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rPackages.buildRPackage: patch shebangs automatically in configure

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This commit is contained in:
TomaSajt
2026-07-18 09:43:58 +02:00
parent a60a16a038
commit 04108965e6
2 changed files with 7 additions and 391 deletions
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392
pkgs/development/r-modules/default.nix
View File

@@ -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

6
pkgs/development/r-modules/generic-builder.nix
View File

@@ -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
'';