Merge remote-tracking branch 'origin/master' into staging-next

lib/systems/parse.nix

@@ -121,15 +121,20 @@ rec {
     js       = { bits = 32; significantByte = littleEndian; family = "js"; };
   };
 
-  # Determine where two CPUs are compatible with each other. That is,
+  # Determine when two CPUs are compatible with each other. That is,
-  # can we run code built for system b on system a? For that to
+  # can code built for system B run on system A? For that to happen,
-  # happen, then the set of all possible possible programs that system
+  # the programs that system B accepts must be a subset of the
-  # b accepts must be a subset of the set of all programs that system
+  # programs that system A accepts.
-  # a accepts. This compatibility relation forms a category where each
+  #
-  # CPU is an object and each arrow from a to b represents
+  # We have the following properties of the compatibility relation,
-  # compatibility. CPUs with multiple modes of Endianness are
+  # which must be preserved when adding compatibility information for
-  # isomorphic while all CPUs are endomorphic because any program
+  # additional CPUs.
-  # built for a CPU can run on that CPU.
+  # - (reflexivity)
+  #   Every CPU is compatible with itself.
+  # - (transitivity)
+  #   If A is compatible with B and B is compatible with C then A is compatible with C.
+  # - (compatible under multiple endianness)
+  #   CPUs with multiple modes of endianness are pairwise compatible.
   isCompatible = a: b: with cpuTypes; lib.any lib.id [
     # x86
     (b == i386 && isCompatible a i486)

pkgs/applications/graphics/ImageMagick/6.x.nix

@@ -1,7 +1,7 @@
 { lib, stdenv, fetchFromGitHub, pkg-config, libtool
 , bzip2, zlib, libX11, libXext, libXt, fontconfig, freetype, ghostscript, libjpeg, djvulibre
 , lcms2, openexr, libpng, librsvg, libtiff, libxml2, openjpeg, libwebp, fftw, libheif, libde265
-, ApplicationServices
+, ApplicationServices, Foundation
 }:
 
 let
@@ -50,7 +50,8 @@ stdenv.mkDerivation rec {
     ]
     ++ lib.optionals (!stdenv.hostPlatform.isMinGW)
       [ openexr librsvg openjpeg ]
-    ++ lib.optional stdenv.isDarwin ApplicationServices;
+    ++ lib.optionals stdenv.isDarwin
+      [ ApplicationServices Foundation ];
 
   propagatedBuildInputs =
     [ bzip2 freetype libjpeg lcms2 fftw ]

pkgs/applications/networking/cluster/kubernetes/default.nix

@@ -20,13 +20,13 @@
 
 stdenv.mkDerivation rec {
   pname = "kubernetes";
-  version = "1.21.0";
+  version = "1.21.1";
 
   src = fetchFromGitHub {
     owner = "kubernetes";
     repo = "kubernetes";
     rev = "v${version}";
-    sha256 = "sha256-5IUcKVbHxL5qb7M087sZSsd50t5zSaeWATnyLHkVsRU=";
+    sha256 = "sha256-gJjCw28SqU49kIiRH+MZgeYN4VBgKVEaRPr5A/2c5Pc=";
   };
 
   nativeBuildInputs = [ removeReferencesTo makeWrapper which go rsync installShellFiles ];

pkgs/applications/science/biology/cd-hit/default.nix

@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchFromGitHub, makeWrapper, zlib, perl, perlPackages }:
+{ lib, stdenv, fetchFromGitHub, makeWrapper, zlib, perl, perlPackages, openmp }:
 
 stdenv.mkDerivation rec {
   version = "4.8.1";
@@ -14,8 +14,12 @@ stdenv.mkDerivation rec {
   propagatedBuildInputs = [ perl perlPackages.TextNSP perlPackages.PerlMagick ];
 
   nativeBuildInputs = [ zlib makeWrapper ];
+  buildInputs = lib.optional stdenv.cc.isClang openmp;
 
-  makeFlags = [ "PREFIX=$(out)/bin" ];
+  makeFlags = [
+    "CC=${stdenv.cc.targetPrefix}c++" # remove once https://github.com/weizhongli/cdhit/pull/114 is merged
+    "PREFIX=$(out)/bin"
+  ];
 
   preInstall = "mkdir -p $out/bin";
 

pkgs/development/compilers/copper/default.nix

@@ -28,5 +28,6 @@ stdenv.mkDerivation rec {
     homepage = "https://tibleiz.net/copper/";
     license = licenses.bsd2;
     platforms = platforms.x86_64;
+    broken = stdenv.isDarwin;
   };
 }

