R,rPackages: 4.4.2 -> 4.4.3 (#385925) (3b9548ed) · Commits · nix / nixpkgs

pkgs/applications/science/math/R/default.nix

+2 −2

Original line number	Diff line number	Diff line
		@@ -15,13 +15,13 @@ assert (!blas.isILP64) && (!lapack.isILP64);

		stdenv.mkDerivation (finalAttrs: {
		pname = "R";
		version = "4.4.2";
		version = "4.4.3";

		src = let
		inherit (finalAttrs) pname version;
		in fetchurl {
		url = "https://cran.r-project.org/src/base/R-${lib.versions.major version}/${pname}-${version}.tar.gz";
		sha256 = "sha256-FXjNYD6NhmtYdD5J2L+ZxWnoEHm2pgzzPN973/64F+w=";
		sha256 = "sha256-DZPSJEQt6iU8KwhvCI220NPP2bWSzVSW6MshQ+kPyeg=";
		};

		outputs = [ "out" "tex" ];

pkgs/development/r-modules/bioc-experiment-packages.json

+18 −18

Original line number	Diff line number	Diff line
		@@ -749,9 +749,9 @@
		},
		"MetaScope": {
		"name": "MetaScope",
		"version": "1.5.4",
		"sha256": "1f69bkm7qb027pl1c1w9vlvbcw0sxi0da5az21a8i8xrz42aab57",
		"depends": ["BiocFileCache", "Biostrings", "Matrix", "MultiAssayExperiment", "Rbowtie2", "Rsamtools", "S4Vectors", "SummarizedExperiment", "data_table", "dplyr", "ggplot2", "magrittr", "readr", "rlang", "stringr", "tibble", "tidyr"]
		"version": "1.6.0",
		"sha256": "1f7w4dfv6sizpp97vjwm034ha4pcq93b3j0gg1l75s6ans8s89aw",
		"depends": ["BiocFileCache", "Biostrings", "Matrix", "MultiAssayExperiment", "Rbowtie2", "Rsamtools", "S4Vectors", "SummarizedExperiment", "data_table", "dplyr", "ggplot2", "magrittr", "readr", "rlang", "stringr", "taxize", "tibble", "tidyr"]
		},
		"MethylAidData": {
		"name": "MethylAidData",
		@@ -1139,8 +1139,8 @@
		},
		"STexampleData": {
		"name": "STexampleData",
		"version": "1.14.0",
		"sha256": "1n2cq1ia7vi7a2gma9mhwv34dwy0fyxmap5fycy3f8f2bnm373kw",
		"version": "1.14.1",
		"sha256": "14xdinp0ix55lgs0adcxwnjascrpx4s39kghrhbcpjl0ainrdhk3",
		"depends": ["ExperimentHub", "SingleCellExperiment", "SpatialExperiment"]
		},
		"SVM2CRMdata": {
		@@ -1319,9 +1319,9 @@
		},
		"TumourMethData": {
		"name": "TumourMethData",
		"version": "1.3.0",
		"sha256": "01xbsi6x4bafkp0m5xi4l2w62067xnfqnlkaz59ng1hf2ld2p690",
		"depends": ["ExperimentHub", "GenomicRanges", "HDF5Array", "R_utils", "SummarizedExperiment", "rhdf5"]
		"version": "1.4.0",
		"sha256": "14y58qa4khi4jdymilxrb6x57br1gjclw2q3n9mivjrj6z3r3nmw",
		"depends": ["BSgenome_Hsapiens_UCSC_hg19", "ExperimentHub", "ExperimentHubData", "GenomicRanges", "HDF5Array", "R_utils", "SummarizedExperiment", "TCGAutils", "dplyr", "knitr", "methrix", "openxlsx", "readr", "rhdf5", "rmarkdown", "stringr", "tibble", "usethis", "xlsx"]
		},
		"VariantToolsData": {
		"name": "VariantToolsData",
		@@ -1739,9 +1739,9 @@
		},
		"etec16s": {
		"name": "etec16s",
		"version": "1.33.0",
		"sha256": "1xbj8z68006riah51lpk0bh8hq240wl9n1inlss84yj6kn4y5m0w",
		"depends": ["Biobase"]
		"version": "1.34.0",
		"sha256": "114jmrnjm2xpfzx1m10bn73fy1am209c70ws4jwfggrbavg6xp8j",
		"depends": ["Biobase", "metagenomeSeq"]
		},
		"ewceData": {
		"name": "ewceData",
		@@ -1817,8 +1817,8 @@
		},
		"gDRtestData": {
		"name": "gDRtestData",
		"version": "1.4.0",
		"sha256": "1qqk9x8i2g5284p60hxznl95b6sp80qksx4qq724ycmknayg3kxb",
		"version": "1.4.1",
		"sha256": "0ybp2zrkjivrfl62zz7jljs1inlnx3iybwazyh0rxb255r9cg9ns",
		"depends": ["checkmate", "data_table"]
		},
		"gageData": {
		@@ -2117,9 +2117,9 @@
		},
		"msd16s": {
		"name": "msd16s",
		"version": "1.25.0",
		"sha256": "0lzcpwf9rhr8i80hn3dab0fpgx7qmy0q9l8j7fkrazq2paiiikj7",
		"depends": ["Biobase"]
		"version": "1.26.0",
		"sha256": "0wg705d0232d4916d3b84q62pdrzmf8v3k9apyh4fsmg4pk2xw6p",
		"depends": ["Biobase", "metagenomeSeq"]
		},
		"msdata": {
		"name": "msdata",
		@@ -2207,8 +2207,8 @@
		},
		"pRolocdata": {
		"name": "pRolocdata",
		"version": "1.44.0",
		"sha256": "0dh5zgwr248gnlygja7ly66dyhh4b4xf72n9ycp0xa02xdl0mwi3",
		"version": "1.44.1",
		"sha256": "01n9p4a02lq96rhz97skzs79mvnki3vqyn3b4b89vhrp8idgmli0",
		"depends": ["Biobase", "MSnbase"]
		},
		"parathyroidSE": {

