgs/development/libraries/mesa-darwin/default.nix
index 0b0cf5f2822..f259a397c84 100644
--- a/pkgs/development/libraries/mesa-darwin/default.nix
+++ b/pkgs/development/libraries/mesa-darwin/default.nix
@@ -41,6 +41,8 @@ let
       ./patches/patch-src-mapi-vgapi-Makefile.diff
     ];
 
+    postPatch = "patchShebangs .";
+
     configurePhase = ":";
 
     makeFlags = "INSTALL_DIR=\${out} CC=cc CXX=c++";
diff --git a/pkgs/development/libraries/mesa/default.nix b/pkgs/development/libraries/mesa/default.nix
index 4db3b003f2f..a3b40eb612c 100644
--- a/pkgs/development/libraries/mesa/default.nix
+++ b/pkgs/development/libraries/mesa/default.nix
@@ -38,6 +38,7 @@ stdenv.mkDerivation {
     sha256 = "f6031f8b7113a92325b60635c504c510490eebb2e707119bbff7bd86aa34657d";
   };
 
+  prePatch = "patchShebangs .";
 
   patches = [
     ./static-gallium.patch
diff --git a/pkgs/development/libraries/polkit/default.nix b/pkgs/development/libraries/polkit/default.nix
index 6a0cc50c412..7fe16cec56b 100644
--- a/pkgs/development/libraries/polkit/default.nix
+++ b/pkgs/development/libraries/polkit/default.nix
@@ -35,7 +35,9 @@ stdenv.mkDerivation rec {
     ( map (var: ''-DPACKAGE_${var}_DIR=\""${builtins.getAttr var foolVars}"\"'')
         (builtins.attrNames foolVars) );
 
-  preConfigure = stdenv.lib.optionalString useSystemd /* bogus chroot detection */ ''
+  preConfigure = ''
+    patchShebangs .
+  '' + stdenv.lib.optionalString useSystemd /* bogus chroot detection */ ''
     sed '/libsystemd-login autoconfigured, but system does not appear to use systemd/s/.*/:/' -i configure
   ''
     # ‘libpolkit-agent-1.so’ should call the setuid wrapper on
diff --git a/pkgs/development/libraries/qpdf/default.nix b/pkgs/development/libraries/qpdf/default.nix
index 2f481503670..63ba58f2343 100644
--- a/pkgs/development/libraries/qpdf/default.nix
+++ b/pkgs/development/libraries/qpdf/default.nix
@@ -15,9 +15,11 @@ stdenv.mkDerivation rec {
   buildInputs = [ pcre zlib ];
 
   postPatch = ''
+    patchShebangs qpdf/fix-qdf
   '';
 
   preCheck = ''
+    patchShebangs qtest/bin/qtest-driver
   '';
 
   doCheck = true;
diff --git a/pkgs/development/libraries/sword/default.nix b/pkgs/development/libraries/sword/default.nix
index a91474d054c..6faf2224b0c 100644
--- a/pkgs/development/libraries/sword/default.nix
+++ b/pkgs/development/libraries/sword/default.nix
@@ -13,6 +13,10 @@ stdenv.mkDerivation rec {
 
   buildInputs = [ pkgconfig icu clucene_core curl ];
 
+  prePatch = ''
+    patchShebangs .;
+  '';
+
   configureFlags = "--without-conf --enable-tests=no CXXFLAGS=-Wno-unused-but-set-variable";
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/libraries/webkitgtk/2.4.6.nix b/pkgs/development/libraries/webkitgtk/2.4.6.nix
index bb8e95fb1ec..a2344f71f88 100644
--- a/pkgs/development/libraries/webkitgtk/2.4.6.nix
+++ b/pkgs/development/libraries/webkitgtk/2.4.6.nix
@@ -28,6 +28,10 @@ stdenv.mkDerivation rec {
 
   CC = "cc";
 
+  prePatch = ''
+    patchShebangs Tools/gtk
+  '';
+
   configureFlags = with stdenv.lib; [
     "--disable-geolocation"
     (optionalString enableIntrospection "--enable-introspection")
diff --git a/pkgs/development/libraries/webkitgtk/default.nix b/pkgs/development/libraries/webkitgtk/default.nix
index 08576c2ebc3..3cbf3698732 100644
--- a/pkgs/development/libraries/webkitgtk/default.nix
+++ b/pkgs/development/libraries/webkitgtk/default.nix
@@ -17,6 +17,8 @@ stdenv.mkDerivation rec {
     maintainers = with maintainers; [ iyzsong koral ];
   };
 
+  preConfigure = "patchShebangs Tools";
+
   src = fetchurl {
     url = "http://webkitgtk.org/releases/${name}.tar.xz";
     sha256 = "1f9qm5g1mbjm2hrnlzymas99piws4h4y3yxz4p6f6gavnsvfjwji";
diff --git a/pkgs/development/libraries/zeitgeist/default.nix b/pkgs/development/libraries/zeitgeist/default.nix
index ecdcd7804e5..d0de624890b 100644
--- a/pkgs/development/libraries/zeitgeist/default.nix
+++ b/pkgs/development/libraries/zeitgeist/default.nix
@@ -21,6 +21,8 @@ stdenv.mkDerivation rec {
                   libtool python dbus_libs telepathy_glib vala dbus_glib
                   gtk3 json_glib librdf_raptor2 pythonPackages.rdflib ];
 
