R: use replace-fail for substitutions

pkgs/by-name/r/R/package.nix

@@ -117,11 +117,11 @@ stdenv.mkDerivation (finalAttrs: {
   # https://github.com/NixOS/nixpkgs/issues/146131
   postPatch = lib.optionalString stdenv.hostPlatform.isDarwin ''
     substituteInPlace configure \
-      --replace "-install_name libRblas.dylib" "-install_name $out/lib/R/lib/libRblas.dylib" \
+      --replace-fail "-install_name libRblas.dylib" "-install_name $out/lib/R/lib/libRblas.dylib" \
-      --replace "-install_name libRlapack.dylib" "-install_name $out/lib/R/lib/libRlapack.dylib" \
+      --replace-fail "-install_name libRlapack.dylib" "-install_name $out/lib/R/lib/libRlapack.dylib" \
-      --replace "-install_name libR.dylib" "-install_name $out/lib/R/lib/libR.dylib"
+      --replace-fail "-install_name libR.dylib" "-install_name $out/lib/R/lib/libR.dylib"
     substituteInPlace tests/Examples/Makefile.in \
-      --replace "test-Examples: test-Examples-Base" "test-Examples:" # do not test the examples
+      --replace-fail "test-Examples: test-Examples-Base" "test-Examples:" # do not test the examples
   '';
 
   dontDisableStatic = static;
@@ -163,8 +163,8 @@ stdenv.mkDerivation (finalAttrs: {
   ''
   + ''
     )
-    echo >>etc/Renviron.in "TCLLIBPATH=${tk}/lib"
+    echo >>etc/Renviron.in 'TCLLIBPATH="${tk}/lib ''${TCLLIBPATH}"'
-    echo >>etc/Renviron.in "TZDIR=${tzdata}/share/zoneinfo"
+    echo >>etc/Renviron.in 'TZDIR=${tzdata}/share/zoneinfo'
   '';
 
   installTargets = [

pkgs/development/r-modules/default.nix

@@ -25,7 +25,6 @@ let
 
   buildRPackage = pkgs.callPackage ./generic-builder.nix {
     inherit R;
-    inherit (pkgs) gettext gfortran;
   };
 
   # Generates package templates given per-repository settings
@@ -64,7 +63,6 @@ let
         };
         inherit doCheck requireX;
         propagatedBuildInputs = depends;
-        nativeBuildInputs = depends;
         meta.homepage = mkHomepage (args // { inherit name; });
         meta.platforms = platforms;
         meta.hydraPlatforms = hydraPlatforms;
@@ -142,7 +140,7 @@ let
   #
   # {
   #   foo = old.foo.overrideAttrs (attrs: {
-  #     nativeBuildInputs = attrs.nativeBuildInputs ++ [ pkgs.bar ];
+  #     nativeBuildInputs = (attrs.nativeBuildInputs or [ ]) ++ [ pkgs.bar ];
   #   });
   # }
   overrideNativeBuildInputs =
@@ -150,7 +148,7 @@ let
     lib.mapAttrs (
       name: value:
       (builtins.getAttr name old).overrideAttrs (attrs: {
-        nativeBuildInputs = attrs.nativeBuildInputs ++ value;
+        nativeBuildInputs = (attrs.nativeBuildInputs or [ ]) ++ value;
       })
     ) overrides;
 
@@ -165,7 +163,7 @@ let
   #
   # {
   #   foo = old.foo.overrideAttrs (attrs: {
-  #     buildInputs = attrs.buildInputs ++ [ pkgs.bar ];
+  #     buildInputs = (attrs.buildInputs or [ ]) ++ [ pkgs.bar ];
   #   });
   # }
   overrideBuildInputs =
@@ -173,7 +171,7 @@ let
     lib.mapAttrs (
       name: value:
       (builtins.getAttr name old).overrideAttrs (attrs: {
-        buildInputs = attrs.buildInputs ++ value;
+        buildInputs = (attrs.buildInputs or [ ]) ++ value;
       })
     ) overrides;
 