pkgs/development/r-modules/bioc-packages.json

+226 −238

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pkgs/development/r-modules/cran-packages.json

+6876 −4681

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pkgs/development/r-modules/default.nix

+136 −22

Original line number	Diff line number	Diff line
		@@ -370,11 +370,12 @@ let
		diversitree = with pkgs; [ gsl fftw ];
		exactextractr = [ pkgs.geos ];
		EMCluster = [ pkgs.lapack ];
		fangs = [ pkgs.cargo ];
		fangs = with pkgs; [ cargo rustc ];
		fastpng = [ pkgs.zlib.dev ];
		fcl = with pkgs; [ cargo rustc ];
		fftw = [ pkgs.fftw.dev ];
		fftwtools = with pkgs; [ fftw.dev pkg-config ];
		flint = with pkgs; [ pkg-config gmp.dev mpfr.dev flint3 ];
		fingerPro = [ pkgs.gsl ];
		Formula = [ pkgs.gmp ];
		frailtyMMpen = [ pkgs.gsl ];
		@@ -401,6 +402,7 @@ let
		RNiftyReg = with pkgs; [ zlib.dev ];
		highs = [ pkgs.which pkgs.cmake ];
		crc32c = [ pkgs.which pkgs.cmake ];
		cpp11bigwig = with pkgs; [ zlib.dev curl.dev ];
		rbedrock = [ pkgs.zlib.dev pkgs.which pkgs.cmake ];
		HiCseg = [ pkgs.gsl ];
		imager = [ pkgs.xorg.libX11.dev ];
		@@ -450,6 +452,7 @@ let
		PKI = [ pkgs.openssl.dev ];
		png = [ pkgs.libpng.dev ];
		protolite = [ pkgs.protobuf ];
		prqlr = with pkgs; [ cargo rustc ];
		R2SWF = with pkgs; [ zlib libpng freetype.dev ];
		RAppArmor = [ pkgs.libapparmor ];
		rapportools = [ pkgs.which ];
		@@ -495,9 +498,9 @@ let
		httpuv = [ pkgs.zlib.dev ];
		clustermq = [ pkgs.zeromq ];
		SAVE = with pkgs; [ zlib bzip2 icu xz pcre ];
		salso = [ pkgs.cargo ];
		salso = with pkgs; [ cargo rustc ];
		ymd = with pkgs; [ cargo rustc ];
		arcpbf = [ pkgs.cargo ];
		arcpbf = with pkgs; [ cargo rustc ];
		sdcTable = with pkgs; [ gmp glpk ];
		seewave = with pkgs; [ fftw.dev libsndfile.dev ];
		seqinr = [ pkgs.zlib.dev ];
		@@ -513,6 +516,7 @@ let
		arcgisutils = with pkgs; [ cargo rustc ];
		arcgisgeocode = with pkgs; [ cargo rustc ];
		arcgisplaces = with pkgs; [ pkg-config openssl.dev cargo rustc ];
		awdb = [ pkgs.cargo ];
		apcf = with pkgs; [ geos ];
		SemiCompRisks = [ pkgs.gsl ];
		showtext = with pkgs; [ zlib libpng icu freetype.dev ];
		@@ -521,6 +525,7 @@ let
