From 04108965e63d3a6e2f28fa81f7a53cdd396dd3d1 Mon Sep 17 00:00:00 2001
From: TomaSajt <62384384+TomaSajt@users.noreply.github.com>
Date: Sat, 18 Jul 2026 09:43:58 +0200
Subject: [PATCH] rPackages.buildRPackage: patch shebangs automatically in
 configure

---
 pkgs/development/r-modules/default.nix        | 392 +-----------------
 .../development/r-modules/generic-builder.nix |   6 +
 2 files changed, 7 insertions(+), 391 deletions(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 098ab6a0ac9a..d6ed55e92899 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -1919,10 +1919,6 @@ let
       '';
     });
 
-    BigDataStatMeth = old.BigDataStatMeth.overrideAttrs (_: {
-      preConfigure = "patchShebangs configure";
-    });
-
     BiocParallel = old.BiocParallel.overrideAttrs (attrs: {
       env = (attrs.env or { }) // {
         NIX_CFLAGS_COMPILE =
@@ -1957,14 +1953,6 @@ let
       };
     });
 
-    Colossus = old.Colossus.overrideAttrs (_: {
-      postPatch = "patchShebangs configure";
-    });
-
-    Cyclops = old.Cyclops.overrideAttrs (attrs: {
-      preConfigure = "patchShebangs configure";
-    });
-
     FLAMES = old.FLAMES.overrideAttrs (attrs: {
       patches = [ ./patches/FLAMES.patch ];
     });
@@ -2018,9 +2006,6 @@ let
         # needed to avoid "log limit exceeded" on Hydra
         NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -Wno-ignored-attributes";
       };
-      preConfigure = ''
-        patchShebangs configure
-      '';
     });
 
     PICS = old.PICS.overrideAttrs (attrs: {
@@ -2074,18 +2059,10 @@ let
       ];
     });
 
-    RPesto = old.RPesto.overrideAttrs (_: {
-      preConfigure = "patchShebangs configure";
-    });
-
     RProtoBuf = old.RProtoBuf.overrideAttrs (attrs: {
       configureFlags = [ "ac_cv_prog_cxx_cxx11=" ];
     });
 
-    RSQLite = old.RSQLite.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
     RVowpalWabbit = old.RVowpalWabbit.overrideAttrs (attrs: {
       configureFlags = [
         "--with-boost=${pkgs.boost.dev}"
@@ -2106,22 +2083,6 @@ let
       '';
     });
 
-    RcppArmadillo = old.RcppArmadillo.overrideAttrs (attrs: {
-      patchPhase = "patchShebangs configure";
-    });
-
-    RcppCGAL = old.RcppCGAL.overrideAttrs (_: {
-      postPatch = "patchShebangs configure";
-    });
-
-    RcppGetconf = old.RcppGetconf.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
-    RcppParallel = old.RcppParallel.overrideAttrs (attrs: {
-      preConfigure = "patchShebangs configure";
-    });
-
     Rdisop = old.Rdisop.overrideAttrs (_: {
       hardeningDisable = [ "format" ];
     });
@@ -2184,10 +2145,6 @@ let
       hardeningDisable = [ "format" ];
     });
 
-    SQLFormatteR = old.SQLFormatteR.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
     SamplerCompare = old.SamplerCompare.overrideAttrs (attrs: {
       env = (attrs.env or { }) // {
         PKG_LIBS = "-L${pkgs.blas}/lib -lblas -L${pkgs.lapack}/lib -llapack";
@@ -2202,10 +2159,6 @@ let
       '';
     });
 
-    SpliceWiz = old.SpliceWiz.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
     SynExtend = old.SynExtend.overrideAttrs (attrs: {
       # build might fail due to race condition
       enableParallelBuilding = false;
@@ -2215,7 +2168,6 @@ let
       preConfigure = ''
         export V8_PKG_CFLAGS="$(pkg-config --cflags v8)";
         export V8_PKG_LIBS="$(pkg-config --libs v8)";
-        patchShebangs configure
       '';
 
       env = (attrs.env or { }) // {
@@ -2304,34 +2256,12 @@ let
         '';
       });
 