+  prePatch = "patchShebangs .";
+
   patches = [ ./dbus_glib.patch ];
 
   patchFlags = [ "-p0" ];
diff --git a/pkgs/development/ocaml-modules/javalib/default.nix b/pkgs/development/ocaml-modules/javalib/default.nix
index 960824731f6..7272e668aa2 100644
--- a/pkgs/development/ocaml-modules/javalib/default.nix
+++ b/pkgs/development/ocaml-modules/javalib/default.nix
@@ -20,6 +20,8 @@ stdenv.mkDerivation rec {
 
   createFindlibDestdir = true;
 
+  preConfigure = "patchShebangs ./configure.sh";
+
   configureScript = "./configure.sh";
   dontAddPrefix = "true";
 
diff --git a/pkgs/development/ocaml-modules/sawja/default.nix b/pkgs/development/ocaml-modules/sawja/default.nix
index 2ee035aadb6..534a7684cec 100644
--- a/pkgs/development/ocaml-modules/sawja/default.nix
+++ b/pkgs/development/ocaml-modules/sawja/default.nix
@@ -22,6 +22,8 @@ stdenv.mkDerivation rec {
 
   createFindlibDestdir = true;
 
+  preConfigure = "patchShebangs ./configure.sh";
+
   configureScript = "./configure.sh";
   dontAddPrefix = "true";
 
diff --git a/pkgs/development/python-modules/dbus/default.nix b/pkgs/development/python-modules/dbus/default.nix
index 9a6e25d13a4..bc386e7e5ac 100644
--- a/pkgs/development/python-modules/dbus/default.nix
+++ b/pkgs/development/python-modules/dbus/default.nix
@@ -8,6 +8,8 @@ if isPyPy then throw "dbus-python not supported for interpreter ${python.executa
     sha256 = "1py62qir966lvdkngg0v8k1khsqxwk5m4s8nflpk1agk5f5nqb71";
   };
 
+  postPatch = "patchShebangs .";
+
   buildInputs = [ python pkgconfig dbus dbus_glib ]
     ++ stdenv.lib.optional doCheck dbus_tools;
 
diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 46bed164fef..1ec48bcc06f 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -916,6 +916,14 @@ let
   ];
 
   otherOverrides = old: new: {
+    RcppArmadillo = old.RcppArmadillo.overrideDerivation (attrs: {
+      patchPhase = "patchShebangs configure";
+    });
+
+    rpf = old.rpf.overrideDerivation (attrs: {
+      patchPhase = "patchShebangs configure";
+    });
+
     BayesXsrc = old.BayesXsrc.overrideDerivation (attrs: {
       patches = [ ./patches/BayesXsrc.patch ];
     });
diff --git a/pkgs/development/tools/build-managers/icmake/default.nix b/pkgs/development/tools/build-managers/icmake/default.nix
index 929e68ed4e0..a32ea9a3add 100644
--- a/pkgs/development/tools/build-managers/icmake/default.nix
+++ b/pkgs/development/tools/build-managers/icmake/default.nix
@@ -10,6 +10,7 @@ stdenv.mkDerivation rec {
   };
 
   preConfigure = ''
+    patchShebangs ./
     sed -i "s;usr/;;g" INSTALL.im
   '';
 
@@ -24,4 +25,4 @@ stdenv.mkDerivation rec {
     maintainers = with maintainers; [ pSub ];
     platforms = platforms.linux;
   };
-}
+}
\ No newline at end of file
diff --git a/pkgs/development/tools/documentation/doxygen/default.nix b/pkgs/development/tools/documentation/doxygen/default.nix
index 65ae4b61b4f..50f2037b271 100644
--- a/pkgs/development/tools/documentation/doxygen/default.nix
+++ b/pkgs/development/tools/documentation/doxygen/default.nix
@@ -24,7 +24,9 @@ stdenv.mkDerivation {
     ++ stdenv.lib.optional (qt4 != null) "--with-doxywizard";
 
   preConfigure =
-    stdenv.lib.optionalString (qt4 != null)
+    ''
+      patchShebangs .
+    '' + stdenv.lib.optionalString (qt4 != null)
     ''
       echo "using QTDIR=${qt4}..."
       export QTDIR=${qt4}
diff --git a/pkgs/development/tools/misc/yodl/default.nix b/pkgs/development/tools/misc/yodl/default.nix
index f16c961f4cf..691974353e1 100644
--- a/pkgs/development/tools/misc/yodl/default.nix
+++ b/pkgs/development/tools/misc/yodl/default.nix
@@ -12,6 +12,7 @@ stdenv.mkDerivation rec {
   };
 
   preConfigure = ''
+    patchShebangs scripts/.
     sed -i 's;/usr;;g' INSTALL.im
     substituteInPlace build --replace /usr/bin/icmake ${icmake}/bin/icmake
     substituteInPlace macros/rawmacros/startdoc.pl --replace /usr/bin/perl ${perl}/bin/perl