r-modules: Fix a number of popular R packages
The R V8 package still depends on V8 3.14 so this is also included.
This commit is contained in:
Hamish Mackenzie
committed by
Domen Kožar
Domen Kožar
parent
43f94ff5a9
commit
8870d1a67d
@@ -253,6 +253,7 @@ let
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fftwtools = [ pkgs.fftw.dev ];
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Formula = [ pkgs.gmp ];
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geoCount = [ pkgs.gsl_1 ];
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gdtools = [ pkgs.cairo.dev pkgs.fontconfig.lib pkgs.freetype.dev ];
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git2r = [ pkgs.zlib.dev pkgs.openssl.dev ];
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GLAD = [ pkgs.gsl_1 ];
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glpkAPI = [ pkgs.gmp pkgs.glpk ];
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@@ -260,32 +261,37 @@ let
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graphscan = [ pkgs.gsl_1 ];
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gsl = [ pkgs.gsl_1 ];
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h5 = [ pkgs.hdf5-cpp pkgs.which ];
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haven = [ pkgs.libiconv ];
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h5vc = [ pkgs.zlib.dev ];
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HiCseg = [ pkgs.gsl_1 ];
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imager = [ pkgs.x11 ];
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iBMQ = [ pkgs.gsl_1 ];
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igraph = [ pkgs.gmp ];
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igraph = [ pkgs.gmp pkgs.libxml2.dev ];
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JavaGD = [ pkgs.jdk ];
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jpeg = [ pkgs.libjpeg.dev ];
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KFKSDS = [ pkgs.gsl_1 ];
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kza = [ pkgs.fftw.dev ];
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libamtrack = [ pkgs.gsl_1 ];
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magick = [ pkgs.imagemagick.dev ];
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mixcat = [ pkgs.gsl_1 ];
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mvabund = [ pkgs.gsl_1 ];
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mwaved = [ pkgs.fftw.dev ];
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ncdf4 = [ pkgs.netcdf ];
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nloptr = [ pkgs.nlopt ];
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openssl = [ pkgs.openssl.dev ];
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odbc = [ pkgs.unixODBC ];
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openssl = [ pkgs.openssl pkgs.openssl.dev ];
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outbreaker = [ pkgs.gsl_1 ];
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pander = [ pkgs.pandoc pkgs.which ];
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pbdMPI = [ pkgs.openmpi ];
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pbdNCDF4 = [ pkgs.netcdf ];
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pbdPROF = [ pkgs.openmpi ];
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pbdZMQ = [ pkgs.which ];
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pdftools = [ pkgs.poppler.dev ];
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PKI = [ pkgs.openssl.dev ];
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png = [ pkgs.libpng.dev ];
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PopGenome = [ pkgs.zlib.dev ];
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proj4 = [ pkgs.proj ];
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protolite = [ pkgs.protobuf ];
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qtbase = [ pkgs.qt4 ];
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qtpaint = [ pkgs.qt4 ];
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R2GUESS = [ pkgs.gsl_1 ];
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@@ -293,6 +299,7 @@ let
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RAppArmor = [ pkgs.libapparmor ];
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rapportools = [ pkgs.which ];
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rapport = [ pkgs.which ];
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readxl = [ pkgs.libiconv ];
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rbamtools = [ pkgs.zlib.dev ];
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rcdd = [ pkgs.gmp.dev ];
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RcppCNPy = [ pkgs.zlib.dev ];
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@@ -315,14 +322,15 @@ let
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rmatio = [ pkgs.zlib.dev ];
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Rmpfr = [ pkgs.gmp pkgs.mpfr.dev ];
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Rmpi = [ pkgs.openmpi ];
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RMySQL = [ pkgs.zlib pkgs.mysql.lib ];
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RMySQL = [ pkgs.zlib pkgs.mysql.lib pkgs.mariadb pkgs.openssl.dev ];
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RNetCDF = [ pkgs.netcdf pkgs.udunits ];
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RODBCext = [ pkgs.libiodbc ];
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RODBC = [ pkgs.libiodbc ];
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rpanel = [ pkgs.bwidget ];
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rpg = [ pkgs.postgresql ];
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rphast = [ pkgs.pcre.dev pkgs.zlib pkgs.bzip2 pkgs.gzip pkgs.readline ];
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Rpoppler = [ pkgs.poppler ];
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RPostgreSQL = [ pkgs.postgresql ];
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RPostgreSQL = [ pkgs.postgresql pkgs.postgresql ];
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RProtoBuf = [ pkgs.protobuf ];
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rPython = [ pkgs.python ];
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RSclient = [ pkgs.openssl.dev ];
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@@ -331,6 +339,7 @@ let
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rtfbs = [ pkgs.zlib pkgs.pcre.dev pkgs.bzip2 pkgs.gzip pkgs.readline ];
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rtiff = [ pkgs.libtiff.dev ];
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runjags = [ pkgs.jags ];
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RSymphony = [ pkgs.symphony ];
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RVowpalWabbit = [ pkgs.zlib.dev pkgs.boost ];
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rzmq = [ pkgs.zeromq3 ];
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SAVE = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre ];
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@@ -338,6 +347,7 @@ let
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seewave = [ pkgs.fftw.dev pkgs.libsndfile.dev ];
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seqinr = [ pkgs.zlib.dev ];
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seqminer = [ pkgs.zlib.dev pkgs.bzip2 ];
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sf = [ pkgs.gdal pkgs.proj pkgs.geos ];
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showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype.dev ];
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simplexreg = [ pkgs.gsl_1 ];
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SOD = [ pkgs.opencl-headers ];
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@@ -349,12 +359,13 @@ let
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survSNP = [ pkgs.gsl_1 ];
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sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ];
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TAQMNGR = [ pkgs.zlib.dev ];