-    acs = old.acs.overrideAttrs (attrs: {
-      preConfigure = ''
-        patchShebangs configure
-      '';
-    });
-
     alcyon = old.alcyon.overrideAttrs (attrs: {
       configureFlags = [
         "--enable-force-openmp"
       ];
     });
 
-    arcgisgeocode = old.arcgisgeocode.overrideAttrs (_: {
-      postPatch = "patchShebangs configure";
-    });
-
-    arcgisplaces = old.arcgisplaces.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
-    arcgisutils = old.arcgisutils.overrideAttrs (_: {
-      postPatch = "patchShebangs configure";
-    });
-
-    arcpbf = old.arcpbf.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
     # it can happen that the major version of arrow-cpp is ahead of the
     # rPackages.arrow that would be built from CRAN sources; therefore, to avoid
     # build failures and manual updates of the hash, we use the R source at
@@ -2345,62 +2275,15 @@ let
       src = pkgs.arrow-cpp.src;
       name = "r-arrow-${pkgs.arrow-cpp.version}";
       prePatch = "cd r";
-      postPatch = ''
-        patchShebangs configure
-      '';
       buildInputs = attrs.buildInputs ++ [
         pkgs.arrow-cpp
       ];
     });
 
-    astgrepr = old.astgrepr.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
-    awdb = old.awdb.overrideAttrs (attrs: {
-      postPatch = ''
-        patchShebangs configure
-      '';
-    });
-
-    b32 = old.b32.overrideAttrs (_: {
-      preConfigure = "patchShebangs configure";
-    });
-
-    b64 = old.b64.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
-    bigPLSR = old.bigPLSR.overrideAttrs (_: {
-      preConfigure = "patchShebangs configure";
-    });
-
-    cartogramR = old.cartogramR.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
-    caugi = old.caugi.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
-    ciflyr = old.ciflyr.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
     cisPath = old.cisPath.overrideAttrs (attrs: {
       hardeningDisable = [ "format" ];
     });
 
-    clarabel = old.clarabel.overrideAttrs (attrs: {
-      postPatch = ''
-        patchShebangs configure
-      '';
-    });
-
-    clustermq = old.clustermq.overrideAttrs (attrs: {
-      preConfigure = "patchShebangs configure";
-    });
-
     covidsymptom = old.covidsymptom.overrideAttrs (attrs: {
       preConfigure = "rm R/covidsymptomdata.R";
     });
@@ -2409,27 +2292,14 @@ let
       enableParallelBuilding = false;
     });
 
-    curl = old.curl.overrideAttrs (attrs: {
-      preConfigure = "patchShebangs configure";
-    });
-
     data_table = old.data_table.overrideAttrs (attrs: {
       env = (attrs.env or { }) // {
         NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -fopenmp";
       };
-      patchPhase = "patchShebangs configure";
-    });
-
-    datefixR = old.datefixR.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
     });
 
     dbarts = old.dbarts.override { platforms = lib.platforms.x86_64 ++ lib.platforms.x86; };
 
-    enderecobr = old.enderecobr.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
     exifr = old.exifr.overrideAttrs (attrs: {
       postPatch = ''
         for f in .onLoad .onAttach ; do
@@ -2445,10 +2315,6 @@ let
       '';
     });
 
-    fcl = old.fcl.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
     findpython = old.findpython.overrideAttrs (attrs: {
       postPatch = ''
         substituteInPlace "R/find_python_cmd.r" \
@@ -2458,28 +2324,13 @@ let
       '';
     });
 
-    fio = old.fio.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
-    fixest = old.fixest.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
     float = old.float.overrideAttrs (attrs: {
       enableParallelBuilding = false;
     });
 
     flowClust = old.flowClust.override { platforms = lib.platforms.x86_64 ++ lib.platforms.x86; };
 
