Justin Bedő
GitHub
commit
0689e7368d
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@ -119,6 +119,6 @@ stdenv.mkDerivation rec {
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platforms = platforms.all;
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maintainers = with maintainers; teams.sage.members;
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maintainers = with maintainers; [ jbedo ] ++ teams.sage.members;
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};
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}
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@ -158,6 +158,38 @@ let
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in
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builtins.listToAttrs nameValuePairs;
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# Overrides package definition requiring a home directory to install or to
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# run tests.
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# For example,
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#
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# overrideRequireHome [
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# "foo"
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# ] old
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#
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# results in
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#
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# {
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# foo = old.foo.overrideAttrs (oldAttrs: {
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# preInstall = ''
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# ${oldAttrs.preInstall or ""}
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# export HOME=$(mktemp -d)
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# '';
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# });
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# }
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overrideRequireHome = packageNames: old:
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let
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nameValuePairs = map (name: {
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inherit name;
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value = (builtins.getAttr name old).overrideAttrs (oldAttrs: {
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preInstall = ''
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${oldAttrs.preInstall or ""}
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export HOME=$(mktemp -d)
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'';
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});
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}) packageNames;
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in
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builtins.listToAttrs nameValuePairs;
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# Overrides package definition to skip check.
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# For example,
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#
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@ -211,13 +243,14 @@ let
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defaultOverrides = old: new:
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let old0 = old; in
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let
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old1 = old0 // (overrideRequireX packagesRequireingX old0);
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old2 = old1 // (overrideSkipCheck packagesToSkipCheck old1);
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old3 = old2 // (overrideRDepends packagesWithRDepends old2);
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old4 = old3 // (overrideNativeBuildInputs packagesWithNativeBuildInputs old3);
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old5 = old4 // (overrideBuildInputs packagesWithBuildInputs old4);
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old6 = old5 // (overrideBroken brokenPackages old5);
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old = old6;
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old1 = old0 // (overrideRequireX packagesRequiringX old0);
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old2 = old1 // (overrideRequireHome packagesRequiringHome old1);
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old3 = old2 // (overrideSkipCheck packagesToSkipCheck old2);
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old4 = old3 // (overrideRDepends packagesWithRDepends old3);
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old5 = old4 // (overrideNativeBuildInputs packagesWithNativeBuildInputs old4);
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old6 = old5 // (overrideBuildInputs packagesWithBuildInputs old5);
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old7 = old6 // (overrideBroken brokenPackages old6);
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old = old7;
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in old // (otherOverrides old new);
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# Recursive override pattern.
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@ -243,14 +276,14 @@ let
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adimpro = [ pkgs.imagemagick ];
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animation = [ pkgs.which ];
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audio = [ pkgs.portaudio ];
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BayesSAE = [ pkgs.gsl_1 ];
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BayesVarSel = [ pkgs.gsl_1 ];
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BayesSAE = [ pkgs.gsl ];
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BayesVarSel = [ pkgs.gsl ];
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BayesXsrc = with pkgs; [ readline.dev ncurses ];
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bigGP = [ pkgs.mpi ];
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bio3d = [ pkgs.zlib ];
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BiocCheck = [ pkgs.which ];
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Biostrings = [ pkgs.zlib ];
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bnpmr = [ pkgs.gsl_1 ];
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bnpmr = [ pkgs.gsl ];
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cairoDevice = [ pkgs.gtk2.dev ];
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Cairo = with pkgs; [ libtiff libjpeg cairo.dev x11 fontconfig.lib ];
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Cardinal = [ pkgs.which ];
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@ -259,37 +292,39 @@ let
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curl = [ pkgs.curl.dev ];
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data_table = [ pkgs.zlib.dev ] ++ lib.optional stdenv.isDarwin pkgs.llvmPackages.openmp;
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devEMF = with pkgs; [ xorg.libXft.dev x11 ];
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diversitree = with pkgs; [ gsl_1 fftw ];
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diversitree = with pkgs; [ gsl fftw ];
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exactextractr = [ pkgs.geos ];
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EMCluster = [ pkgs.lapack ];
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fftw = [ pkgs.fftw.dev ];
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fftwtools = with pkgs; [ fftw.dev pkg-config ];
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Formula = [ pkgs.gmp ];
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gdtools = with pkgs; [ cairo.dev fontconfig.lib freetype.dev ];
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ggiraph = with pkgs; [ pkgs.libpng.dev ];
