diff options
Diffstat (limited to 'pkgs/applications/science')
8 files changed, 87 insertions, 17 deletions
diff --git a/pkgs/applications/science/biology/megahit/default.nix b/pkgs/applications/science/biology/megahit/default.nix index 7f054a51d5e05..5fa9420bc87cb 100644 --- a/pkgs/applications/science/biology/megahit/default.nix +++ b/pkgs/applications/science/biology/megahit/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchFromGitHub, cmake, zlib }: +{ lib, stdenv, fetchFromGitHub, fetchpatch, cmake, zlib }: stdenv.mkDerivation rec { pname = "megahit"; @@ -11,6 +11,16 @@ stdenv.mkDerivation rec { sha256 = "1r5d9nkdmgjsbrpj43q9hy3s8jwsabaz3ji561v18hy47v58923c"; }; + patches = [ + # Fix gcc-13 build failure: + # https://github.com/voutcn/megahit/pull/366 + (fetchpatch { + name = "gcc-13.patch"; + url = "https://github.com/voutcn/megahit/commit/4cb2f793503087163bda8592222f105f27e33e66.patch"; + hash = "sha256-b5mhzif+OPcMjmg+BnaUc5CB6Acn/KTBOJEw+WYEhbs="; + }) + ]; + nativeBuildInputs = [ cmake ]; buildInputs = [ zlib ]; diff --git a/pkgs/applications/science/biology/svaba/default.nix b/pkgs/applications/science/biology/svaba/default.nix index 441c7ed6dcc3d..d36c4b668ec3b 100644 --- a/pkgs/applications/science/biology/svaba/default.nix +++ b/pkgs/applications/science/biology/svaba/default.nix @@ -14,6 +14,13 @@ stdenv.mkDerivation rec { buildInputs = [ zlib bzip2 xz ]; + postPatch = '' + # Fix gcc-13 build failure due to missing includes + sed -e '1i #include <cstdint>' -i \ + SeqLib/src/non_api/Histogram.h \ + src/svaba/Histogram.h + ''; + # Workaround build failure on -fno-common toolchains like upstream # gcc-10. Otherwise build fails as: # ld: ./libfml.a(rle.o):/build/source/SeqLib/fermi-lite/rle.h:33: multiple definition of diff --git a/pkgs/applications/science/chemistry/openmolcas/default.nix b/pkgs/applications/science/chemistry/openmolcas/default.nix index 0aeb01c2916b5..cefe83446662e 100644 --- a/pkgs/applications/science/chemistry/openmolcas/default.nix +++ b/pkgs/applications/science/chemistry/openmolcas/default.nix @@ -13,7 +13,7 @@ , libxc , makeWrapper , gsl -, boost175 +, boost180 , autoPatchelfHook # Note that the CASPT2 module is broken with MPI # See https://gitlab.com/Molcas/OpenMolcas/-/issues/169 @@ -93,7 +93,7 @@ stdenv.mkDerivation { armadillo libxc gsl.dev - boost175 + boost180 ] ++ lib.optionals enableMpi [ mpi globalarrays @@ -155,7 +155,7 @@ stdenv.mkDerivation { homepage = "https://gitlab.com/Molcas/OpenMolcas"; maintainers = [ maintainers.markuskowa ]; license = with licenses; [ lgpl21Only bsd3 ]; - platforms = [ "x86_64-linux" ]; + platforms = [ "aarch64-linux" "x86_64-linux" ]; mainProgram = "pymolcas"; }; } diff --git a/pkgs/applications/science/logic/cryptoverif/default.nix b/pkgs/applications/science/logic/cryptoverif/default.nix index 66ba807c8dd81..5c15b8a17241f 100644 --- a/pkgs/applications/science/logic/cryptoverif/default.nix +++ b/pkgs/applications/science/logic/cryptoverif/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "cryptoverif"; - version = "2.07"; + version = "2.08pl1"; src = fetchurl { url = "http://prosecco.gforge.inria.fr/personal/bblanche/cryptoverif/cryptoverif${version}.tar.gz"; - hash = "sha256-GXXql4+JZ396BM6W2I3kN0u59xos7UCAtzR0IjMIETY="; + hash = "sha256-rmORSZuhds9W2WpNgYf4AJM2jgEUPoJit4G64qLqj5w="; }; /* Fix up the frontend to load the 'default' cryptoverif library diff --git a/pkgs/applications/science/logic/stp/default.nix b/pkgs/applications/science/logic/stp/default.nix index 4646f7178f560..fb41ea07f5a15 100644 --- a/pkgs/applications/science/logic/stp/default.nix +++ b/pkgs/applications/science/logic/stp/default.nix @@ -18,6 +18,14 @@ stdenv.mkDerivation rec { ./stdint.patch ]; + postPatch = '' + # Upstream fix for gcc-13 support: + # https://github.com/stp/stp/pull/462 + # Can't apply