diff options
Diffstat (limited to 'pkgs/development/r-modules/default.nix')
| -rw-r--r-- | pkgs/development/r-modules/default.nix | 100 |
1 files changed, 99 insertions, 1 deletions
diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index aaa37c9bc7eb8..ce5f581be1bcf 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -308,6 +308,7 @@ let FactoMineR = [ self.car ]; pander = [ self.codetools ]; rmsb = [ self.rstantools ]; + gastempt = [ self.rstantools ]; interactiveDisplay = [ self.BiocManager ]; }; @@ -334,6 +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 ]; @@ -378,6 +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 ]; @@ -412,6 +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 ]; @@ -532,6 +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 ]; @@ -561,11 +566,13 @@ 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 ]; RPushbullet = [ pkgs.which ]; stpphawkes = [ pkgs.gsl ]; + registr = with pkgs; [ icu.dev zlib.dev bzip2.dev xz.dev ]; RCurl = [ pkgs.curl.dev ]; R2SWF = [ pkgs.pkg-config ]; rDEA = [ pkgs.glpk ]; @@ -583,12 +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 ]; @@ -616,7 +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 ]; @@ -706,9 +715,11 @@ let RcppCWB = with pkgs; [ pcre.dev glib.dev ]; redux = [ pkgs.hiredis ]; RmecabKo = [ pkgs.mecab ]; + markets = [ pkgs.gsl ]; PoissonBinomial = [ pkgs.fftw.dev ]; poisbinom = [ pkgs.fftw.dev ]; PoissonMultinomial = [ pkgs.fftw.dev ]; + psbcGroup = [ pkgs.gsl.dev ]; rrd = [ pkgs.rrdtool ]; flowWorkspace = [ pkgs.zlib.dev ]; RITCH = [ pkgs.zlib.dev ]; @@ -933,6 +944,7 @@ let "aroma_affymetrix" "aroma_cn" "aroma_core" + "ceramic" "connections" "csodata" "DiceView" @@ -966,6 +978,9 @@ let "Quartet" "ShinyQuickStarter" "TIN" + "cfdnakit" + "CaDrA" + "GNOSIS" "TotalCopheneticIndex" "TreeDist" "biocthis" @@ -995,6 +1010,8 @@ let "PhIPData" # tries to download something from a DB "RBioFormats" # tries to download jar during load test "pbdMPI" # tries to run MPI processes + "CTdata" # tries to connect to ExperimentHub + "rfaRm" # tries to connect to Ebi "data_table" # fails to rename shared library before check "coMethDMR" # tries to connect to ExperimentHub "multiMiR" # tries to connect to DB @@ -1080,6 +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"; @@ -1137,6 +1169,11 @@ let patchPhase = "patchShebangs configure"; }); + luajr = old.luajr.overrideAttrs (attrs: { + hardeningDisable = [ "format" ]; + postPatch = "patchShebangs configure"; + }); + RcppArmadillo = old.RcppArmadillo.overrideAttrs (attrs: { patchPhase = "patchShebangs configure"; }); @@ -1166,6 +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 @@ -1261,6 +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"; @@ -1416,6 +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 ''; @@ -1437,6 +1498,43 @@ let buildInputs = [ cacert ] ++ attrs.buildInputs; }); + + immunotation = let + MHC41alleleList = fetchurl { + url = "https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/allele.list"; + hash = "sha256-CRZ+0uHzcq5zK5eONucAChXIXO8tnq5sSEAS80Z7jhg="; + }; + + MHCII40alleleList = fetchurl { + url = "https://services.healthtech.dtu.dk/services/NetMHCIIpan-4.0/alleles_name.list"; + hash = "sha256-K4Ic2NUs3P4IkvOODwZ0c4Yh8caex5Ih0uO5jXRHp40="; + }; + + # List of valid countries, regions and ethnic groups + # The original page is changing a bit every day, but the relevant + # content does not. Use archive.org to get a stable snapshot. + # It can be updated from time to time, or when the package becomes + # deficient. This may be difficult to know. + # Update the snapshot date, and add id_ after it, as described here: + # https://web.archive.org/web/20130806040521/http://faq.web.archive.org/page-without-wayback-code/ + validGeographics = fetchurl { + url = "https://web.archive.org/web/20240418194005id_/http://www.allelefrequencies.net/hla6006a.asp"; + hash = "sha256-m7Wkmh/cPxeqn94LwoznIh+fcFXskmSGErUYj6kTqak="; + }; + in old.immunotation.overrideAttrs (attrs: { + patches = [ ./patches/immunotation.patch ]; + postPatch = '' + substituteInPlace "R/external_resources_input.R" --replace-fail \ + "nix-NetMHCpan-4.1-allele-list" ${MHC41alleleList} + + substituteInPlace "R/external_resources_input.R" --replace-fail \ + "nix-NETMHCIIpan-4.0-alleles-name-list" ${MHCII40alleleList} + + substituteInPlace "R/AFND_interface.R" --replace-fail \ + "nix-valid-geographics" ${validGeographics} + ''; + }); + rstan = old.rstan.overrideAttrs (attrs: { env = (attrs.env or { }) // { NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION"; |