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author | Justin Bedo <cu@cua0.org> | 2018-02-15 16:22:52 +1100 |
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committer | Justin Bedo <cu@cua0.org> | 2018-02-21 09:58:17 +1100 |
commit | cfc07bcf0eee0a9c767cc9157b7785a264090d86 (patch) | |
tree | b655e9bf898dba489ef87677095792e2da57ece4 /pkgs/development/r-modules/default.nix | |
parent | 5bede1a25280d3ce57d9140babdd2ecac6c1333a (diff) | |
download | nixlib-cfc07bcf0eee0a9c767cc9157b7785a264090d86.tar nixlib-cfc07bcf0eee0a9c767cc9157b7785a264090d86.tar.gz nixlib-cfc07bcf0eee0a9c767cc9157b7785a264090d86.tar.bz2 nixlib-cfc07bcf0eee0a9c767cc9157b7785a264090d86.tar.lz nixlib-cfc07bcf0eee0a9c767cc9157b7785a264090d86.tar.xz nixlib-cfc07bcf0eee0a9c767cc9157b7785a264090d86.tar.zst nixlib-cfc07bcf0eee0a9c767cc9157b7785a264090d86.zip |
bioconductor: 3.4 -> 3.6
Diffstat (limited to 'pkgs/development/r-modules/default.nix')
-rw-r--r-- | pkgs/development/r-modules/default.nix | 39 |
1 files changed, 8 insertions, 31 deletions
diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index ee1fb24b3098..fbc4ed2dc469 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -42,16 +42,16 @@ let # from the name, version, sha256, and optional per-package arguments above # deriveBioc = mkDerive { - mkHomepage = {name, rVersion}: "https://bioconductor.org/packages/${rVersion}/bioc/html/${name}.html"; - mkUrls = {name, version, rVersion}: [ "mirror://bioc/${rVersion}/bioc/src/contrib/${name}_${version}.tar.gz" ]; + mkHomepage = {name, biocVersion}: "https://bioconductor.org/packages/${biocVersion}/bioc/html/${name}.html"; + mkUrls = {name, version, biocVersion}: [ "mirror://bioc/${biocVersion}/bioc/src/contrib/${name}_${version}.tar.gz" ]; }; deriveBiocAnn = mkDerive { - mkHomepage = {name, rVersion}: "http://www.bioconductor.org/packages/${name}.html"; - mkUrls = {name, version, rVersion}: [ "mirror://bioc/${rVersion}/data/annotation/src/contrib/${name}_${version}.tar.gz" ]; + mkHomepage = {name, biocVersion}: "http://www.bioconductor.org/packages/${name}.html"; + mkUrls = {name, version, biocVersion}: [ "mirror://bioc/${biocVersion}/data/annotation/src/contrib/${name}_${version}.tar.gz" ]; }; deriveBiocExp = mkDerive { - mkHomepage = {name, rVersion}: "http://www.bioconductor.org/packages/${name}.html"; - mkUrls = {name, version, rVersion}: [ "mirror://bioc/${rVersion}/data/experiment/src/contrib/${name}_${version}.tar.gz" ]; + mkHomepage = {name, biocVersion}: "http://www.bioconductor.org/packages/${name}.html"; + mkUrls = {name, version, biocVersion}: [ "mirror://bioc/${biocVersion}/data/experiment/src/contrib/${name}_${version}.tar.gz" ]; }; deriveCran = mkDerive { mkHomepage = {name, snapshot}: "http://mran.revolutionanalytics.com/snapshot/${snapshot}/web/packages/${name}/"; @@ -230,6 +230,7 @@ let packagesWithNativeBuildInputs = { abn = [ pkgs.gsl_1 ]; adimpro = [ pkgs.imagemagick ]; + animation = [ pkgs.which ]; audio = [ pkgs.portaudio ]; BayesSAE = [ pkgs.gsl_1 ]; BayesVarSel = [ pkgs.gsl_1 ]; @@ -313,7 +314,7 @@ let RGtk2 = [ pkgs.gtk2.dev ]; rhdf5 = [ pkgs.zlib ]; Rhpc = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.openmpi pkgs.pcre.dev ]; - Rhtslib = [ pkgs.zlib.dev ]; + Rhtslib = [ pkgs.zlib.dev pkgs.automake pkgs.autoconf ]; RJaCGH = [ pkgs.zlib.dev ]; rjags = [ pkgs.jags ]; rJava = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.pcre.dev pkgs.jdk pkgs.libzip ]; @@ -350,7 +351,6 @@ let simplexreg = [ pkgs.gsl_1 ]; SOD = [ pkgs.opencl-headers ]; spate = [ pkgs.fftw.dev ]; - sprint = [ pkgs.openmpi ]; ssanv = [ pkgs.proj ]; stsm = [ pkgs.gsl_1 ]; stringi = [ pkgs.icu.dev ]; @@ -384,7 +384,6 @@ let affyio = [ pkgs.zlib.dev ]; VariantAnnotation = [ pkgs.zlib.dev ]; snpStats = [ pkgs.zlib.dev ]; - gputools = [ pkgs.pcre.dev pkgs.lzma.dev pkgs.zlib.dev pkgs.bzip2.dev pkgs.icu.dev ]; }; packagesWithBuildInputs = { @@ -398,7 +397,6 @@ let RPushbullet = [ pkgs.which ]; qtpaint = [ pkgs.cmake ]; qtbase = [ pkgs.cmake pkgs.perl ]; - gmatrix = [ pkgs.cudatoolkit pkgs.which ]; RCurl = [ pkgs.curl.dev ]; R2SWF = [ pkgs.pkgconfig ]; rggobi = [ pkgs.pkgconfig ]; @@ -427,12 +425,10 @@ let tesseract = [ pkgs.pkgconfig ]; Cairo = [ pkgs.pkgconfig ]; Rsymphony = [ pkgs.pkgconfig pkgs.doxygen pkgs.graphviz pkgs.subversion ]; - qtutils = [ pkgs.qt4 ]; tcltk2 = [ pkgs.tcl pkgs.tk ]; tikzDevice = [ pkgs.which pkgs.texlive.combined.scheme-medium ]; rPython = [ pkgs.which ]; gridGraphics = [ pkgs.which ]; - gputools = [ pkgs.which pkgs.cudatoolkit ]; adimpro = [ pkgs.which pkgs.xorg.xdpyinfo ]; PET = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ]; dti = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ]; @@ -498,7 +494,6 @@ let "EnQuireR" "eVenn" "exactLoglinTest" - "FAiR" "fat2Lpoly" "fbati" "FD" @@ -519,7 +514,6 @@ let "geoR" "geoRglm" "georob" - "GeoXp" "GGEBiplotGUI" "gnm" "GPCSIV" @@ -535,7 +529,6 @@ let "HH" "HiveR" "HomoPolymer" - "iBUGS" "ic50" "iDynoR" "in2extRemes" @@ -591,10 +584,8 @@ let "prefmod" "PrevMap" "ProbForecastGOP" - "QCAGUI" "qtbase" "qtpaint" - "qtutils" "R2STATS" "r4ss" "RandomFields" @@ -700,16 +691,11 @@ let packagesToSkipCheck = [ "Rmpi" # tries to run MPI processes - "gmatrix" # requires CUDA runtime - "gputools" # requires CUDA runtime - "sprint" # tries to run MPI processes "pbdMPI" # tries to run MPI processes ]; # Packages which cannot be installed due to lack of dependencies or other reasons. brokenPackages = [ - "gputools" # depends on non-free cudatoolkit-8.0.61 - "gmatrix" # depends on non-free cudatoolkit-8.0.61 ]; otherOverrides = old: new: { @@ -840,15 +826,6 @@ let patches = [ ./patches/spMC.patch ]; }); - BayesLogit = old.BayesLogit.overrideDerivation (attrs: { - patches = [ ./patches/BayesLogit.patch ]; - buildInputs = (attrs.buildInputs or []) ++ [ pkgs.openblasCompat ]; - }); - - BayesBridge = old.BayesBridge.overrideDerivation (attrs: { - patches = [ ./patches/BayesBridge.patch ]; - }); - openssl = old.openssl.overrideDerivation (attrs: { PKGCONFIG_CFLAGS = "-I${pkgs.openssl.dev}/include"; PKGCONFIG_LIBS = "-Wl,-rpath,${pkgs.openssl.out}/lib -L${pkgs.openssl.out}/lib -lssl -lcrypto"; |