@@ -211,7 +209,6 @@ let
   #
   # {
   #   foo = old.foo.overrideAttrs (attrs: {
-  #     nativeBuildInputs = attrs.nativeBuildInputs ++ [ self.bar ];
   #     propagatedBuildInputs = attrs.propagatedBuildInputs ++ [ self.bar ];
   #   });
   # }
@@ -220,7 +217,6 @@ let
     lib.mapAttrs (
       name: value:
       (builtins.getAttr name old).overrideAttrs (attrs: {
-        nativeBuildInputs = (attrs.nativeBuildInputs or [ ]) ++ value;
         propagatedBuildInputs = (attrs.propagatedBuildInputs or [ ]) ++ value;
       })
     ) overrides;
@@ -434,7 +430,6 @@ let
     JMcmprsk = [ pkgs.gsl ]; # for gsl-config
     KSgeneral = with pkgs; [ pkg-config ];
     LCMCR = [ pkgs.gsl ]; # for gsl-config
-    ModelMetrics = lib.optional stdenv.hostPlatform.isDarwin pkgs.llvmPackages.openmp;
     PEPBVS = [ pkgs.gsl ]; # for gsl-config
     PICS = [ pkgs.gsl ];
     QF = [ pkgs.gsl ]; # for gsl-config
@@ -616,13 +611,7 @@ let
       pkgs.which
       pkgs.cmake
     ];
-    data_table = (
+    data_table = [ pkgs.pkg-config ];
-      # added extra parentheses so that `keep-sorted` doesn't get tripped up
-      [
-        pkgs.pkg-config
-      ]
-      ++ lib.optional stdenv.hostPlatform.isDarwin pkgs.llvmPackages.openmp
-    );
     datefixR = with pkgs; [
       cargo
       rustc
@@ -721,6 +710,7 @@ let
       pkgs.which
       pkgs.cmake
     ];
+    httpuv = [ pkgs.pkg-config ];
     hypergeo2 = [ pkgs.pkg-config ];
     iBMQ = [ pkgs.gsl ]; # for gsl-config
     image_textlinedetector = [ pkgs.pkg-config ];
@@ -766,6 +756,7 @@ let
     mixlink = [ pkgs.gsl ]; # for gsl-config
     mixture = [ pkgs.gsl ]; # for gsl-config
     mmpca = [ pkgs.gsl ]; # for gsl-config via RcppGSL
+    mongolite = [ pkgs.pkg-config ];
     monoreg = [ pkgs.gsl ]; # for gsl-config
     multibridge = [ pkgs.pkg-config ];
     mvabund = [ pkgs.gsl ]; # for gsl-config via RcppGSL
@@ -786,6 +777,7 @@ let
     ];
     odbc = [ pkgs.pkg-config ];
     opencv = [ pkgs.pkg-config ];
+    openssl = [ pkgs.pkg-config ];
     orbweaver = with pkgs; [
       cargo
       rustc
@@ -857,7 +849,6 @@ let
       cargo
       rustc
     ];
-    rpanel = [ pkgs.tclPackages.bwidget ];
     rrd = [ pkgs.pkg-config ];
     rsamplr = with pkgs; [
       cargo
@@ -985,6 +976,7 @@ let
       rustc
     ];
     webp = [ pkgs.pkg-config ];
+    websocket = [ pkgs.pkg-config ];
     xactonomial = with pkgs; [
       cargo
       rustc
@@ -1082,6 +1074,7 @@ let
       ncurses
       zlib
     ];
+    ModelMetrics = lib.optional stdenv.hostPlatform.isDarwin pkgs.llvmPackages.openmp;
     NanoMethViz = [ pkgs.zlib ];
     OpenCL = with pkgs; [
       opencl-clhpp
@@ -1300,7 +1293,13 @@ let
       curl
     ];
     curl = [ pkgs.curl ];
-    data_table = [ pkgs.zlib ];
+    data_table = (
+      # added extra parentheses so that `keep-sorted` doesn't get tripped up
+      [
+        pkgs.zlib
+      ]
+      ++ lib.optional stdenv.hostPlatform.isDarwin pkgs.llvmPackages.openmp
+    );
     deepSNV = with pkgs; [
       xz
       bzip2
@@ -1378,7 +1377,10 @@ let
     hadron = [ pkgs.gsl ];
     haven = [ pkgs.zlib ];
     hipread = [ pkgs.zlib ];
-    httpuv = [ pkgs.zlib ];
+    httpuv = with pkgs; [
+      libuv
+      zlib
+    ];
     hypergeo2 = with pkgs; [
       gmp
       mpfr
@@ -1477,6 +1479,11 @@ let
       zlib
     ];
     mixcat = [ pkgs.gsl ];
+    mongolite = with pkgs; [
+      cyrus_sasl
+      openssl
+      zlib
+    ];
     multibridge = [ pkgs.mpfr ];
     mutscan = [ pkgs.zlib ];
     mvabund = [ pkgs.gsl ];
@@ -1494,6 +1501,7 @@ let
     npRmpi = [ pkgs.mpi ];
     odbc = [ pkgs.unixodbc ];
     oligo = [ pkgs.zlib ];
+    openssl = [ pkgs.openssl ];
     otelsdk = with pkgs; [
       curl
       protobuf
@@ -1770,6 +1778,7 @@ let
     ];
     vdiffr = [ pkgs.libpng ];
     webp = [ pkgs.libwebp ];
+    websocket = [ pkgs.openssl ];
     writexl = with pkgs; [ zlib ];
     xdvir = [ pkgs.freetype ];
     xml2 = [ pkgs.libxml2 ];
@@ -2010,7 +2019,7 @@ let
     ACME = old.ACME.overrideAttrs (attrs: {
       env = (attrs.env or { }) // {
         # Avoid incompatible pointer type error
-        NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -Wno-incompatible-pointer-types";
+        NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE or "" + " -Wno-incompatible-pointer-types";
       };
     });
 