		ssanv = [ pkgs.proj ];
		stsm = [ pkgs.gsl ];
		stringi = [ pkgs.icu.dev ];
		parseLatex = [ pkgs.icu.dev ];
		survSNP = [ pkgs.gsl ];
		svglite = [ pkgs.libpng.dev ];
		sysfonts = with pkgs; [ zlib libpng freetype.dev ];
		@@ -588,6 +593,7 @@ let
		rrd = [ pkgs.pkg-config ];
		surveyvoi = [ pkgs.pkg-config ];
		Rbwa = [ pkgs.zlib.dev ];
		tergo = with pkgs; [ cargo rustc ];
		trackViewer = [ pkgs.zlib.dev ];
		themetagenomics = [ pkgs.zlib.dev ];
		Rsymphony = [ pkgs.pkg-config ];
		@@ -599,9 +605,11 @@ let
		qqconf = [ pkgs.pkg-config ];
		qspray = [ pkgs.pkg-config ];
		ratioOfQsprays = [ pkgs.pkg-config ];
		watcher = with pkgs; [ cmake which ];
		symbolicQspray = [ pkgs.pkg-config ];
		sphereTessellation = [ pkgs.pkg-config ];
		vapour = [ pkgs.pkg-config ];
		xdvir = [ pkgs.freetype.dev ];
		};

		packagesWithBuildInputs = {
		@@ -908,6 +916,7 @@ let
		"MSnID"
		"OmnipathR"
		"orthGS"
		"pannotator"
		"precommit"
		"protGear"
		"PCRA"
		@@ -982,6 +991,7 @@ let
		"HierO"
		"HIBAG"
		"HiveR"
		"minired" # deprecated on CRAN

		# Impure network access during build
		"waddR"
		@@ -1016,6 +1026,17 @@ let
		];

		otherOverrides = old: new: {
		ACME = old.ACME.overrideAttrs (attrs: {
		env = (attrs.env or { }) // {
		# Avoid incompatible pointer type error
		NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -Wno-incompatible-pointer-types";
		};
		});

		vegan3d = old.vegan3d.overrideAttrs (attrs: {
		RGL_USE_NULL = "true";
		});

		# it can happen that the major version of arrow-cpp is ahead of the
		# rPackages.arrow that would be built from CRAN sources; therefore, to avoid
		# build failures and manual updates of the hash, we use the R source at
		@@ -1025,11 +1046,6 @@ let
		# this is a straightforward approach. Example where patching was necessary
		# -> arrow 14.0.0.2 on CRAN; was lagging behind libarrow release:
		# https://github.com/apache/arrow/issues/39698 )

		vegan3d = old.vegan3d.overrideAttrs (attrs: {
		RGL_USE_NULL = "true";
		});

		arrow = old.arrow.overrideAttrs (attrs: {
		src = pkgs.arrow-cpp.src;
		name = "r-arrow-${pkgs.arrow-cpp.version}";
		@@ -1058,6 +1074,14 @@ let
		];
		});

