Merge branch 'nixos-unstable' of https://github.com/NixOS/nixpkgs

Conflicts:
	nixpkgs/nixos/modules/config/console.nix
	nixpkgs/nixos/modules/services/mail/mailman.nix
	nixpkgs/nixos/modules/services/mail/public-inbox.nix
	nixpkgs/nixos/modules/services/mail/rss2email.nix
	nixpkgs/nixos/modules/services/networking/ssh/sshd.nix
	nixpkgs/pkgs/applications/networking/instant-messengers/dino/default.nix
	nixpkgs/pkgs/applications/networking/irc/weechat/default.nix
	nixpkgs/pkgs/applications/window-managers/sway/default.nix
	nixpkgs/pkgs/build-support/go/module.nix
	nixpkgs/pkgs/build-support/rust/build-rust-package/default.nix
	nixpkgs/pkgs/development/interpreters/python/default.nix
	nixpkgs/pkgs/development/node-packages/overrides.nix
	nixpkgs/pkgs/development/tools/b4/default.nix
	nixpkgs/pkgs/servers/dict/dictd-db.nix
	nixpkgs/pkgs/servers/mail/public-inbox/default.nix
	nixpkgs/pkgs/tools/security/pinentry/default.nix
	nixpkgs/pkgs/tools/text/unoconv/default.nix
	nixpkgs/pkgs/top-level/all-packages.nix

1 files changed, 15 insertions, 3 deletions

diff --git a/nixpkgs/pkgs/applications/science/biology/bedops/default.nix b/nixpkgs/pkgs/applications/science/biology/bedops/default.nix
index bde774c622bd..d455e98264cc 100644
--- a/nixpkgs/pkgs/applications/science/biology/bedops/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/bedops/default.nix
@@ -18,7 +18,20 @@ stdenv.mkDerivation rec {
     # We use nixpkgs versions of these libraries
     rm -r third-party
     sed -i '/^LIBS/d' system.mk/*
-    sed -i 's|^LIBRARIES.*$|LIBRARIES = -lbz2 -lz -ljansson|' */*/*/*/Makefile
+    sed -i 's|^LIBRARIES.*$|LIBRARIES = -lbz2 -lz -ljansson|' */*/*/*/Makefile*
+
+    # `make support` installs above libraries
+    substituteInPlace system.mk/* \
+      --replace ": support" ":"
+
+    # Variable name is different in this makefile
+    substituteInPlace applications/bed/sort-bed/src/Makefile.darwin \
+      --replace "DIST_DIR" "BINDIR"
+
+    # `mkdir -p $BINDIR` is missing
+    substituteInPlace applications/bed/sort-bed/src/Makefile.darwin \
+      --replace 'mkdir -p ''${OBJ_DIR}' 'mkdir -p ''${OBJ_DIR} ''${BINDIR}'
+
     substituteInPlace applications/bed/starch/src/Makefile --replace '$(LIBRARIES)' ""
 
     # Function name is different in nixpkgs provided libraries
@@ -27,7 +40,7 @@ stdenv.mkDerivation rec {
     done
 
     # Don't force static
-    for f in */*/*/*/Makefile ; do
+    for f in */*/*/*/Makefile* ; do
       substituteInPlace $f --replace '-static' ""
     done
   '';
@@ -46,6 +59,5 @@ stdenv.mkDerivation rec {
     license = licenses.gpl2Only;
     maintainers = with maintainers; [ jbedo ];
     platforms = platforms.x86_64;
-    broken = stdenv.isDarwin;
   };
 }