rPackages: s/overrideDerivation/overrideAttrs (5110d8b6) · Commits · nix / nixpkgs

pkgs/development/r-modules/default.nix

+74 −69

Original line number	Diff line number	Diff line
		@@ -84,13 +84,13 @@ let
		# results in
		#
		# {
		# foo = old.foo.overrideDerivation (attrs: {
		# foo = old.foo.overrideAttrs (attrs: {
		# nativeBuildInputs = attrs.nativeBuildInputs ++ [ pkgs.bar ];
		# });
		# }
		overrideNativeBuildInputs = overrides: old:
		lib.mapAttrs (name: value:
		(builtins.getAttr name old).overrideDerivation (attrs: {
		(builtins.getAttr name old).overrideAttrs (attrs: {
		nativeBuildInputs = attrs.nativeBuildInputs ++ value;
		})
		) overrides;
		@@ -105,13 +105,13 @@ let
		# results in
		#
		# {
		# foo = old.foo.overrideDerivation (attrs: {
		# foo = old.foo.overrideAttrs (attrs: {
		# buildInputs = attrs.buildInputs ++ [ pkgs.bar ];
		# });
		# }
		overrideBuildInputs = overrides: old:
		lib.mapAttrs (name: value:
		(builtins.getAttr name old).overrideDerivation (attrs: {
		(builtins.getAttr name old).overrideAttrs (attrs: {
		buildInputs = attrs.buildInputs ++ value;
		})
		) overrides;
		@@ -146,14 +146,14 @@ let
		# results in
		#
		# {
		# foo = old.foo.overrideDerivation (attrs: {
		# foo = old.foo.overrideAttrs (attrs: {
		# nativeBuildInputs = attrs.nativeBuildInputs ++ [ self.bar ];
		# propagatedNativeBuildInputs = attrs.propagatedNativeBuildInputs ++ [ self.bar ];
		# });
		# }
		overrideRDepends = overrides: old:
		lib.mapAttrs (name: value:
		(builtins.getAttr name old).overrideDerivation (attrs: {
		(builtins.getAttr name old).overrideAttrs (attrs: {
		nativeBuildInputs = attrs.nativeBuildInputs ++ value;
		propagatedNativeBuildInputs = attrs.propagatedNativeBuildInputs ++ value;
		})
		@@ -913,7 +913,7 @@ let
		];

		otherOverrides = old: new: {
		gifski = old.gifski.overrideDerivation (attrs: {
		gifski = old.gifski.overrideAttrs (attrs: {
		cargoDeps = pkgs.rustPlatform.fetchCargoTarball {
		src = attrs.src;
		sourceRoot = "gifski/src/myrustlib";
		@@ -929,7 +929,7 @@ let
		];
		});

		stringi = old.stringi.overrideDerivation (attrs: {
		stringi = old.stringi.overrideAttrs (attrs: {
		postInstall = let
		icuName = "icudt52l";
		icuSrc = pkgs.fetchzip {
		@@ -943,72 +943,75 @@ let
		'';
		});

		xml2 = old.xml2.overrideDerivation (attrs: {
		xml2 = old.xml2.overrideAttrs (attrs: {
		preConfigure = ''
		export LIBXML_INCDIR=${pkgs.libxml2.dev}/include/libxml2
		patchShebangs configure
		'';
		});

		rzmq = old.rzmq.overrideDerivation (attrs: {
		rzmq = old.rzmq.overrideAttrs (attrs: {
		preConfigure = "patchShebangs configure";
		});

		clustermq = old.clustermq.overrideDerivation (attrs: {
		clustermq = old.clustermq.overrideAttrs (attrs: {
		preConfigure = "patchShebangs configure";
		});

		Cairo = old.Cairo.overrideDerivation (attrs: {
		Cairo = old.Cairo.overrideAttrs (attrs: {
		NIX_LDFLAGS = "-lfontconfig";
		});

		curl = old.curl.overrideDerivation (attrs: {
		curl = old.curl.overrideAttrs (attrs: {
		preConfigure = "patchShebangs configure";
		});

		RcppParallel = old.RcppParallel.overrideDerivation (attrs: {
		RcppParallel = old.RcppParallel.overrideAttrs (attrs: {
		preConfigure = "patchShebangs configure";
		});

		RcppArmadillo = old.RcppArmadillo.overrideDerivation (attrs: {
		RcppArmadillo = old.RcppArmadillo.overrideAttrs (attrs: {
		patchPhase = "patchShebangs configure";
		});

		data_table = old.data_table.overrideDerivation (attrs: {
		env.NIX_CFLAGS_COMPILE = attrs.NIX_CFLAGS_COMPILE + " -fopenmp";
		data_table = old.data_table.overrideAttrs (attrs: {
		env = (attrs.env or { }) // {
		NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -fopenmp";
		};
		patchPhase = "patchShebangs configure";
		});