pkgs/development/interpreters/lua-5/5.4.darwin.patch

@@ -0,0 +1,48 @@
+--- a/Makefile	2021-05-14 22:39:14.407200562 +0300
++++ b/Makefile	2021-05-14 22:36:23.828513407 +0300
+@@ -41,7 +41,7 @@
+ # What to install.
+ TO_BIN= lua luac
+ TO_INC= lua.h luaconf.h lualib.h lauxlib.h lua.hpp
+-TO_LIB= liblua.a
++TO_LIB= liblua.${version}.dylib
+ TO_MAN= lua.1 luac.1
+ 
+ # Lua version and release.
+@@ -60,6 +60,8 @@
+ 	cd src && $(INSTALL_DATA) $(TO_INC) $(INSTALL_INC)
+ 	cd src && $(INSTALL_DATA) $(TO_LIB) $(INSTALL_LIB)
+ 	cd doc && $(INSTALL_DATA) $(TO_MAN) $(INSTALL_MAN)
++	ln -s -f liblua.${version}.dylib $(INSTALL_LIB)/liblua.${luaversion}.dylib
++	ln -s -f liblua.${luaversion}.dylib $(INSTALL_LIB)/liblua.dylib
+ 
+ uninstall:
+ 	cd src && cd $(INSTALL_BIN) && $(RM) $(TO_BIN)
+--- a/src/Makefile	2021-05-14 22:35:38.575051882 +0300
++++ b/src/Makefile	2021-05-14 22:35:33.584631206 +0300
+@@ -32,7 +32,7 @@
+ 
+ PLATS= guess aix bsd c89 freebsd generic linux linux-readline macosx mingw posix solaris
+ 
+-LUA_A=	liblua.a
++LUA_A=	liblua.${version}.dylib
+ CORE_O=	lapi.o lcode.o lctype.o ldebug.o ldo.o ldump.o lfunc.o lgc.o llex.o lmem.o lobject.o lopcodes.o lparser.o lstate.o lstring.o ltable.o ltm.o lundump.o lvm.o lzio.o
+ LIB_O=	lauxlib.o lbaselib.o lcorolib.o ldblib.o liolib.o lmathlib.o loadlib.o loslib.o lstrlib.o ltablib.o lutf8lib.o linit.o
+ BASE_O= $(CORE_O) $(LIB_O) $(MYOBJS)
+@@ -57,11 +57,13 @@
+ a:	$(ALL_A)
+ 
+ $(LUA_A): $(BASE_O)
+-	$(AR) $@ $(BASE_O)
+-	$(RANLIB) $@
++	$(CC) -dynamiclib -install_name $(out)/lib/liblua.${version}.dylib \
++		-compatibility_version ${version} -current_version ${version} \
++		-o liblua.${version}.dylib $^
+ 
+ $(LUA_T): $(LUA_O) $(LUA_A)
+-	$(CC) -o $@ $(LDFLAGS) $(LUA_O) $(LUA_A) $(LIBS)
++	$(CC) -fno-common $(MYLDFLAGS) \
++		-o $@ $(LUA_O) $(LUA_A) -L. -llua.${version} $(LIBS)
+ 
+ $(LUAC_T): $(LUAC_O) $(LUA_A)
+ 	$(CC) -o $@ $(LDFLAGS) $(LUAC_O) $(LUA_A) $(LIBS)

pkgs/development/interpreters/lua-5/default.nix

@@ -5,6 +5,12 @@ rec {
   lua5_4 = callPackage ./interpreter.nix {
     sourceVersion = { major = "5"; minor = "4"; patch = "2"; };
     hash = "0ksj5zpj74n0jkamy3di1p6l10v4gjnd2zjnb453qc6px6bhsmqi";
+
+    patches = if stdenv.isDarwin then [ ./5.4.darwin.patch ] else [
+      # build lua as a shared library as well, MIT-licensed from
+      # https://github.com/archlinux/svntogit-packages/tree/packages/lua/trunk
+      ./liblua.so.patch
+    ];
   };
 
   lua5_4_compat = lua5_4.override({

pkgs/development/tools/ecpdap/default.nix

@@ -1,4 +1,4 @@
-{ lib, fetchFromGitHub, rustPlatform, pkg-config, libusb1 }:
+{ lib, stdenv, fetchFromGitHub, rustPlatform, pkg-config, libusb1, AppKit }:
 
 rustPlatform.buildRustPackage rec {
   pname = "ecpdap";
@@ -15,7 +15,8 @@ rustPlatform.buildRustPackage rec {
 
   nativeBuildInputs = [ pkg-config ];
 
