diff options
Diffstat (limited to 'infra/libkookie/nixpkgs/pkgs/development/r-modules/default.nix')
| -rw-r--r-- | infra/libkookie/nixpkgs/pkgs/development/r-modules/default.nix | 49 |
1 files changed, 11 insertions, 38 deletions
diff --git a/infra/libkookie/nixpkgs/pkgs/development/r-modules/default.nix b/infra/libkookie/nixpkgs/pkgs/development/r-modules/default.nix index 2d2839c0e007..292653d75e51 100644 --- a/infra/libkookie/nixpkgs/pkgs/development/r-modules/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/development/r-modules/default.nix @@ -44,6 +44,7 @@ let deriveBioc = mkDerive { mkHomepage = {name, biocVersion, ...}: "https://bioconductor.org/packages/${biocVersion}/bioc/html/${name}.html"; mkUrls = {name, version, biocVersion}: [ "mirror://bioc/${biocVersion}/bioc/src/contrib/${name}_${version}.tar.gz" + "mirror://bioc/${biocVersion}/bioc/src/contrib/Archive/${name}/${name}_${version}.tar.gz" "mirror://bioc/${biocVersion}/bioc/src/contrib/Archive/${name}_${version}.tar.gz" ]; }; deriveBiocAnn = mkDerive { @@ -230,7 +231,6 @@ let }; packagesWithNativeBuildInputs = { - abn = [ pkgs.gsl_1 ]; adimpro = [ pkgs.imagemagick ]; animation = [ pkgs.which ]; audio = [ pkgs.portaudio ]; @@ -281,7 +281,6 @@ let ncdf4 = [ pkgs.netcdf ]; nloptr = [ pkgs.nlopt pkgs.pkgconfig ]; odbc = [ pkgs.unixODBC ]; - outbreaker = [ pkgs.gsl_1 ]; pander = [ pkgs.pandoc pkgs.which ]; pbdMPI = [ pkgs.openmpi ]; pbdNCDF4 = [ pkgs.netcdf ]; @@ -293,8 +292,6 @@ let png = [ pkgs.libpng.dev ]; proj4 = [ pkgs.proj ]; protolite = [ pkgs.protobuf ]; - qtbase = [ pkgs.qt4 ]; - qtpaint = [ pkgs.qt4 ]; R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ]; RAppArmor = [ pkgs.libapparmor ]; rapportools = [ pkgs.which ]; @@ -307,13 +304,12 @@ let reprex = [ pkgs.which ]; rgdal = [ pkgs.proj.dev pkgs.gdal ]; rgeos = [ pkgs.geos ]; - rggobi = [ pkgs.ggobi pkgs.gtk2.dev pkgs.libxml2.dev ]; Rglpk = [ pkgs.glpk ]; RGtk2 = [ pkgs.gtk2.dev ]; rhdf5 = [ pkgs.zlib ]; Rhdf5lib = [ pkgs.zlib ]; Rhpc = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.openmpi pkgs.pcre.dev ]; - Rhtslib = [ pkgs.zlib.dev pkgs.automake pkgs.autoconf ]; + Rhtslib = [ pkgs.zlib.dev pkgs.automake pkgs.autoconf pkgs.bzip2.dev pkgs.lzma.dev pkgs.curl.dev ]; rjags = [ pkgs.jags ]; rJava = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.pcre.dev pkgs.jdk pkgs.libzip ]; Rlibeemd = [ pkgs.gsl_1 ]; @@ -353,7 +349,6 @@ let TAQMNGR = [ pkgs.zlib.dev ]; tesseract = [ pkgs.tesseract pkgs.leptonica ]; tiff = [ pkgs.libtiff.dev ]; - TKF = [ pkgs.gsl_1 ]; tkrplot = [ pkgs.xorg.libX11 pkgs.tk.dev ]; topicmodels = [ pkgs.gsl_1 ]; udunits2 = [ pkgs.udunits pkgs.expat ]; @@ -371,10 +366,10 @@ let gmapR = [ pkgs.zlib.dev ]; Rsubread = [ pkgs.zlib.dev ]; XVector = [ pkgs.zlib.dev ]; - Rsamtools = [ pkgs.zlib.dev ]; + Rsamtools = [ pkgs.zlib.dev pkgs.curl.dev ]; rtracklayer = [ pkgs.zlib.dev ]; affyio = [ pkgs.zlib.dev ]; - VariantAnnotation = [ pkgs.zlib.dev ]; + VariantAnnotation = [ pkgs.zlib.dev pkgs.curl.dev ]; snpStats = [ pkgs.zlib.dev ]; }; @@ -391,12 +386,9 @@ let pbdZMQ = lib.optionals stdenv.isDarwin [ pkgs.darwin.binutils ]; RMark = [ pkgs.which ]; RPushbullet = [ pkgs.which ]; - qtpaint = [ pkgs.cmake ]; - qtbase = [ pkgs.cmake pkgs.perl ]; RcppEigen = [ pkgs.libiconv ]; RCurl = [ pkgs.curl.dev ]; R2SWF = [ pkgs.pkgconfig ]; - rggobi = [ pkgs.pkgconfig ]; rgl = [ pkgs.libGLU pkgs.libGLU.dev pkgs.libGL pkgs.xlibsWrapper ]; RGtk2 = [ pkgs.pkgconfig ]; RProtoBuf = [ pkgs.pkgconfig ]; @@ -458,9 +450,7 @@ let "AnthropMMD" "aplpack" "asbio" - "AtelieR" "BAT" - "bayesDem" "BCA" "betapart" "BiodiversityR" @@ -495,7 +485,6 @@ let "dynBiplotGUI" "EasyqpcR" "EcoVirtual" - "ENiRG" "exactLoglinTest" "fat2Lpoly" "fbati" @@ -505,7 +494,6 @@ let "FFD" "fgui" "fisheyeR" - "fit4NM" "forams" "forensim" "FreeSortR" @@ -518,15 +506,12 @@ let "GGEBiplotGUI" "gnm" "GPCSIV" - "GrammR" "GrapheR" "GroupSeq" "gsubfn" "GUniFrac" "gWidgets2RGtk2" "gWidgets2tcltk" - "gWidgetsRGtk2" - "gWidgetstcltk" "HH" "HiveR" "ic50" @@ -542,14 +527,10 @@ let "LS2Wstat" "MareyMap" "memgene" - "MergeGUI" "metacom" "Meth27QC" - "MetSizeR" - "MicroStrategyR" "migui" "miniGUI" - "MissingDataGUI" "mixsep" "MplusAutomation" "mpmcorrelogram" @@ -567,7 +548,6 @@ let "pez" "phylotools" "picante" - "PKgraph" "plotSEMM" "plsRbeta" "plsRglm" @@ -578,8 +558,6 @@ let "prefmod" "PrevMap" "ProbForecastGOP" - "qtbase" - "qtpaint" "r4ss" "RandomFields" "rareNMtests" @@ -598,7 +576,6 @@ let "RcmdrPlugin_KMggplot2" "RcmdrPlugin_lfstat" "RcmdrPlugin_MA" - "RcmdrPlugin_mosaic" "RcmdrPlugin_MPAStats" "RcmdrPlugin_orloca" "RcmdrPlugin_plotByGroup" @@ -616,16 +593,12 @@ let "RcmdrPlugin_UCA" "recluster" "relimp" - "RenextGUI" - "reshapeGUI" "rgl" "RHRV" "rich" "RNCEP" - "RQDA" "RSDA" "RSurvey" - "RunuranGUI" "simba" "Simile" "SimpleTable" @@ -662,13 +635,13 @@ let "vegan" "vegan3d" "vegclust" - "WMCapacity" "x12GUI" ]; packagesToSkipCheck = [ "Rmpi" # tries to run MPI processes "pbdMPI" # tries to run MPI processes + "data_table" # fails to rename shared library before check ]; # Packages which cannot be installed due to lack of dependencies or other reasons. @@ -723,8 +696,9 @@ let }); data_table = old.data_table.overrideDerivation (attrs: { - NIX_CFLAGS_COMPILE = attrs.NIX_CFLAGS_COMPILE - + lib.optionalString stdenv.isDarwin " -fopenmp"; + NIX_CFLAGS_COMPILE = attrs.NIX_CFLAGS_COMPILE + " -fopenmp"; + patchPhase = "patchShebangs configure"; + postInstall = "mv $out/library/data.table/libs/{data.table,datatable}.so"; }); ModelMetrics = old.ModelMetrics.overrideDerivation (attrs: { @@ -772,10 +746,6 @@ let ''; }); - qtbase = old.qtbase.overrideDerivation (attrs: { - patches = [ ./patches/qtbase.patch ]; - }); - Rmpi = old.Rmpi.overrideDerivation (attrs: { configureFlags = [ "--with-Rmpi-type=OPENMPI" @@ -828,6 +798,9 @@ let }); openssl = old.openssl.overrideDerivation (attrs: { + preConfigure = '' + patchShebangs configure + ''; PKGCONFIG_CFLAGS = "-I${pkgs.openssl.dev}/include"; PKGCONFIG_LIBS = "-Wl,-rpath,${pkgs.openssl.out}/lib -L${pkgs.openssl.out}/lib -lssl -lcrypto"; }); |