@@ -2025,7 +2034,7 @@ let
     BiocParallel = old.BiocParallel.overrideAttrs (attrs: {
       env = (attrs.env or { }) // {
         NIX_CFLAGS_COMPILE =
-          attrs.env.NIX_CFLAGS_COMPILE
+          attrs.env.NIX_CFLAGS_COMPILE or ""
           + lib.optionalString stdenv.hostPlatform.isDarwin " -Wno-error=missing-template-arg-list-after-template-kw";
       };
     });
@@ -2063,7 +2072,7 @@ let
     FlexReg = old.FlexReg.overrideAttrs (attrs: {
       env = (attrs.env or { }) // {
         # needed to avoid "log limit exceeded" on Hydra
-        NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -Wno-ignored-attributes";
+        NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE or "" + " -Wno-ignored-attributes";
       };
 
       # consumes a lot of resources in parallel
@@ -2092,7 +2101,7 @@ let
     ModelMetrics = old.ModelMetrics.overrideAttrs (attrs: {
       env = (attrs.env or { }) // {
         NIX_CFLAGS_COMPILE =
-          attrs.env.NIX_CFLAGS_COMPILE + lib.optionalString stdenv.hostPlatform.isDarwin " -fopenmp";
+          attrs.env.NIX_CFLAGS_COMPILE or "" + lib.optionalString stdenv.hostPlatform.isDarwin " -fopenmp";
       };
     });
 
@@ -2107,7 +2116,7 @@ let
     OpenMx = old.OpenMx.overrideAttrs (attrs: {
       env = (attrs.env or { }) // {
         # needed to avoid "log limit exceeded" on Hydra
-        NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -Wno-ignored-attributes";
+        NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE or "" + " -Wno-ignored-attributes";
       };
     });
 