		ModelMetrics = old.ModelMetrics.overrideDerivation (attrs: {
		env.NIX_CFLAGS_COMPILE = attrs.NIX_CFLAGS_COMPILE
		+ lib.optionalString stdenv.isDarwin " -fopenmp";
		ModelMetrics = old.ModelMetrics.overrideAttrs (attrs: {
		env = (attrs.env or { }) // {
		NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + lib.optionalString stdenv.isDarwin " -fopenmp";
		};
		});

		rpf = old.rpf.overrideDerivation (attrs: {
		rpf = old.rpf.overrideAttrs (attrs: {
		patchPhase = "patchShebangs configure";
		});

		rJava = old.rJava.overrideDerivation (attrs: {
		rJava = old.rJava.overrideAttrs (attrs: {
		preConfigure = ''
		export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/
		export JAVA_HOME=${pkgs.jdk}
		'';
		});

		JavaGD = old.JavaGD.overrideDerivation (attrs: {
		JavaGD = old.JavaGD.overrideAttrs (attrs: {
		preConfigure = ''
		export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/
		export JAVA_HOME=${pkgs.jdk}
		'';
		});

		jqr = old.jqr.overrideDerivation (attrs: {
		jqr = old.jqr.overrideAttrs (attrs: {
		preConfigure = ''
		patchShebangs configure
		'';
		});

		pbdZMQ = old.pbdZMQ.overrideDerivation (attrs: {
		pbdZMQ = old.pbdZMQ.overrideAttrs (attrs: {
		postPatch = lib.optionalString stdenv.isDarwin ''
		for file in R/*.{r,r.in}; do
		sed -i 's#system("which $\w\+$"[^)]*)#"${pkgs.darwin.cctools}/bin/\1"#g' $file
		@@ -1016,42 +1019,42 @@ let
		'';
		});

		quarto = old.quarto.overrideDerivation (attrs: {
		quarto = old.quarto.overrideAttrs (attrs: {
		postPatch = ''
		substituteInPlace "R/quarto.R" \
		--replace "path_env <- Sys.getenv(\"QUARTO_PATH\", unset = NA)" "path_env <- Sys.getenv(\"QUARTO_PATH\", unset = '${lib.getBin pkgs.quarto}/bin/quarto')"
		'';
		});

		s2 = old.s2.overrideDerivation (attrs: {
		s2 = old.s2.overrideAttrs (attrs: {
		PKGCONFIG_CFLAGS = "-I${pkgs.openssl.dev}/include";
		PKGCONFIG_LIBS = "-Wl,-rpath,${lib.getLib pkgs.openssl}/lib -L${lib.getLib pkgs.openssl}/lib -lssl -lcrypto";
		});

		Rmpi = old.Rmpi.overrideDerivation (attrs: {
		Rmpi = old.Rmpi.overrideAttrs (attrs: {
		configureFlags = [
		"--with-Rmpi-type=OPENMPI"
		];
		});

		Rmpfr = old.Rmpfr.overrideDerivation (attrs: {
		Rmpfr = old.Rmpfr.overrideAttrs (attrs: {
		configureFlags = [
		"--with-mpfr-include=${pkgs.mpfr.dev}/include"
		];
		});

		RVowpalWabbit = old.RVowpalWabbit.overrideDerivation (attrs: {
		RVowpalWabbit = old.RVowpalWabbit.overrideAttrs (attrs: {
		configureFlags = [
		"--with-boost=${pkgs.boost.dev}" "--with-boost-libdir=${pkgs.boost.out}/lib"
		];
		});

		RAppArmor = old.RAppArmor.overrideDerivation (attrs: {
		RAppArmor = old.RAppArmor.overrideAttrs (attrs: {
		patches = [ ./patches/RAppArmor.patch ];
		LIBAPPARMOR_HOME = pkgs.libapparmor;
		});

		RMySQL = old.RMySQL.overrideDerivation (attrs: {
		RMySQL = old.RMySQL.overrideAttrs (attrs: {
		MYSQL_DIR = "${pkgs.libmysqlclient}";
		PKGCONFIG_CFLAGS = "-I${pkgs.libmysqlclient.dev}/include/mysql";
		NIX_CFLAGS_LINK = "-L${pkgs.libmysqlclient}/lib/mysql -lmysqlclient";
		@@ -1060,24 +1063,24 @@ let
		'';
		});

		devEMF = old.devEMF.overrideDerivation (attrs: {
		devEMF = old.devEMF.overrideAttrs (attrs: {
		NIX_CFLAGS_LINK = "-L${pkgs.xorg.libXft.out}/lib -lXft";
		NIX_LDFLAGS = "-lX11";
		});

		slfm = old.slfm.overrideDerivation (attrs: {
		slfm = old.slfm.overrideAttrs (attrs: {
		PKG_LIBS = "-L${pkgs.blas}/lib -lblas -L${pkgs.lapack}/lib -llapack";
		});

