rPackages: CRAN and BioC update (#434138)

pkgs/development/r-modules/bioc-experiment-packages.json

@@ -899,8 +899,8 @@
     },
     "PhyloProfileData": {
       "name": "PhyloProfileData",
-      "version": "1.22.0",
-      "sha256": "0zbs9aaf8xmz3is9vf54d0iib00ypa6vly5s207dbcj7l1x4h0yc",
+      "version": "1.22.3",
+      "sha256": "0bc702idbsnqs2fga4jd9qwqphc0hrv3j1hidwz26awkfwb8yv59",
       "depends": ["BiocStyle", "Biostrings", "ExperimentHub"]
     },
     "ProData": {
@@ -911,8 +911,8 @@
     },
     "ProteinGymR": {
       "name": "ProteinGymR",
-      "version": "1.2.1",
-      "sha256": "1xwva9gnfldgx2bw62zwz3wlc84k4jlnybq81nr0xqa6xdr9fycl",
+      "version": "1.2.4",
+      "sha256": "0czlxm1z5bpb096alwb96a3gwpv9244h0b8isbbfdiy70rcd21rm",
       "depends": ["AnnotationHub", "ComplexHeatmap", "ExperimentHub", "bio3d", "circlize", "dplyr", "forcats", "ggExtra", "ggdist", "gghalves", "ggplot2", "htmltools", "lifecycle", "pals", "purrr", "queryup", "r3dmol", "rlang", "spdl", "stringr", "tidyr", "tidyselect"]
     },
     "PtH2O2lipids": {

pkgs/development/r-modules/default.nix

@@ -451,7 +451,10 @@ let
       libjpeg
     ];
     bnpmr = [ pkgs.gsl ];
-    caviarpd = [ pkgs.cargo ];
+    caviarpd = with pkgs; [
+      cargo
+      rustc
+    ];
     cairoDevice = [ pkgs.gtk2.dev ];
     Cairo = with pkgs; [
       libtiff
@@ -569,6 +572,11 @@ let
     ];
     Rigraphlib = [ pkgs.cmake ];
     HiCseg = [ pkgs.gsl ];
+    hypergeo2 = with pkgs; [
+      gmp.dev
+      mpfr.dev
+      pkg-config
+    ];
     imager = [ pkgs.xorg.libX11.dev ];
     imbibe = [ pkgs.zlib.dev ];
     image_CannyEdges = with pkgs; [
@@ -586,7 +594,10 @@ let
     leidenAlg = [ pkgs.gmp.dev ];
     Libra = [ pkgs.gsl ];
     libstable4u = [ pkgs.gsl ];
-    heck = [ pkgs.cargo ];
+    heck = with pkgs; [
+      cargo
+      rustc
+    ];
     LOMAR = [ pkgs.gmp.dev ];
     littler = [ pkgs.libdeflate ];
     lpsymphony = with pkgs; [
@@ -678,6 +689,11 @@ let
     gdalcubes = [ pkgs.pkg-config ];
     rgeos = [ pkgs.geos ];
     Rglpk = [ pkgs.glpk ];
+    RcppPlanc = with pkgs; [
+      which
+      cmake
+      pkg-config
+    ];
     RGtk2 = [ pkgs.gtk2.dev ];
     rhdf5 = [ pkgs.zlib ];
     Rhdf5lib = with pkgs; [ zlib.dev ];
@@ -1106,7 +1122,10 @@ let
       fftw.dev
     ];
     specklestar = [ pkgs.fftw.dev ];
-    cartogramR = [ pkgs.fftw.dev ];
+    cartogramR = with pkgs; [
+      fftw.dev
+      pkg-config
+    ];
     jqr = [ pkgs.jq.out ];
     kza = [ pkgs.pkg-config ];
     igraph = with pkgs; [
@@ -1114,7 +1133,10 @@ let
       libxml2.dev
       glpk
     ];
-    interpolation = [ pkgs.gmp ];
+    interpolation = with pkgs; [
+      gmp
+      mpfr
+    ];
     image_textlinedetector = with pkgs; [
       pkg-config
       opencv
@@ -1364,6 +1386,10 @@ let
     crandep = [ pkgs.gsl ];
     catSurv = [ pkgs.gsl ];
     ccfindR = [ pkgs.gsl ];
+    RcppPlanc = with pkgs; [
+      hwloc
+      hdf5.dev
+    ];
     screenCounter = [ pkgs.zlib.dev ];
     SPARSEMODr = [ pkgs.gsl ];
     RKHSMetaMod = [ pkgs.gsl ];
@@ -1424,7 +1450,11 @@ let
     ];
     DropletUtils = [ pkgs.zlib.dev ];
     RMariaDB = [ pkgs.libmysqlclient.dev ];
-    ijtiff = [ pkgs.libtiff ];
+    ijtiff = with pkgs; [
+      libtiff
+      libjpeg
+      zlib
+    ];
     ragg =
       with pkgs;
       [
@@ -1644,6 +1674,7 @@ let
     "minired" # deprecated on CRAN
 
     # Impure network access during build
+    "BulkSignalR"
     "waddR"
     "tiledb"
     "switchr"
@@ -1753,6 +1784,14 @@ let
       postPatch = "patchShebangs configure";
     });
 
+    arcgisplaces = old.arcgisplaces.overrideAttrs (attrs: {
+      postPatch = "patchShebangs configure";
+    });
+
+    cartogramR = old.cartogramR.overrideAttrs (attrs: {
+      postPatch = "patchShebangs configure";
+    });
+
     rshift = old.rshift.overrideAttrs (attrs: {
       postPatch = "patchShebangs configure";
     });
@@ -1790,6 +1829,10 @@ let
       '';
     });
 
+    fcl = old.fcl.overrideAttrs (attrs: {
+      postPatch = "patchShebangs configure";
+    });
+
     fio = old.fio.overrideAttrs (attrs: {
       postPatch = "patchShebangs configure";
     });
@@ -1976,7 +2019,11 @@ let
     });
 
     zoomerjoin = old.zoomerjoin.overrideAttrs (attrs: {
-      nativeBuildInputs = [ pkgs.cargo ] ++ attrs.nativeBuildInputs;
+      nativeBuildInputs = [
+        pkgs.cargo
+        pkgs.rustc
+      ]
+      ++ attrs.nativeBuildInputs;
       postPatch = "patchShebangs configure";
     });
 
@@ -1999,13 +2046,6 @@ let
       postPatch = "patchShebangs configure";
     });
 
-    graper = old.graper.overrideAttrs (attrs: {
-      postPatch = ''
-        substituteInPlace "src/Makevars" \
-          --replace-fail "CXX_STD=CXX11" "CXX_STD=CXX14"
-      '';
-    });
-
     ocf = old.ocf.overrideAttrs (attrs: {
       postPatch = "patchShebangs configure";
     });
@@ -2705,6 +2745,10 @@ let
       '';
     });
 
+    webfakes = old.webfakes.overrideAttrs (_: {
+      postPatch = "patchShebangs configure";
+    });
+
     redland = old.redland.overrideAttrs (_: {
       PKGCONFIG_CFLAGS = "-I${pkgs.redland}/include -I${pkgs.librdf_raptor2}/include/raptor2 -I${pkgs.librdf_rasqal}/include/rasqal";
       PKGCONFIG_LIBS = "-L${pkgs.redland}/lib -L${pkgs.librdf_raptor2}/lib -L${pkgs.librdf_rasqal}/lib -lrdf -lraptor2 -lrasqal";