		gmapR = old.gmapR.overrideAttrs (attrs: {
		env = (attrs.env or { }) // {
		# Avoid incompatible pointer type error
		NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE +
		" -Wno-implicit-function-declaration -Wno-incompatible-pointer-types";
		};
		});

		timeless = old.timeless.overrideAttrs (attrs: {
		preConfigure = "patchShebangs configure";
		cargoDeps = pkgs.rustPlatform.fetchCargoVendor {
		@@ -1074,6 +1098,10 @@ let
		];
		});

		arcpbf = old.arcpbf.overrideAttrs (attrs: {
		postPatch = "patchShebangs configure";
		});

		stringi = old.stringi.overrideAttrs (attrs: {
		postInstall = let
		icuName = "icudt52l";
		@@ -1095,18 +1123,51 @@ let
		'';
		});

		findpython = old.findpython.overrideAttrs (attrs: {
		postPatch = ''
		substituteInPlace "R/find_python_cmd.r" \
		--replace-fail 'python_cmds[which(python_cmds != "")]' \
		'python_cmds <- c(python_cmds, file.path("${lib.getBin pkgs.python3}", "bin", "python3"))
		python_cmds[which(python_cmds != "")]'
		'';
		});

		alcyon = old.alcyon.overrideAttrs (attrs: {
		configureFlags = [
		"--enable-force-openmp"
		];
		});

		awdb = old.awdb.overrideAttrs (attrs: {
		postPatch = ''
		patchShebangs configure
		'';
		});

		clarabel = old.clarabel.overrideAttrs (attrs: {
		postPatch = ''
		patchShebangs configure
		'';
		});

		lwgeom = old.lwgeom.overrideAttrs (attrs: {
		configureFlags = [
		"--with-proj-lib=${pkgs.lib.getLib pkgs.proj}/lib"
		];
		});

		scDDboost = old.scDDboost.overrideAttrs (attrs: {
		postPatch = ''
		# https://code.bioconductor.org/browse/scDDboost/commit/f704a727c906075a2e271e9e2db93cf31e3822f5
		substituteInPlace "DESCRIPTION" \
		--replace-fail "c++11" "c++14"
		# https://code.bioconductor.org/browse/scDDboost/commit/74d46e266957b38fe77185fa3ce683f891706538
		substituteInPlace "src/Makevars" \
		--replace-fail "#CXX_STD = CXX11" "CXX_STD = CXX14"
		'';
		});


		sf = old.sf.overrideAttrs (attrs: {
		configureFlags = [
		"--with-proj-lib=${pkgs.lib.getLib pkgs.proj}/lib"
		@@ -1129,6 +1190,10 @@ let
		preConfigure = "patchShebangs configure";
		});

		nanoparquet = old.nanoparquet.overrideAttrs (attrs: {
		postPatch = "patchShebangs configure";
		});

		clustermq = old.clustermq.overrideAttrs (attrs: {
		preConfigure = "patchShebangs configure";
		});
		@@ -1161,10 +1226,25 @@ let
		postPatch = "patchShebangs configure";
		});

		EBSeq = old.EBSeq.overrideAttrs (attrs: {
		postPatch = ''
		# https://code.bioconductor.org/browse/EBSeq/commit/d18c41cc3eb96ca82a7c55f0d60287e28785281e
		substituteInPlace "DESCRIPTION" \
		--replace-fail "c++11" "c++14"
		# https://code.bioconductor.org/browse/EBSeq/commit/fd9ccf425b3c8c0f209de77e7d6e9a1d0c839d68
		substituteInPlace "src/Makevars" \
		--replace-fail "#CXX_STD = CXX11" "CXX_STD = CXX14"
		'';
		});

		gmailr = old.gmailr.overrideAttrs (attrs: {
		postPatch = "patchShebangs configure";
		});

		prqlr = old.prqlr.overrideAttrs (attrs: {
		postPatch = "patchShebangs configure";
		});