-    gadjid = old.gadjid.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
     gdtools = old.gdtools.overrideAttrs (attrs: {
-      preConfigure = ''
-        patchShebangs configure
-      '';
       env = (attrs.env or { }) // {
         NIX_LDFLAGS = "-lfontconfig -lfreetype";
       };
@@ -2504,10 +2355,6 @@ let
       };
     });
 
-    gmailr = old.gmailr.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
     gmapR = old.gmapR.overrideAttrs (attrs: {
       env = (attrs.env or { }) // {
         # Avoid incompatible pointer type error
@@ -2534,10 +2381,6 @@ let
       '';
     });
 
-    h3o = old.h3o.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
     harbinger = old.harbinger.overrideAttrs (attrs: {
       env = (attrs.env or { }) // {
         LC_ALL = "en_US.UTF-8";
@@ -2549,26 +2392,6 @@ let
       buildInputs = attrs.buildInputs ++ [ new.Rhdf5lib.hdf5 ];
     });
 
-    heck = old.heck.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
-    httpuv = old.httpuv.overrideAttrs (_: {
-      preConfigure = ''
-        patchShebangs configure
-      '';
-    });
-
-    httr2 = old.httr2.overrideAttrs (attrs: {
-      preConfigure = "patchShebangs configure";
-    });
-
-    ijtiff = old.ijtiff.overrideAttrs (_: {
-      preConfigure = ''
-        patchShebangs configure
-      '';
-    });
-
     immunotation =
       let
         MHC41alleleList = fetchurl {
@@ -2607,14 +2430,6 @@ let
         '';
       });
 
-    instantiate = old.instantiate.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
-    ironseed = old.ironseed.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
     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
@@ -2623,28 +2438,6 @@ let
         ++ [ pkgs.htslib ];
     });
 
-    jqr = old.jqr.overrideAttrs (attrs: {
-      preConfigure = ''
-        patchShebangs configure
-      '';
-    });
-
-    keyring = old.keyring.overrideAttrs (attrs: {
-      preConfigure = ''
-        patchShebangs configure
-      '';
-    });
-
-    libdeflate = old.libdeflate.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
-    libgeos = old.libgeos.overrideAttrs (attrs: {
-      preConfigure = ''
-        patchShebangs configure
-      '';
-    });
-
     littler = old.littler.overrideAttrs (attrs: {
       postInstall = ''
         install -d $out/bin $out/share/man/man1
@@ -2661,19 +2454,11 @@ let
         substituteInPlace configure \
           --replace-fail '--libs SYMPHONY' '--libs symphony' \
           --replace-fail '--cflags SYMPHONY' '--cflags symphony'
-        patchShebangs configure
       '';
     });
 
     luajr = old.luajr.overrideAttrs (attrs: {
       hardeningDisable = [ "format" ];
-      postPatch = "patchShebangs configure";
-    });
-
-    magick = old.magick.overrideAttrs (attrs: {
-      preConfigure = ''
-        patchShebangs configure
-      '';
     });
 
     metahdep = old.metahdep.overrideAttrs (attrs: {
@@ -2684,9 +2469,6 @@ let
     });
 
     mongolite = old.mongolite.overrideAttrs (attrs: {
-      preConfigure = ''
-        patchShebangs configure
-      '';
       env = (attrs.env or { }) // {
         PKGCONFIG_CFLAGS = "-I${pkgs.openssl.dev}/include -I${pkgs.cyrus_sasl.dev}/include -I${pkgs.zlib.dev}/include";
         PKGCONFIG_LIBS = "-Wl,-rpath,${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";
@@ -2699,10 +2481,6 @@ let
       };
     });
 
-    nanoparquet = old.nanoparquet.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
     nearfar =
       let
         angrist = fetchurl {
@@ -2727,16 +2505,6 @@ let
       enableParallelBuilding = false;
     });
 
-    ocf = old.ocf.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
-    odbc = old.odbc.overrideAttrs (attrs: {
-      preConfigure = ''
-        patchShebangs configure
-      '';
-    });
-
     oligo = old.oligo.overrideAttrs (_: {
       hardeningDisable = [ "format" ];
     });
@@ -2758,23 +2526,9 @@ let
       };
     });
 