		SamplerCompare = old.SamplerCompare.overrideDerivation (attrs: {
		SamplerCompare = old.SamplerCompare.overrideAttrs (attrs: {
		PKG_LIBS = "-L${pkgs.blas}/lib -lblas -L${pkgs.lapack}/lib -llapack";
		});

		spMC = old.spMC.overrideDerivation (attrs: {
		spMC = old.spMC.overrideAttrs (attrs: {
		patches = [ ./patches/spMC.patch ];
		});

		openssl = old.openssl.overrideDerivation (attrs: {
		openssl = old.openssl.overrideAttrs (attrs: {
		preConfigure = ''
		patchShebangs configure
		'';
		@@ -1085,19 +1088,19 @@ let
		PKGCONFIG_LIBS = "-Wl,-rpath,${lib.getLib pkgs.openssl}/lib -L${lib.getLib pkgs.openssl}/lib -lssl -lcrypto";
		});

		websocket = old.websocket.overrideDerivation (attrs: {
		websocket = old.websocket.overrideAttrs (attrs: {
		PKGCONFIG_CFLAGS = "-I${pkgs.openssl.dev}/include";
		PKGCONFIG_LIBS = "-Wl,-rpath,${lib.getLib pkgs.openssl}/lib -L${lib.getLib pkgs.openssl}/lib -lssl -lcrypto";
		});

		Rserve = old.Rserve.overrideDerivation (attrs: {
		Rserve = old.Rserve.overrideAttrs (attrs: {
		patches = [ ./patches/Rserve.patch ];
		configureFlags = [
		"--with-server" "--with-client"
		];
		});

		V8 = old.V8.overrideDerivation (attrs: {
		V8 = old.V8.overrideAttrs (attrs: {
		postPatch = ''
		substituteInPlace configure \
		--replace " -lv8_libplatform" ""
		@@ -1115,45 +1118,45 @@ let
		'');
		});

		acs = old.acs.overrideDerivation (attrs: {
		acs = old.acs.overrideAttrs (attrs: {
		preConfigure = ''
		patchShebangs configure
		'';
		});

		gdtools = old.gdtools.overrideDerivation (attrs: {
		gdtools = old.gdtools.overrideAttrs (attrs: {
		preConfigure = ''
		patchShebangs configure
		'';
		NIX_LDFLAGS = "-lfontconfig -lfreetype";
		});

		magick = old.magick.overrideDerivation (attrs: {
		magick = old.magick.overrideAttrs (attrs: {
		preConfigure = ''
		patchShebangs configure
		'';
		});

		libgeos = old.libgeos.overrideDerivation (attrs: {
		libgeos = old.libgeos.overrideAttrs (attrs: {
		preConfigure = ''
		patchShebangs configure
		'';
		});

		protolite = old.protolite.overrideDerivation (attrs: {
		protolite = old.protolite.overrideAttrs (attrs: {
		preConfigure = ''
		patchShebangs configure
		'';
		});

		rpanel = old.rpanel.overrideDerivation (attrs: {
		rpanel = old.rpanel.overrideAttrs (attrs: {
		preConfigure = ''
		export TCLLIBPATH="${pkgs.bwidget}/lib/bwidget${pkgs.bwidget.version}"
		'';
		TCLLIBPATH = "${pkgs.bwidget}/lib/bwidget${pkgs.bwidget.version}";
		});

		RPostgres = old.RPostgres.overrideDerivation (attrs: {
		RPostgres = old.RPostgres.overrideAttrs (attrs: {
		preConfigure = ''
		export INCLUDE_DIR=${pkgs.postgresql}/include
		export LIB_DIR=${pkgs.postgresql.lib}/lib
		@@ -1161,33 +1164,35 @@ let
		'';
		});

		OpenMx = old.OpenMx.overrideDerivation (attrs: {
		OpenMx = old.OpenMx.overrideAttrs (attrs: {
		preConfigure = ''
		patchShebangs configure
		'';
		});

		odbc = old.odbc.overrideDerivation (attrs: {
		odbc = old.odbc.overrideAttrs (attrs: {
		preConfigure = ''
		patchShebangs configure
		'';
		});

		x13binary = old.x13binary.overrideDerivation (attrs: {
		x13binary = old.x13binary.overrideAttrs (attrs: {
		preConfigure = ''
		patchShebangs configure
		'';
		});

		geojsonio = old.geojsonio.overrideDerivation (attrs: {
		geojsonio = old.geojsonio.overrideAttrs (attrs: {
		buildInputs = [ cacert ] ++ attrs.buildInputs;
		});