@@ -2193,15 +2202,15 @@ let
     Rhdf5lib =
       let
         hdf5 = pkgs.hdf5.overrideAttrs (attrs: {
-          cmakeFlags = attrs.cmakeFlags ++ [ "-DHDF5_ENABLE_ROS3_VFD:BOOL=TRUE" ];
+          cmakeFlags = (attrs.cmakeFlags or [ ]) ++ [ "-DHDF5_ENABLE_ROS3_VFD:BOOL=TRUE" ];
-          buildInputs = attrs.buildInputs ++ [ pkgs.curl ];
+          buildInputs = (attrs.buildInputs or [ ]) ++ [ pkgs.curl ];
-          postInstall = attrs.postInstall or "" + ''
+          postInstall = (attrs.postInstall or "") + ''
             cp src/libhdf5.settings $dev/lib
           '';
         });
       in
       old.Rhdf5lib.overrideAttrs (attrs: {
-        propagatedBuildInputs = attrs.propagatedBuildInputs ++ [
+        propagatedBuildInputs = (attrs.propagatedBuildInputs or [ ]) ++ [
           hdf5
           pkgs.libaec
         ];
@@ -2222,16 +2231,26 @@ let
     Rrdrand = old.Rrdrand.override { platforms = lib.platforms.x86_64 ++ lib.platforms.x86; };
 
     Rserve = old.Rserve.overrideAttrs (attrs: {
-      patches = [ ./patches/Rserve.patch ];
       configureFlags = [
         "--with-server"
         "--with-client"
       ];
+
+      patches = [
+        # Don't try to copy the Rserve binaries into $R_HOME/bin
+        ./patches/Rserve.patch
+      ];
+
+      # Instead, we symlink them into $out/bin
+      postInstall = ''
+        mkdir -p "$out/bin/"
+        ln -s "$out"/library/Rserve/libs/Rserve{,.dbg} "$out/bin/"
+      '';
     });
 
     SAIGEgds = old.SAIGEgds.overrideAttrs (attrs: {
       env = (attrs.env or { }) // {
-        NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -fpermissive";
+        NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE or "" + " -fpermissive";
       };
     });
 
@@ -2372,7 +2391,7 @@ let
       src = pkgs.arrow-cpp.src;
       name = "r-arrow-${pkgs.arrow-cpp.version}";
       prePatch = "cd r";
-      buildInputs = attrs.buildInputs ++ [
+      buildInputs = (attrs.buildInputs or [ ]) ++ [
         pkgs.arrow-cpp
       ];
     });
@@ -2391,7 +2410,7 @@ let
 
     data_table = old.data_table.overrideAttrs (attrs: {
       env = (attrs.env or { }) // {
-        NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -fopenmp";
+        NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE or "" + " -fopenmp";
       };
     });
 
@@ -2443,7 +2462,7 @@ let
     });
 
     geojsonio = old.geojsonio.overrideAttrs (attrs: {
-      buildInputs = [ cacert ] ++ attrs.buildInputs;
+      buildInputs = (attrs.buildInputs or [ ]) ++ [ cacert ];
     });
 
     geomorph = old.geomorph.overrideAttrs (attrs: {
@@ -2456,7 +2475,7 @@ let
       env = (attrs.env or { }) // {
         # Avoid incompatible pointer type error
         NIX_CFLAGS_COMPILE =
-          attrs.env.NIX_CFLAGS_COMPILE
+          attrs.env.NIX_CFLAGS_COMPILE or ""
           + " -Wno-implicit-function-declaration -Wno-incompatible-pointer-types";
       };
     });
@@ -2485,8 +2504,8 @@ let
     });
 
     hdf5r = old.hdf5r.overrideAttrs (attrs: {
-      nativeBuildInputs = attrs.nativeBuildInputs ++ [ new.Rhdf5lib.hdf5 ];
+      nativeBuildInputs = (attrs.nativeBuildInputs or [ ]) ++ [ new.Rhdf5lib.hdf5 ];
-      buildInputs = attrs.buildInputs ++ [ new.Rhdf5lib.hdf5 ];
+      buildInputs = (attrs.buildInputs or [ ]) ++ [ new.Rhdf5lib.hdf5 ];
     });
 
     immunotation =
@@ -2514,25 +2533,26 @@ let
         };
       in
       old.immunotation.overrideAttrs (attrs: {
-        patches = [ ./patches/immunotation.patch ];
+        patches = [
-        postPatch = ''
+          (pkgs.replaceVars ./patches/immunotation.patch {
-          substituteInPlace "R/external_resources_input.R" --replace-fail \
+            "mhc41_allele_list" = MHC41alleleList;
-            "nix-NetMHCpan-4.1-allele-list" ${MHC41alleleList}
+            "mhcii40_alleles_name_list" = MHCII40alleleList;
-
+            "valid_geographics" = validGeographics;
-          substituteInPlace "R/external_resources_input.R" --replace-fail \
+          })
-            "nix-NETMHCIIpan-4.0-alleles-name-list" ${MHCII40alleleList}
+        ];
-
-          substituteInPlace "R/AFND_interface.R" --replace-fail \
-            "nix-valid-geographics" ${validGeographics}
-        '';
       });
 