-    orbweaver = old.orbweaver.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
-    otelsdk = old.otelsdk.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
     pak = old.pak.overrideAttrs (attrs: {
       preConfigure = ''
-        patchShebangs configure
-        patchShebangs src/library/curl/configure
-        patchShebangs src/library/keyring/configure
-        patchShebangs src/library/pkgdepends/configure
-        patchShebangs src/library/ps/configure
-        patchShebangs src/library/tsitter/configure
-        patchShebangs src/library/tstoml/configure
+        patchShebangs src/library/*/configure
       '';
     });
 
@@ -2786,34 +2540,6 @@ let
       '';
     });
 
-    pingr = old.pingr.overrideAttrs (_: {
-      postPatch = "patchShebangs configure";
-    });
-
-    pkgdepends = old.pkgdepends.overrideAttrs (attrs: {
-      postPatch = ''
-        patchShebangs configure
-      '';
-    });
-
-    protolite = old.protolite.overrideAttrs (attrs: {
-      preConfigure = ''
-        patchShebangs configure
-      '';
-    });
-
-    prqlr = old.prqlr.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
-    ps = old.ps.overrideAttrs (attrs: {
-      preConfigure = "patchShebangs configure";
-    });
-
-    purrr = old.purrr.overrideAttrs (attrs: {
-      patchPhase = "patchShebangs configure";
-    });
-
     quarto = old.quarto.overrideAttrs (attrs: {
       propagatedBuildInputs = attrs.propagatedBuildInputs ++ [ pkgs.quarto ];
       postPatch = ''
@@ -2837,10 +2563,6 @@ let
       '';
     });
 
-    ramr = old.ramr.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
     rawrr = old.rawrr.overrideAttrs (attrs: {
       postPatch = ''
         substituteInPlace "R/zzz.R" "R/dotNetAssembly.R" --replace-warn \
@@ -2858,10 +2580,6 @@ let
       '';
     });
 
-    rbm25 = old.rbm25.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
     redatamx = old.redatamx.overrideAttrs (
       finalAttrs: previousAttrs:
       let
@@ -2944,10 +2662,6 @@ let
       patches = [ ./patches/rhdf5filters.patch ];
     });
 
-    rlang = old.rlang.overrideAttrs (attrs: {
-      preConfigure = "patchShebangs configure";
-    });
-
     rmarkdown = old.rmarkdown.overrideAttrs (_: {
       preConfigure = ''
         substituteInPlace R/pandoc.R \
@@ -2959,7 +2673,6 @@ let
       env = (attrs.env or { }) // {
         LIBCLANG_PATH = "${lib.getLib pkgs.libclang}/lib";
       };
-      postPatch = "patchShebangs configure";
     });
 
     rpanel = old.rpanel.overrideAttrs (attrs: {
@@ -2971,34 +2684,12 @@ let
       };
     });
 
-    rpf = old.rpf.overrideAttrs (attrs: {
-      patchPhase = "patchShebangs configure";
-    });
-
-    rrd = old.rrd.overrideAttrs (attrs: {
-      preConfigure = ''
-        patchShebangs configure
-      '';
-    });
-
-    rsgeo = old.rsgeo.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
-    rshift = old.rshift.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
     rstan = old.rstan.overrideAttrs (attrs: {
       env = (attrs.env or { }) // {
         NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION";
       };
     });
 
-    rtiktoken = old.rtiktoken.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
     rvisidata = old.rvisidata.overrideAttrs (attrs: {
       postPatch = ''
         substituteInPlace R/main.r --replace-fail \
@@ -3008,10 +2699,6 @@ let
       '';
     });
 
-    rzmq = old.rzmq.overrideAttrs (attrs: {
-      preConfigure = "patchShebangs configure";
-    });
-
     s2 = old.s2.overrideAttrs (attrs: {
       preConfigure = ''
         substituteInPlace "configure" \
@@ -3025,16 +2712,6 @@ let
       };
     });
 