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tesseract = [ pkgs.tesseract pkgs.leptonica ];
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tiff = [ pkgs.libtiff.dev ];
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TKF = [ pkgs.gsl_1 ];
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tkrplot = [ pkgs.xorg.libX11 pkgs.tk.dev ];
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topicmodels = [ pkgs.gsl_1 ];
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udunits2 = [ pkgs.udunits pkgs.expat ];
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V8 = [ pkgs.v8 ];
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V8 = [ pkgs.v8_3_14 ];
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VBLPCM = [ pkgs.gsl_1 ];
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VBmix = [ pkgs.gsl_1 pkgs.fftw pkgs.qt4 ];
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WhopGenome = [ pkgs.zlib.dev ];
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@@ -401,12 +412,20 @@ let
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chebpol = [ pkgs.pkgconfig ];
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fftw = [ pkgs.pkgconfig ];
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geoCount = [ pkgs.pkgconfig ];
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gdtools = [ pkgs.pkgconfig ];
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kza = [ pkgs.pkgconfig ];
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magick = [ pkgs.pkgconfig ];
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mwaved = [ pkgs.pkgconfig ];
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odbc = [ pkgs.pkgconfig ];
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openssl = [ pkgs.pkgconfig ];
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pdftools = [ pkgs.pkgconfig ];
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sf = [ pkgs.pkgconfig ];
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showtext = [ pkgs.pkgconfig ];
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spate = [ pkgs.pkgconfig ];
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stringi = [ pkgs.pkgconfig ];
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sys = [ pkgs.libapparmor ];
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sysfonts = [ pkgs.pkgconfig ];
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tesseract = [ pkgs.pkgconfig ];
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Cairo = [ pkgs.pkgconfig ];
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Rsymphony = [ pkgs.pkgconfig pkgs.doxygen pkgs.graphviz pkgs.subversion ];
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qtutils = [ pkgs.qt4 ];
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@@ -782,8 +801,10 @@ let
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});
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RMySQL = old.RMySQL.overrideDerivation (attrs: {
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patches = [ ./patches/RMySQL.patch ];
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MYSQL_DIR="${pkgs.mysql.lib}";
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preConfigure = ''
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patchShebangs configure
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'';
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});
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devEMF = old.devEMF.overrideDerivation (attrs: {
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@@ -818,6 +839,9 @@ let
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openssl = old.openssl.overrideDerivation (attrs: {
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OPENSSL_INCLUDES = "${pkgs.openssl.dev}/include";
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preConfigure = ''
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sed -i.bak 's|^\( *PKG_LIBS_VERSIONED=\).*$|\1$PKG_LIBS|' configure
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'';
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});
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Rserve = old.Rserve.overrideDerivation (attrs: {
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@@ -835,7 +859,71 @@ let
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});
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V8 = old.V8.overrideDerivation (attrs: {
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preConfigure = "export V8_INCLUDES=${pkgs.v8}/include";
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preConfigure = ''
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export INCLUDE_DIR=${pkgs.v8_3_14}/include
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export LIB_DIR=${pkgs.v8_3_14}/lib
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patchShebangs configure
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'';
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});
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acs = old.acs.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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gdtools = old.gdtools.overrideDerivation (attrs: {
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preConfigure = ''
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patchShebangs configure
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'';
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NIX_LDFLAGS = "-lfontconfig -lfreetype";
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});
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magick = old.magick.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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protolite = old.protolite.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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rpanel = old.rpanel.overrideDerivation (attrs: {
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preConfigure = ''
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export TCLLIBPATH="${pkgs.bwidget}/lib/bwidget${pkgs.bwidget.version}"
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'';
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TCLLIBPATH = "${pkgs.bwidget}/lib/bwidget${pkgs.bwidget.version}";
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});
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OpenMx = old.OpenMx.overrideDerivation (attrs: {
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preConfigure = ''
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patchShebangs configure
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'';
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});
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odbc = old.odbc.overrideDerivation (attrs: {
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preConfigure = ''
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patchShebangs configure
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'';
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});
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x13binary = old.x13binary.overrideDerivation (attrs: {
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preConfigure = ''
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patchShebangs configure
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'';
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});
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geojsonio = old.geojsonio.overrideDerivation (attrs: {
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preConfigure = ''
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export SSL_CERT_FILE=${pkgs.cacert}/etc/ssl/certs/ca-bundle.crt
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'';
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});
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rstan = old.rstan.overrideDerivation (attrs: {
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NIX_CFLAGS_COMPILE = "${attrs.NIX_CFLAGS_COMPILE} -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION";
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});
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};
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