     iscream = old.iscream.overrideAttrs (attrs: {
       # https://huishenlab.github.io/iscream/articles/htslib.html
       # Rhtslib (in LinkingTo) is not needed if we provide a proper htslib
-      propagatedBuildInputs =
+      propagatedBuildInputs = builtins.filter (el: el.pname != "Rhtslib") attrs.propagatedBuildInputs;
-        builtins.filter (el: el != pkgs.rPackages.Rhtslib) attrs.propagatedBuildInputs
+
-        ++ [ pkgs.htslib ];
+      buildInputs = (attrs.buildInputs or [ ]) ++ [ pkgs.htslib ];
+
+      postPatch = ''
+        substituteInPlace "DESCRIPTION" \
+          --replace-fail ", Rhtslib" ""
+      '';
     });
 
     littler = old.littler.overrideAttrs (attrs: {
@@ -2561,14 +2581,7 @@ let
     metahdep = old.metahdep.overrideAttrs (attrs: {
       env = (attrs.env or { }) // {
         # Avoid incompatible pointer type error
-        NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -Wno-int-conversion";
+        NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE or "" + " -Wno-int-conversion";
-      };
-    });
-
-    mongolite = old.mongolite.overrideAttrs (attrs: {
-      env = (attrs.env or { }) // {
-        PKGCONFIG_CFLAGS = "-I${lib.getDev pkgs.openssl}/include -I${lib.getDev pkgs.cyrus_sasl}/include -I${lib.getDev pkgs.zlib}/include";
-        PKGCONFIG_LIBS = "-Wl,-rpath,${lib.getLib pkgs.openssl}/lib -L${lib.getLib pkgs.openssl}/lib -L${pkgs.cyrus_sasl.out}/lib -L${pkgs.zlib.out}/lib -lssl -lcrypto -lsasl2 -lz";
       };
     });
 
@@ -2595,7 +2608,7 @@ let
     networkscaleup = old.networkscaleup.overrideAttrs (attrs: {
       env = (attrs.env or { }) // {
         # needed to avoid "log limit exceeded" on Hydra
-        NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -Wno-ignored-attributes";
+        NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE or "" + " -Wno-ignored-attributes";
       };
 
       # consumes a lot of resources in parallel
@@ -2613,14 +2626,15 @@ let
         });
       in
       old.opencv.overrideAttrs (attrs: {
-        buildInputs = attrs.buildInputs ++ [ opencvGtk ];
+        buildInputs = (attrs.buildInputs or [ ]) ++ [ opencvGtk ];
       });
 
     openssl = old.openssl.overrideAttrs (attrs: {
-      env = (attrs.env or { }) // {
+      # RPATH will be incorrect if the configure script replaces -lssl with -l:libssl.so.{n}
-        PKGCONFIG_CFLAGS = "-I${lib.getDev pkgs.openssl}/include";
+      postPatch = ''
-        PKGCONFIG_LIBS = "-Wl,-rpath,${lib.getLib pkgs.openssl}/lib -L${lib.getLib pkgs.openssl}/lib -lssl -lcrypto";
+        substituteInPlace configure \
-      };
+          --replace-fail 'PKG_LIBS="''${PKG_LIBS_VERSIONED}"' ':'
+      '';
     });
 
     pak = old.pak.overrideAttrs (attrs: {
@@ -2752,7 +2766,8 @@ let
 
     rhdf5 = old.rhdf5.overrideAttrs (attrs: {
       patches = [ ./patches/rhdf5.patch ];
-      env.NIX_CFLAGS_COMPILE = "-Wno-error=implicit-function-declaration";
+      env.NIX_CFLAGS_COMPILE =
+        attrs.env.NIX_CFLAGS_COMPILE or "" + " -Wno-error=implicit-function-declaration";
     });
 