		pingr = old.pingr.overrideAttrs (_: {
		postPatch = "patchShebangs configure";
		});
		@@ -1216,6 +1296,21 @@ let
		postPatch = "patchShebangs configure";
		});

		bandle = old.bandle.overrideAttrs (attrs: {
		postPatch = ''
		# https://code.bioconductor.org/browse/bandle/commit/e8f7aaa29c1ba772cee5d51e09b1f500bfee44b8
		substituteInPlace "src/Makevars" \
		--replace-fail "CXX_STD = CXX11" "CXX_STD = CXX14"
		'';
		});

		graper = old.graper.overrideAttrs (attrs: {
		postPatch = ''
		substituteInPlace "src/Makevars" \
		--replace-fail "CXX_STD=CXX11" "CXX_STD=CXX14"
		'';
		});

		ocf = old.ocf.overrideAttrs (attrs: {
		postPatch = "patchShebangs configure";
		});
		@@ -1279,6 +1374,14 @@ let
		'';
		});

		metahdep = old.metahdep.overrideAttrs (attrs: {
		env = (attrs.env or { }) // {
		# Avoid incompatible pointer type error
		NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -Wno-int-conversion";
		};
		});


		ModelMetrics = old.ModelMetrics.overrideAttrs (attrs: {
		env = (attrs.env or { }) // {
		NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + lib.optionalString stdenv.hostPlatform.isDarwin " -fopenmp";
		@@ -1566,6 +1669,21 @@ let
		buildInputs = [ cacert ] ++ attrs.buildInputs;
		});

		float = old.float.overrideAttrs (attrs: {
		enableParallelBuilding = false;
		});

		redatamx = old.redatamx.overrideAttrs (attrs: {
		preConfigure = let
		redatam-core = pkgs.fetchzip {
		url = "https://redatam-core.s3.us-west-2.amazonaws.com/core-dev/linux/redatamx-core-linux-20241222.zip";
		hash = "sha256-CagDpv7v5fj/NgaC5fmYc5UuKuBVlT3gauH2ItVnIIY=";
		};
		in ''
		mkdir -p ./inst/redengine/
		cp ${redatam-core}/lib/libredengine-1.0.0-rc2.so ./inst/redengine/libredengine-1.0.0-rc2.so
		'';
		});

		immunotation = let
		MHC41alleleList = fetchurl {
		@@ -1779,6 +1897,16 @@ let
		RGL_USE_NULL = "true";
		});

		methylKit = old.methylKit.overrideAttrs (attrs: {
		# resolve missing function from data.table
		patches = [
		(pkgs.fetchpatch {
		url = "https://github.com/al2na/methylKit/commit/5c30347630bc064d7aefc918923f723671f35253.patch";
		sha256 = "sha256-hwtybBmSYwVInMIEZ7i7zudJWjiRJmrD0/tU7v78pPc=";
		})
		];
		});

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

		symengine = old.symengine.overrideAttrs (_: {
		@@ -1799,20 +1927,6 @@ let
		postPatch = "patchShebangs configure";
		});

		SharedObject = old.SharedObject.overrideAttrs (attrs: {
		# backport PR resolving build issues: https://github.com/Jiefei-Wang/SharedObject/pull/17
		patches = let inherit (pkgs) fetchpatch; in [
		(fetchpatch {
		url = "https://github.com/Jiefei-Wang/SharedObject/pull/17/commits/50c4b2964649d7f5a14d843bd7089ab62650fcd3.patch";
		sha256 = "sha256-zn535IeOYRvyQ2yxgoGEq2wccrl9xdu9nREmy7sV+PQ=";
		})
		(fetchpatch {
		url = "https://github.com/Jiefei-Wang/SharedObject/pull/17/commits/bf096a39858e9210cbe246d4b136905d4cfbfaf4.patch";
		sha256 = "sha256-Z+BZOkFnLgIBiVuPsAHp7bMXzADcvuHV4hILdmLvd+k=";
		})
		];
		});

		httr2 = old.httr2.overrideAttrs (attrs: {
		preConfigure = "patchShebangs configure";
		});