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git2r = with pkgs; [ zlib.dev openssl.dev libssh2.dev libgit2 pkg-config ];
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GLAD = [ pkgs.gsl_1 ];
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GLAD = [ pkgs.gsl ];
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glpkAPI = with pkgs; [ gmp glpk ];
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gmp = [ pkgs.gmp.dev ];
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graphscan = [ pkgs.gsl_1 ];
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gsl = [ pkgs.gsl_1 ];
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graphscan = [ pkgs.gsl ];
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gsl = [ pkgs.gsl ];
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gert = [ pkgs.libgit2 ];
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haven = with pkgs; [ libiconv zlib.dev ];
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h5vc = [ pkgs.zlib.dev ];
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HiCseg = [ pkgs.gsl_1 ];
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HiCseg = [ pkgs.gsl ];
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imager = [ pkgs.x11 ];
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iBMQ = [ pkgs.gsl_1 ];
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iBMQ = [ pkgs.gsl ];
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igraph = with pkgs; [ gmp libxml2.dev ];
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JavaGD = [ pkgs.jdk ];
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jpeg = [ pkgs.libjpeg.dev ];
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jqr = [ pkgs.jq.dev ];
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KFKSDS = [ pkgs.gsl_1 ];
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KFKSDS = [ pkgs.gsl ];
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kza = [ pkgs.fftw.dev ];
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lpsymphony = with pkgs; [ pkg-config gfortran gettext ];
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lwgeom = with pkgs; [ proj geos gdal ];
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magick = [ pkgs.imagemagick.dev ];
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ModelMetrics = lib.optional stdenv.isDarwin pkgs.llvmPackages.openmp;
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mvabund = [ pkgs.gsl_1 ];
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mvabund = [ pkgs.gsl ];
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mwaved = [ pkgs.fftw.dev ];
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mzR = with pkgs; [ zlib boost159.dev netcdf ];
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ncdf4 = [ pkgs.netcdf ];
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nloptr = with pkgs; [ nlopt pkg-config ];
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n1qn1 = [ pkgs.gfortran ];
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@ -311,8 +346,8 @@ let
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readxl = [ pkgs.libiconv ];
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rcdd = [ pkgs.gmp.dev ];
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RcppCNPy = [ pkgs.zlib.dev ];
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RcppGSL = [ pkgs.gsl_1 ];
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RcppZiggurat = [ pkgs.gsl_1 ];
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RcppGSL = [ pkgs.gsl ];
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RcppZiggurat = [ pkgs.gsl ];
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reprex = [ pkgs.which ];
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rgdal = with pkgs; [ proj.dev gdal ];
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rgeos = [ pkgs.geos ];
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@ -324,7 +359,7 @@ let
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Rhtslib = with pkgs; [ zlib.dev automake autoconf bzip2.dev xz.dev curl.dev ];
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rjags = [ pkgs.jags ];
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rJava = with pkgs; [ zlib bzip2.dev icu xz.dev pcre.dev jdk libzip ];
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Rlibeemd = [ pkgs.gsl_1 ];
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Rlibeemd = [ pkgs.gsl ];
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rmatio = [ pkgs.zlib.dev ];
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Rmpfr = with pkgs; [ gmp mpfr.dev ];
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Rmpi = [ pkgs.mpi ];
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@ -352,12 +387,12 @@ let
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sf = with pkgs; [ gdal proj geos ];
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terra = with pkgs; [ gdal proj geos ];
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showtext = with pkgs; [ zlib libpng icu freetype.dev ];
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simplexreg = [ pkgs.gsl_1 ];
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simplexreg = [ pkgs.gsl ];
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spate = [ pkgs.fftw.dev ];
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ssanv = [ pkgs.proj ];
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stsm = [ pkgs.gsl_1 ];
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stsm = [ pkgs.gsl ];
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stringi = [ pkgs.icu.dev ];
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survSNP = [ pkgs.gsl_1 ];
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survSNP = [ pkgs.gsl ];
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svglite = [ pkgs.libpng.dev ];
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sysfonts = with pkgs; [ zlib libpng freetype.dev ];
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systemfonts = with pkgs; [ fontconfig.dev freetype.dev ];
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@ -365,7 +400,7 @@ let
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tesseract = with pkgs; [ tesseract leptonica ];
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tiff = [ pkgs.libtiff.dev ];
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tkrplot = with pkgs; [ xorg.libX11 tk.dev ];
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topicmodels = [ pkgs.gsl_1 ];
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topicmodels = [ pkgs.gsl ];
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udunits2 = with pkgs; [ udunits expat ];
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units = [ pkgs.udunits ];
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V8 = [ pkgs.v8 ];
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@ -444,7 +479,6 @@ let
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tikzDevice = with pkgs; [ which texlive.combined.scheme-medium ];
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gridGraphics = [ pkgs.which ];
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adimpro = with pkgs; [ which xorg.xdpyinfo ];
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mzR = [ pkgs.netcdf ];
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cluster = [ pkgs.libiconv ];
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KernSmooth = [ pkgs.libiconv ];
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nlme = [ pkgs.libiconv ];
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@ -478,9 +512,12 @@ let
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Rbowtie = with pkgs; [ zlib.dev ];
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gaston = with pkgs; [ zlib.dev ];
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csaw = with pkgs; [ zlib.dev curl ];
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DirichletMultinomial = with pkgs; [ gsl ];
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DiffBind = with pkgs; [ zlib.dev ];
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CNEr = with pkgs; [ zlib ];