     rhdf5filters = old.rhdf5filters.overrideAttrs (attrs: {
@@ -2779,24 +2794,25 @@ let
     });
 
     rpanel = old.rpanel.overrideAttrs (attrs: {
-      preConfigure = ''
+      postPatch = ''
-        export TCLLIBPATH="${pkgs.tclPackages.bwidget}/lib/bwidget${pkgs.tclPackages.bwidget.version}"
+        cat >> R/zzz.R <<EOF
+        .onLoad <- function(...) {
+          tcltk::tcl("lappend", "auto_path", "${pkgs.tclPackages.bwidget}/lib/bwidget${pkgs.tclPackages.bwidget.version}")
+        }
+        EOF
       '';
-      env = (attrs.env or { }) // {
-        TCLLIBPATH = "${pkgs.tclPackages.bwidget}/lib/bwidget${pkgs.tclPackages.bwidget.version}";
-      };
     });
 
     rstan = old.rstan.overrideAttrs (attrs: {
       env = (attrs.env or { }) // {
-        NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION";
+        NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE or "" + " -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION";
       };
     });
 
     rstanarm = old.rstanarm.overrideAttrs (attrs: {
       env = (attrs.env or { }) // {
         # needed to avoid "log limit exceeded" on Hydra
-        NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -Wno-ignored-attributes";
+        NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE or "" + " -Wno-ignored-attributes";
       };
     });
 
@@ -2914,15 +2930,16 @@ let
     });
 
     websocket = old.websocket.overrideAttrs (attrs: {
-      env = (attrs.env or { }) // {
+      # RPATH will be incorrect if the configure script replaces -lssl with -l:libssl.so.{n}
-        PKGCONFIG_CFLAGS = "-I${lib.getDev pkgs.openssl}/include";
+      postPatch = ''
-        PKGCONFIG_LIBS = "-Wl,-rpath,${lib.getLib pkgs.openssl}/lib -L${lib.getLib pkgs.openssl}/lib -lssl -lcrypto";
+        substituteInPlace configure \
-      };
+          --replace-fail 'PKG_LIBS="''${PKG_LIBS_VERSIONED}"' ':'
+      '';
     });
 
     xslt = old.xslt.overrideAttrs (attrs: {
       env = (attrs.env or { }) // {
-        NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -fpermissive";
+        NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE or "" + " -fpermissive";
       };
     });
     # keep-sorted end

pkgs/development/r-modules/generic-builder.nix

@@ -4,38 +4,48 @@
   R,
   xvfb-run,
   util-linux,
-  gettext,
+  libintl,
-  gfortran,
-  libiconv,
 }:
 
-{
+attrs:
-  buildInputs ? [ ],
-  requireX ? false,
-  ...
-}@attrs:
 
 stdenv.mkDerivation (
+  finalAttrs:
   {
-    buildInputs =
+    __structuredAttrs = true;
-      buildInputs
+    strictDeps = true;
+
+    name = "r-${attrs.name or "${attrs.pname}-${attrs.version}"}";
+
+    requireX = false;
+
+    nativeBuildInputs =
+      (attrs.nativeBuildInputs or [ ])
       ++ [
         R
-        gettext
       ]
-      ++ lib.optionals requireX [
+      ++ lib.optionals finalAttrs.requireX [
         util-linux
         xvfb-run
-      ]
-      ++ lib.optionals stdenv.hostPlatform.isDarwin [
-        gfortran
-        libiconv
       ];
 
-    env.NIX_CFLAGS_COMPILE = lib.optionalString stdenv.hostPlatform.isDarwin "-I${lib.getInclude stdenv.cc.libcxx}/include/c++/v1";
+    buildInputs =
+      (attrs.buildInputs or [ ])
+      ++ lib.optionals stdenv.hostPlatform.isDarwin [
+        libintl
+      ];
 
     enableParallelBuilding = true;
 
