diff options
Diffstat (limited to 'nixpkgs/pkgs/development/r-modules/default.nix')
-rw-r--r-- | nixpkgs/pkgs/development/r-modules/default.nix | 53 |
1 files changed, 52 insertions, 1 deletions
diff --git a/nixpkgs/pkgs/development/r-modules/default.nix b/nixpkgs/pkgs/development/r-modules/default.nix index f2c398c0f452..8d4004d7580f 100644 --- a/nixpkgs/pkgs/development/r-modules/default.nix +++ b/nixpkgs/pkgs/development/r-modules/default.nix @@ -335,6 +335,7 @@ let Cardinal = [ pkgs.which ]; chebpol = [ pkgs.fftw.dev ]; ChemmineOB = [ pkgs.pkg-config ]; + interpolation = [ pkgs.pkg-config ]; clarabel = [ pkgs.cargo ]; curl = [ pkgs.curl.dev ]; CytoML = [ pkgs.libxml2.dev ]; @@ -379,6 +380,7 @@ let LOMAR = [ pkgs.gmp.dev ]; lpsymphony = with pkgs; [ pkg-config gfortran gettext ]; lwgeom = with pkgs; [ proj geos gdal ]; + rsbml = [ pkgs.pkg-config ]; rvg = [ pkgs.libpng.dev ]; MAGEE = [ pkgs.zlib.dev pkgs.bzip2.dev ]; magick = [ pkgs.imagemagick.dev ]; @@ -413,6 +415,7 @@ let RcppZiggurat = [ pkgs.gsl ]; reprex = [ pkgs.which ]; rgdal = with pkgs; [ proj.dev gdal ]; + Rhisat2 = [ pkgs.which pkgs.hostname ]; gdalcubes = [ pkgs.pkg-config ]; rgeos = [ pkgs.geos ]; Rglpk = [ pkgs.glpk ]; @@ -533,6 +536,7 @@ let Rbwa = [ pkgs.zlib.dev ]; trackViewer = [ pkgs.zlib.dev ]; themetagenomics = [ pkgs.zlib.dev ]; + Rsymphony = [ pkgs.pkg-config ]; NanoMethViz = [ pkgs.zlib.dev ]; RcppMeCab = [ pkgs.pkg-config ]; HilbertVisGUI = with pkgs; [ pkg-config which ]; @@ -562,6 +566,7 @@ let deepSNV = with pkgs; [ xz.dev bzip2.dev zlib.dev ]; epialleleR = with pkgs; [ xz.dev bzip2.dev zlib.dev ]; gdalraster = with pkgs; [ gdal proj.dev sqlite.dev ]; + mitoClone2 = with pkgs; [ xz.dev bzip2.dev zlib.dev ]; gpg = [ pkgs.gpgme ]; webp = [ pkgs.libwebp ]; RMark = [ pkgs.which ]; @@ -585,12 +590,14 @@ let gdtools = [ pkgs.pkg-config ]; archive = [ pkgs.libarchive]; gdalcubes = with pkgs; [ proj.dev gdal sqlite.dev netcdf ]; + rsbml = [ pkgs.libsbml ]; SuperGauss = [ pkgs.pkg-config pkgs.fftw.dev]; specklestar = [ pkgs.fftw.dev ]; cartogramR = [ pkgs.fftw.dev ]; jqr = [ pkgs.jq.lib ]; kza = [ pkgs.pkg-config ]; igraph = with pkgs; [ gmp libxml2.dev glpk ]; + interpolation = [ pkgs.gmp ]; image_textlinedetector = with pkgs; [ pkg-config opencv ]; lwgeom = with pkgs; [ pkg-config proj.dev sqlite.dev ]; magick = [ pkgs.pkg-config ]; @@ -618,7 +625,7 @@ let mashr = [ pkgs.gsl ]; hadron = [ pkgs.gsl ]; AMOUNTAIN = [ pkgs.gsl ]; - Rsymphony = with pkgs; [ pkg-config doxygen graphviz subversion ]; + Rsymphony = with pkgs; [ symphony doxygen graphviz subversion cgl clp]; tcltk2 = with pkgs; [ tcl tk ]; rswipl = with pkgs; [ ncurses.dev libxcrypt zlib.dev ]; tikzDevice = with pkgs; [ which texliveMedium ]; @@ -1090,6 +1097,21 @@ let ]; }); + timeless = old.timeless.overrideAttrs (attrs: { + cargoDeps = pkgs.rustPlatform.fetchCargoTarball { + src = attrs.src; + sourceRoot = "timeless/src/rust"; + hash = "sha256-n0/52CV3NzWe7T3N6VoaURMxWrnqeYaUMPKkUy+LRQs="; + }; + + cargoRoot = "src/rust"; + + nativeBuildInputs = attrs.nativeBuildInputs ++ [ + pkgs.rustPlatform.cargoSetupHook + pkgs.cargo + ]; + }); + stringi = old.stringi.overrideAttrs (attrs: { postInstall = let icuName = "icudt52l"; @@ -1147,6 +1169,11 @@ let patchPhase = "patchShebangs configure"; }); + luajr = old.luajr.overrideAttrs (attrs: { + hardeningDisable = [ "format" ]; + postPatch = "patchShebangs configure"; + }); + RcppArmadillo = old.RcppArmadillo.overrideAttrs (attrs: { patchPhase = "patchShebangs configure"; }); @@ -1176,6 +1203,15 @@ let patchPhase = "patchShebangs configure"; }); + rsgeo = old.rsgeo.overrideAttrs (attrs: { + nativeBuildInputs = [ pkgs.cargo ] ++ attrs.nativeBuildInputs; + postPatch = "patchShebangs configure"; + }); + + instantiate = old.instantiate.overrideAttrs (attrs: { + postPatch = "patchShebangs configure"; + }); + exifr = old.exifr.overrideAttrs (attrs: { postPatch = '' for f in .onLoad .onAttach ; do @@ -1271,6 +1307,17 @@ let ''; }); + # backported patch from 1.9 + Rhisat2= old.Rhisat2.overrideAttrs (attrs: { + patches = [ (pkgs.fetchpatch { + url = "https://github.com/fmicompbio/Rhisat2/commit/a0f27b018831b39f080f99e6db8a4b876fd56fc3.patch"; + sha256 = "sha256-FbYkP/WFmbfQmxArkHgushgVgY0XSypbK8Z5ivQK8k4="; + }) ]; + env = (attrs.env or { }) // { + NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -w"; + }; + }); + 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"; @@ -1426,6 +1473,10 @@ let }); OpenMx = old.OpenMx.overrideAttrs (attrs: { + env = (attrs.env or { }) // { + # needed to avoid "log limit exceeded" on Hydra + NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -Wno-ignored-attributes"; + }; preConfigure = '' patchShebangs configure ''; |