-  buildInputs = [ libusb1 ];
+  buildInputs = [ libusb1 ]
+    ++ lib.optional stdenv.isDarwin AppKit;
 
   postInstall = ''
     mkdir -p $out/etc/udev/rules.d

pkgs/servers/irc/inspircd/default.nix

@@ -142,13 +142,13 @@ in
 
 stdenv.mkDerivation rec {
   pname = "inspircd";
-  version = "3.9.0";
+  version = "3.10.0";
 
   src = fetchFromGitHub {
     owner = pname;
     repo = pname;
     rev = "v${version}";
-    sha256 = "0x3paasf4ynx4ddky2nq613vyirbhfnxzkjq148k7154pz3q426s";
+    sha256 = "1817gmxk4v7k5398d2fb6qkwadg0fd980gqmr80wdnppx450ikn7";
   };
 
   outputs = [ "bin" "lib" "man" "doc" "out" ];
@@ -160,6 +160,8 @@ stdenv.mkDerivation rec {
   buildInputs = extraInputs;
 
   configurePhase = ''
+    runHook preConfigure
+
     patchShebangs configure make/*.pl
 
     # configure is executed twice, once to set the extras
@@ -183,6 +185,8 @@ stdenv.mkDerivation rec {
       --module-dir  ${placeholder "lib"}/lib/inspircd \
       --runtime-dir /var/run \
       --script-dir  ${placeholder "bin"}/share/inspircd \
+
+    runHook postConfigure
   '';
 
   postInstall = ''

pkgs/tools/graphics/dmtx-utils/default.nix

@@ -5,6 +5,7 @@
 , pkg-config
 , libdmtx
 , imagemagick
+, Foundation
 }:
 
 stdenv.mkDerivation rec {
@@ -20,7 +21,8 @@ stdenv.mkDerivation rec {
 
   nativeBuildInputs = [ autoreconfHook pkg-config ];
 
-  buildInputs = [ libdmtx imagemagick ];
+  buildInputs = [ libdmtx imagemagick ]
+    ++ lib.optional stdenv.isDarwin Foundation;
 
   meta = {
     description = "Data matrix command-line utilities";

pkgs/tools/misc/code-minimap/default.nix

@@ -1,6 +1,8 @@
 { lib
+, stdenv
 , rustPlatform
 , fetchFromGitHub
+, libiconv
 }:
 
 rustPlatform.buildRustPackage rec {
@@ -16,6 +18,8 @@ rustPlatform.buildRustPackage rec {
 
   cargoSha256 = "sha256-87aRZC4OE3UTVToHi5XDBxVqEH4oFeFR4REf69OBkIw=";
 
+  buildInputs = lib.optional stdenv.isDarwin libiconv;
+
   meta = with lib; {
     description = "A high performance code minimap render";
     homepage = "https://github.com/wfxr/code-minimap";

pkgs/tools/networking/findomain/default.nix

@@ -4,6 +4,7 @@
 , rustPlatform
 , installShellFiles
 , perl
+, libiconv
 , Security
 }:
 
@@ -21,7 +22,7 @@ rustPlatform.buildRustPackage rec {
   cargoSha256 = "sha256-FDiIM1LlWEFmiIvebdCsznkB7egspNKhY6xUXB838g8=";
 
   nativeBuildInputs = [ installShellFiles perl ];
-  buildInputs = lib.optional stdenv.isDarwin Security;
+  buildInputs = lib.optionals stdenv.isDarwin [ libiconv Security ];
 
   postInstall = ''
     installManPage ${pname}.1

pkgs/top-level/all-packages.nix

@@ -22805,7 +22805,8 @@ in
 
   dmrconfig = callPackage ../applications/radio/dmrconfig { };
 
-  dmtx-utils = callPackage (callPackage ../tools/graphics/dmtx-utils) {
+  dmtx-utils = callPackage ../tools/graphics/dmtx-utils {
+    inherit (darwin.apple_sdk.frameworks) Foundation;
   };
 
   inherit (callPackage ../applications/virtualization/docker {})
@@ -22907,7 +22908,9 @@ in
     jdk = jdk11;
   });
 
-  ecpdap = callPackage ../development/tools/ecpdap { };
+  ecpdap = callPackage ../development/tools/ecpdap {
+    inherit (darwin.apple_sdk.frameworks) AppKit;
+  };
 
   ecs-agent = callPackage ../applications/virtualization/ecs-agent { };
 
@@ -24121,7 +24124,7 @@ in
   };
 
   imagemagick6 = callPackage ../applications/graphics/ImageMagick/6.x.nix {
-    inherit (darwin.apple_sdk.frameworks) ApplicationServices;
+    inherit (darwin.apple_sdk.frameworks) ApplicationServices Foundation;
     ghostscript = null;
   };
 
@@ -28952,7 +28955,9 @@ in
 
   bppsuite = callPackage ../applications/science/biology/bppsuite { };
 
-  cd-hit = callPackage ../applications/science/biology/cd-hit { };
+  cd-hit = callPackage ../applications/science/biology/cd-hit {
+    inherit (llvmPackages) openmp;
+  };
 
   cmtk = callPackage ../applications/science/biology/cmtk { };