+    env =
+      (attrs.env or { })
+      // (lib.optionalAttrs (stdenv.hostPlatform.isDarwin) {
+        NIX_CFLAGS_COMPILE = "${
+          attrs.env.NIX_CFLAGS_COMPILE or ""
+        } -I${lib.getInclude stdenv.cc.libcxx}/include/c++/v1";
+
+      });
+
     configurePhase = ''
       runHook preConfigure
 
@@ -54,35 +64,65 @@ stdenv.mkDerivation (
       runHook postBuild
     '';
 
-    installFlags = if attrs.doCheck or true then [ ] else [ "--no-test-load" ];
+    doCheck = true;
+
+    checkPhase = ''
+      # noop since R CMD INSTALL tests packages
+    '';
 
     rCommand =
-      if requireX then
+      if finalAttrs.requireX then
         # Unfortunately, xvfb-run has a race condition even with -a option, so that
         # we acquire a lock explicitly.
         "flock ${xvfb-run} xvfb-run -a -e xvfb-error R"
       else
         "R";
 
+    installFlags = (attrs.installFlags or [ ]) ++ (lib.optional (!finalAttrs.doCheck) "--no-test-load");
+
     installPhase = ''
       runHook preInstall
-      mkdir -p $out/library
+
-      $rCommand CMD INSTALL --built-timestamp='1970-01-01 00:00:00 UTC' $installFlags --configure-args="$configureFlags" -l $out/library .
+      mkdir -p "$out/library"
+
+      # logic inside R CMD INSTALL essentially just expands `./configure $configureArgs` and runs it in a system shell
+      # so we need to escape configureFlags if we want to support things like spaces in arguments
+      local configureArgs=""
+      if ((''${#configureFlags[@]})); then
+        printf -v configureArgs '%q ' "''${configureFlags[@]}"
+      fi
+
+      $rCommand CMD INSTALL \
+        --library="$out/library" \
+        --built-timestamp='1970-01-01 00:00:00 UTC' \
+        --configure-args="$configureArgs" \
+        "''${installFlags[@]}" \
+        .
+
       runHook postInstall
     '';
 
+    stripDebugList = [
+      "library/${attrs.pname}/libs"
+      # Note: this is non-standard, but some packages do place binaries here via custom install logic (e.g. via install.libs.R)
+      "library/${attrs.pname}/bin"
+    ];
+
     postFixup = ''
       if test -e $out/nix-support/propagated-build-inputs; then
-          ln -s $out/nix-support/propagated-build-inputs $out/nix-support/propagated-user-env-packages
+        ln -s $out/nix-support/propagated-build-inputs $out/nix-support/propagated-user-env-packages
       fi
-    '';
+    ''
-
+    + (attrs.postFixup or "");
-    checkPhase = ''
-      # noop since R CMD INSTALL tests packages
-    '';
-  }
-  // attrs
-  // {
-    name = "r-${attrs.name or "${attrs.pname}-${attrs.version}"}";
   }
+  // (lib.removeAttrs attrs [
+    # list of attrs that have custom logic for combining the default and the passed values
+    # if not listed, the passed value will override the default value
+    "name"
+    "nativeBuildInputs"
+    "buildInputs"
+    "env"
+    "installFlags"
+    "postFixup"
+  ])
 )

pkgs/development/r-modules/patches/Rserve.patch

@@ -1,15 +1,13 @@
-diff -ru -x '*~' Rserve_orig/src/Makevars.in Rserve/src/Makevars.in
+diff --git a/src/Makevars.in b/src/Makevars.in
---- Rserve_orig/src/Makevars.in	2013-08-22 06:09:33.000000000 +0900
+index e20c4eb..1013e21 100644
-+++ Rserve/src/Makevars.in	2014-11-09 21:36:31.184590320 +0900
+--- a/src/Makevars.in
-@@ -12,8 +12,9 @@
++++ b/src/Makevars.in
- 	$(CC) -DSTANDALONE_RSERVE -DRSERV_DEBUG -DNODAEMON -I. -Iinclude $(ALL_CPPFLAGS) $(ALL_CFLAGS) $(PKG_CPPFLAGS) $(PKG_CFLAGS) -o Rserve.dbg $(SERVER_SRC) $(ALL_LIBS) $(PKG_LIBS)
+@@ -14,8 +14,6 @@ server:	$(SERVER_SRC) $(SERVER_H)
+ 	$(CC) -DSTANDALONE_RSERVE -DRSERV_DEBUG -DNODAEMON -I. -Iinclude $(ALL_CPPFLAGS) $(ALL_CFLAGS) $(PKG_CPPFLAGS) $(EMBED_CPPFLAGS) $(PKG_CFLAGS) -o Rserve.dbg $(SERVER_SRC) $(LDFLAGS) $(ALL_LIBS) $(PKG_LIBS)
  