-    socratadata = old.socratadata.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
-    sodium = old.sodium.overrideAttrs (attrs: {
-      preConfigure = ''
-        patchShebangs configure
-      '';
-    });
-
     sparklyr = old.sparklyr.overrideAttrs (attrs: {
       # Pyspark's spark is full featured and better maintained than pkgs.spark
       preConfigure = ''
@@ -3052,10 +2729,6 @@ let
       '';
     });
 
-    surtvep = old.surtvep.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
     symengine = old.symengine.overrideAttrs (_: {
       preConfigure = ''
         rm configure
@@ -3066,14 +2739,6 @@ let
       '';
     });
 
-    systemfonts = old.systemfonts.overrideAttrs (attrs: {
-      preConfigure = "patchShebangs configure";
-    });
-
-    tergo = old.tergo.overrideAttrs (attrs: {
-      patchPhase = "patchShebangs configure";
-    });
-
     tesseract = old.tesseract.overrideAttrs (_: {
       preConfigure = ''
         substituteInPlace configure \
@@ -3086,7 +2751,6 @@ let
     });
 
     timeless = old.timeless.overrideAttrs (attrs: {
-      preConfigure = "patchShebangs configure";
       cargoDeps = pkgs.rustPlatform.fetchCargoVendor {
         src = attrs.src;
         sourceRoot = "timeless/src/rust";
@@ -3101,20 +2765,6 @@ let
       ];
     });
 
-    tok = old.tok.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
-    tomledit = old.tomledit.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
-    torch = old.torch.overrideAttrs (attrs: {
-      preConfigure = ''
-        patchShebangs configure
-      '';
-    });
-
     trajeR = old.trajeR.overrideAttrs (attrs: {
       patches = [ ./patches/trajeR.patch ];
     });
@@ -3140,24 +2790,12 @@ let
       '';
     });
 
-    unsum = old.unsum.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
     vegan3d = old.vegan3d.overrideAttrs (attrs: {
       env = (attrs.env or { }) // {
         RGL_USE_NULL = "true";
       };
     });
 
-    waysign = old.waysign.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
-    webfakes = old.webfakes.overrideAttrs (_: {
-      postPatch = "patchShebangs configure";
-    });
-
     websocket = old.websocket.overrideAttrs (attrs: {
       env = (attrs.env or { }) // {
         PKGCONFIG_CFLAGS = "-I${pkgs.openssl.dev}/include";
@@ -3165,39 +2803,11 @@ let
       };
     });
 
-    x13binary = old.x13binary.overrideAttrs (attrs: {
-      preConfigure = ''
-        patchShebangs configure
-      '';
-    });
-
-    xactonomial = old.xactonomial.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
-    xml2 = old.xml2.overrideAttrs (attrs: {
-      preConfigure = ''
-        patchShebangs configure
-      '';
-    });
-
     xslt = old.xslt.overrideAttrs (attrs: {
       env = (attrs.env or { }) // {
         NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -fpermissive";
       };
     });
-
-    yaml12 = old.yaml12.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
-    ymd = old.ymd.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
-
-    zoomerjoin = old.zoomerjoin.overrideAttrs (attrs: {
-      postPatch = "patchShebangs configure";
-    });
     # keep-sorted end
   };
 in
diff --git a/pkgs/development/r-modules/generic-builder.nix b/pkgs/development/r-modules/generic-builder.nix
index df463e2f564b..cda092362821 100644
--- a/pkgs/development/r-modules/generic-builder.nix
+++ b/pkgs/development/r-modules/generic-builder.nix
@@ -38,8 +38,14 @@ stdenv.mkDerivation (
 
     configurePhase = ''
       runHook preConfigure
+
       export MAKEFLAGS+="''${enableParallelBuilding:+-j$NIX_BUILD_CORES}"
       export R_LIBS_SITE="$R_LIBS_SITE''${R_LIBS_SITE:+:}$out/library"
+
+      if [ -f ./configure ] && [ -z "''${dontPatchShebangsInConfigure:-}" ]; then
+        patchShebangs --build ./configure
+      fi
+
       runHook postConfigure
     '';