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};
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packagesRequireingX = [
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packagesRequiringX = [
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"accrual"
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"ade4TkGUI"
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"analogue"
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@ -670,6 +707,27 @@ let
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"x12GUI"
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];
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packagesRequiringHome = [
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"aroma_affymetrix"
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"aroma_cn"
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"aroma_core"
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"csodata"
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"DiceView"
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"MSnID"
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"OmnipathR"
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"precommit"
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"PSCBS"
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"repmis"
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"R_cache"
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"R_filesets"
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"RKorAPClient"
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"R_rsp"
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"scholar"
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"stepR"
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"styler"
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"TreeTools"
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];
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packagesToSkipCheck = [
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"Rmpi" # tries to run MPI processes
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"pbdMPI" # tries to run MPI processes
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@ -678,6 +736,11 @@ let
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# Packages which cannot be installed due to lack of dependencies or other reasons.
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brokenPackages = [
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"av"
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"rgl"
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"NetLogoR"
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"proj4"
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"x13binary"
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];
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otherOverrides = old: new: {
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@ -821,10 +884,6 @@ let
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PKG_LIBS = "-L${pkgs.blas}/lib -lblas -L${pkgs.lapack}/lib -llapack";
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});
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EMCluster = old.EMCluster.overrideDerivation (attrs: {
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patches = [ ./patches/EMCluster.patch ];
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});
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spMC = old.spMC.overrideDerivation (attrs: {
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patches = [ ./patches/spMC.patch ];
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});
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@ -972,12 +1031,6 @@ let
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'';
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});
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R_cache = old.R_cache.overrideDerivation (attrs: {
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preConfigure = ''
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export R_CACHE_ROOTPATH=$TMP
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'';
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});
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lpsymphony = old.lpsymphony.overrideDerivation (attrs: {
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preConfigure = ''
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patchShebangs configure
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@ -992,12 +1045,37 @@ let
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buildInputs = [ libsodium.dev ] ++ attrs.buildInputs;
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});
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keyring = old.keyring.overrideDerivation (attrs: {
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preConfigure = ''
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patchShebangs configure
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'';
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});
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Rhtslib = old.Rhtslib.overrideDerivation (attrs: {
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preConfigure = ''
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substituteInPlace R/zzz.R --replace "-lcurl" "-L${pkgs.curl.out}/lib -lcurl"
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'';
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});
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MatchIt = old.MatchIt.overrideDerivation (attrs: {
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patches = [ (pkgs.fetchpatch {
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url = "https://github.com/kosukeimai/MatchIt/commit/8c15a1afa16b74eb04a45e7e46f8aca64ed89bcb.patch";
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sha256 = "sha256-3UI60n49xuX6LniHpTLOUSsHCEAQ7f1FMBVH0jNlW60=";
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}) ];
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});
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h2o = old.h2o.overrideDerivation (attrs: {
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preConfigure = ''
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# prevent download of jar file during install and postpone to first use
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sed -i '/downloadJar()/d' R/zzz.R
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# during runtime the package directory is not writable as it's in the
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# nix store, so store the jar in the user's cache directory instead
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substituteInPlace R/connection.R --replace \
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'dest_file <- file.path(dest_folder, "h2o.jar")' \
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'dest_file <- file.path("~/.cache/", "h2o.jar")'
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'';
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});
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};
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in
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self
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@ -1,6 +0,0 @@
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diff -ru -x '*~' EMCluster_orig/src/Makevars EMCluster/src/Makevars
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--- EMCluster_orig/src/Makevars 2013-07-05 02:43:25.000000000 +0900
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+++ EMCluster/src/Makevars 2014-10-25 18:10:19.190992120 +0900
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@@ -1 +1 @@
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-PKG_LIBS = $(FLIBS) $(BLAS_LIBS) $(LAPACK_LIBS)
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+PKG_LIBS = $(FLIBS) $(LAPACK_LIBS) $(BLAS_LIBS)
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