		rstan = old.rstan.overrideDerivation (attrs: {
		env.NIX_CFLAGS_COMPILE = "${attrs.NIX_CFLAGS_COMPILE} -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION";
		rstan = old.rstan.overrideAttrs (attrs: {
		env = (attrs.env or { }) // {
		NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION";
		};
		});

		mongolite = old.mongolite.overrideDerivation (attrs: {
		mongolite = old.mongolite.overrideAttrs (attrs: {
		preConfigure = ''
		patchShebangs configure
		'';
		@@ -1195,15 +1200,15 @@ let
		PKGCONFIG_LIBS = "-Wl,-rpath,${lib.getLib pkgs.openssl}/lib -L${lib.getLib pkgs.openssl}/lib -L${pkgs.cyrus_sasl.out}/lib -L${pkgs.zlib.out}/lib -lssl -lcrypto -lsasl2 -lz";
		});

		ps = old.ps.overrideDerivation (attrs: {
		ps = old.ps.overrideAttrs (attrs: {
		preConfigure = "patchShebangs configure";
		});

		rlang = old.rlang.overrideDerivation (attrs: {
		rlang = old.rlang.overrideAttrs (attrs: {
		preConfigure = "patchShebangs configure";
		});

		systemfonts = old.systemfonts.overrideDerivation (attrs: {
		systemfonts = old.systemfonts.overrideAttrs (attrs: {
		preConfigure = "patchShebangs configure";
		});

		@@ -1219,13 +1224,13 @@ let
		'';
		});

		lpsymphony = old.lpsymphony.overrideDerivation (attrs: {
		lpsymphony = old.lpsymphony.overrideAttrs (attrs: {
		preConfigure = ''
		patchShebangs configure
		'';
		});

		sodium = old.sodium.overrideDerivation (attrs: with pkgs; {
		sodium = old.sodium.overrideAttrs (attrs: with pkgs; {
		preConfigure = ''
		patchShebangs configure
		'';
		@@ -1233,19 +1238,19 @@ let
		buildInputs = [ libsodium.dev ] ++ attrs.buildInputs;
		});

		keyring = old.keyring.overrideDerivation (attrs: {
		keyring = old.keyring.overrideAttrs (attrs: {
		preConfigure = ''
		patchShebangs configure
		'';
		});

		Rhtslib = old.Rhtslib.overrideDerivation (attrs: {
		Rhtslib = old.Rhtslib.overrideAttrs (attrs: {
		preConfigure = ''
		substituteInPlace R/zzz.R --replace "-lcurl" "-L${pkgs.curl.out}/lib -lcurl"
		'';
		});

		h2o = old.h2o.overrideDerivation (attrs: {
		h2o = old.h2o.overrideAttrs (attrs: {
		preConfigure = ''
		# prevent download of jar file during install and postpone to first use
		sed -i '/downloadJar()/d' R/zzz.R
		@@ -1258,26 +1263,26 @@ let
		'';
		});

		SICtools = old.SICtools.overrideDerivation (attrs: {
		SICtools = old.SICtools.overrideAttrs (attrs: {
		preConfigure = ''
		substituteInPlace src/Makefile --replace "-lcurses" "-lncurses"
		'';
		});

		arrow = old.arrow.overrideDerivation (attrs: {
		arrow = old.arrow.overrideAttrs (attrs: {
		preConfigure = ''
		patchShebangs configure
		'';
		});

		proj4 = old.proj4.overrideDerivation (attrs: {
		proj4 = old.proj4.overrideAttrs (attrs: {
		preConfigure = ''
		substituteInPlace configure \
		--replace "-lsqlite3" "-L${lib.makeLibraryPath [ pkgs.sqlite ]} -lsqlite3"
		'';
		});

		rrd = old.rrd.overrideDerivation (attrs: {
		rrd = old.rrd.overrideAttrs (attrs: {
		preConfigure = ''
		patchShebangs configure
		'';
		@@ -1285,7 +1290,7 @@ let

		ChIPXpress = old.ChIPXpress.override { hydraPlatforms = []; };

		rgl = old.rgl.overrideDerivation (attrs: {
		rgl = old.rgl.overrideAttrs (attrs: {
		RGL_USE_NULL = "true";
		});

		@@ -1295,11 +1300,11 @@ let

		flowClust = old.flowClust.override { platforms = lib.platforms.x86_64 ++ lib.platforms.x86; };

		geomorph = old.geomorph.overrideDerivation (attrs: {
		geomorph = old.geomorph.overrideAttrs (attrs: {
		RGL_USE_NULL = "true";
		});

		Rhdf5lib = old.Rhdf5lib.overrideDerivation (attrs: {
		Rhdf5lib = old.Rhdf5lib.overrideAttrs (attrs: {
		propagatedBuildInputs = attrs.propagatedBuildInputs ++ [ pkgs.hdf5.dev ];
		});
		};