diff options
Diffstat (limited to 'pkgs/development/r-modules/default.nix')
| -rw-r--r-- | pkgs/development/r-modules/default.nix | 16 |
1 files changed, 15 insertions, 1 deletions
diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index f2c398c0f4526..0549ea253e372 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -413,6 +413,7 @@ 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 ]; @@ -533,6 +534,7 @@ 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 ]; @@ -562,6 +564,7 @@ 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 ]; @@ -618,7 +621,7 @@ 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 ]; @@ -1271,6 +1274,17 @@ 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"; |