  # merging to bin/Rserve works only if installed from sources, won't work for binary
 -	-./mergefat Rserve "$(R_HOME)/bin/Rserve"
 -	-./mergefat Rserve.dbg "$(R_HOME)/bin/Rserve.dbg"
-+	mkdir $(out)/bin
-+	-./mergefat Rserve "$(out)/bin/Rserve"
-+	-./mergefat Rserve.dbg "$(out)/bin/Rserve.dbg"
  
  client: config.h
  	cp config.h client/cxx/

pkgs/development/r-modules/patches/immunotation.patch

@@ -2,38 +2,34 @@ diff --git a/R/AFND_interface.R b/R/AFND_interface.R
 index b62e8e0..0f22d85 100644
 --- a/R/AFND_interface.R
 +++ b/R/AFND_interface.R
-@@ -244,9 +244,9 @@ check_population <- function(hla_population) {
+@@ -244,8 +244,8 @@ check_population <- function(hla_population) {
  #' @return list of valid countries, regions and ethnic origin
  #' @keywords internal
  get_valid_geographics <- function() {
 -    url <- "http://www.allelefrequencies.net/hla6006a.asp?"
 -    html_input <- getURL(url, read_method = "html")
--    
 +    # http://www.allelefrequencies.net/hla6006a.asp?
-+    html_input <- xml2::read_html("nix-valid-geographics")
++    html_input <- xml2::read_html("@valid_geographics@")
-+      
+     
      rvest_tables <- rvest::html_table(html_input, fill = TRUE)
      
-     # country
 diff --git a/R/external_resources_input.R b/R/external_resources_input.R
 index c4b1dc1..8fc5881 100644
 --- a/R/external_resources_input.R
 +++ b/R/external_resources_input.R
-@@ -74,16 +74,17 @@ getURL <- function(URL, N.TRIES=2L,
+@@ -74,16 +74,16 @@ getURL <- function(URL, N.TRIES=2L,
  # MHC I
  # netmhcI_input_template is an internal variable containing list of valid 
  # NetMHCpan input alleles
 -netmhcI_input_template <- getURL(
 -    URL="https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/allele.list",
 -    read_method = "delim", delim = "\t",
--    col_names = c("netmhc_input", "hla_chain_name", "HLA_gene"))
 +netmhcI_input_template <- readr::read_delim(
-+        # https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/allele.list
++    # https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/allele.list
-+	"nix-NetMHCpan-4.1-allele-list",
++    "@mhc41_allele_list@",
-+	delim = "\t",
++    delim = "\t",
-+	skip = 0,
++    skip = 0,
-+        col_names = c("netmhc_input", "hla_chain_name", "HLA_gene")
+     col_names = c("netmhc_input", "hla_chain_name", "HLA_gene"))
-+    )
  
  # MHC II
 -lines <- getURL(
@@ -41,7 +37,7 @@ index c4b1dc1..8fc5881 100644
 -    "NetMHCIIpan-4.0/alleles_name.list"),
 -    read_method = "lines")
 +# https://services.healthtech.dtu.dk/services/NetMHCIIpan-4.0/alleles_name.list
-+lines <- readr::read_lines("nix-NETMHCIIpan-4.0-alleles-name-list")
++lines <- readr::read_lines("@mhcii40_alleles_name_list@")
  lines_rep <- stringr::str_replace_all(lines, "\t+|\\s\\s+", "\t")
  netmhcII_input_template <- suppressWarnings(
      suppressMessages(read.delim(textConnection(lines_rep), sep = "\t")))