From 428045f39b3ad96ce0e9276dbebab317200c3ada Mon Sep 17 00:00:00 2001 From: Sergei Trofimovich Date: Sun, 8 May 2022 08:56:43 +0100 Subject: [PATCH] bwa: pull upstream fix for -fno-common tollchains Without the change build fails on -fno-common toolchains like upstream gcc-10 as: $ nix build -L --impure --expr 'with import ./. {}; bwa.overrideAttrs (oa: { NIX_CFLAGS_COMPILE = (oa.NIX_CFLAGS_COMPILE or "") + "-fno-common"; })' ... ld: ./libbwa.a(rope.o):/build/bwa-0.7.17/rle.h:33: multiple definition of `rle_auxtab'; ./libbwa.a(bwtindex.o):/build/bwa-0.7.17/rle.h:33: first defined here ld: ./libbwa.a(rle.o):/build/bwa-0.7.17/rle.h:33: multiple definition of `rle_auxtab'; ./libbwa.a(bwtindex.o):/build/bwa-0.7.17/rle.h:33: first defined here --- pkgs/applications/science/biology/bwa/default.nix | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/pkgs/applications/science/biology/bwa/default.nix b/pkgs/applications/science/biology/bwa/default.nix index d4727b41bd0..801ad00876b 100644 --- a/pkgs/applications/science/biology/bwa/default.nix +++ b/pkgs/applications/science/biology/bwa/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchurl, zlib }: +{ lib, stdenv, fetchurl, fetchpatch, zlib }: stdenv.mkDerivation rec { pname = "bwa"; @@ -9,6 +9,16 @@ stdenv.mkDerivation rec { sha256 = "1zfhv2zg9v1icdlq4p9ssc8k01mca5d1bd87w71py2swfi74s6yy"; }; + patches = [ + # Pull upstream patch for -fno-common toolchain support like upstream + # gcc-10: https://github.com/lh3/bwa/pull/267 + (fetchpatch { + name = "fno-common.patch"; + url = "https://github.com/lh3/bwa/commit/2a1ae7b6f34a96ea25be007ac9d91e57e9d32284.patch"; + sha256 = "1lihfxai6vcshv5vr3m7yhk833bdivkja3gld6ilwrc4z28f6wqy"; + }) + ]; + buildInputs = [ zlib ]; # Avoid hardcoding gcc to allow environments with a different