it as is as patch context changed in ither patches. + # TODO: remove me on 2.4 release + sed -e '1i #include <cstdint>' -i include/stp/AST/ASTNode.h + ''; + buildInputs = [ boost zlib minisat cryptominisat python3 ]; nativeBuildInputs = [ cmake bison flex perl ]; preConfigure = '' diff --git a/pkgs/applications/science/misc/openmvg/default.nix b/pkgs/applications/science/misc/openmvg/default.nix index c5434c8699093..5cf4dc4377521 100644 --- a/pkgs/applications/science/misc/openmvg/default.nix +++ b/pkgs/applications/science/misc/openmvg/default.nix @@ -1,34 +1,63 @@ -{ lib, stdenv, fetchFromGitHub, pkg-config, cmake, cereal, openmp -, libjpeg ? null -, zlib ? null -, libpng ? null -, eigen ? null -, libtiff ? null +{ lib, stdenv, fetchFromGitHub, pkg-config, cmake +, cereal , ceres-solver +, clp +, coin-utils +, eigen +, lemon-graph +, libjpeg +, libpng +, libtiff +, nix-update-script +, openmp +, osi +, zlib , enableShared ? !stdenv.hostPlatform.isStatic , enableExamples ? false , enableDocs ? false }: stdenv.mkDerivation rec { - version = "unstable-2022-12-30"; + version = "2.1"; pname = "openmvg"; src = fetchFromGitHub { owner = "openmvg"; repo = "openmvg"; - rev = "e1bbfe801986cd7171f36443a1573b0f69f3702d"; - sha256 = "sha256-DngfmejNFw5pogTo7Ec5aUey2LUQIojvJybLmtCfvVY="; - fetchSubmodules = true; + rev = "v${version}"; + hash = "sha256-vG+tW9Gl/DAUL8DeY+rJVDJH/oMPH3XyZMUgzjtwFv0="; }; - buildInputs = [ libjpeg zlib libpng eigen libtiff cereal openmp ceres-solver ]; + # Pretend we checked out the dependency submodules + postPatch = '' + mkdir src/dependencies/cereal/include + ''; + + buildInputs = [ + cereal + ceres-solver + clp + coin-utils + eigen + lemon-graph + libjpeg + libpng + libtiff + openmp + osi + zlib + ]; nativeBuildInputs = [ cmake pkg-config ]; + # flann is missing because the lz4 dependency isn't propagated: https://github.com/openMVG/openMVG/issues/1265 cmakeFlags = [ "-DOpenMVG_BUILD_EXAMPLES=${if enableExamples then "ON" else "OFF"}" "-DOpenMVG_BUILD_DOC=${if enableDocs then "ON" else "OFF"}" "-DTARGET_ARCHITECTURE=generic" + "-DCLP_INCLUDE_DIR_HINTS=${lib.getDev clp}/include" + "-DCOINUTILS_INCLUDE_DIR_HINTS=${lib.getDev coin-utils}/include" + "-DLEMON_INCLUDE_DIR_HINTS=${lib.getDev lemon-graph}/include" + "-DOSI_INCLUDE_DIR_HINTS=${lib.getDev osi}/include" ] ++ lib.optional enableShared "-DOpenMVG_BUILD_SHARED=ON"; cmakeDir = "./src"; @@ -41,6 +70,8 @@ stdenv.mkDerivation rec { # Without hardeningDisable, certain flags are passed to the compile that break the build (primarily string format errors) hardeningDisable = [ "all" ]; + passthru.updateScript = nix-update-script { }; + meta = { broken = stdenv.isDarwin && stdenv.isx86_64; description = "A library for computer-vision scientists and targeted for the Multiple View Geometry community"; diff --git a/pkgs/applications/science/misc/root/default.nix b/pkgs/applications/science/misc/root/default.nix index c5534c18d7bbb..7c9d6f5cb0a66 100644 --- a/pkgs/applications/science/misc/root/default.nix +++ b/pkgs/applications/science/misc/root/default.nix @@ -2,6 +2,7 @@ , lib , callPackage , fetchurl +, fetchpatch , makeWrapper , cmake , coreutils @@ -109,6 +110,17 @@ stdenv.mkDerivation rec { patches = [ ./sw_vers.patch + + # compatibility with recent XRootD + # https://github.com/root-project/root/pull/13752 + (fetchpatch { + url = "https://github.com/root-project/root/commit/3d3cda6c520791282298782189cdb8ca07ace4b9.diff"; + hash = "sha256-O3aXzrOEQiPjZgbAj9TL6Wt/adN1kKFwjooeaFRyT4I="; + }) + (fetchpatch { + url = "https://github.com/root-project/root/commit/6e7798e62dbed1ffa8b91a180fa5a080b7c04ba3.diff"; + hash = "sha256-47/J631DBnVlvM1Pm9iicKXDKAqN8v9hjAstQuHmH8Q="; + }) ]; preConfigure = '' diff --git a/pkgs/applications/science/physics/xfitter/default.nix b/pkgs/applications/science/physics/xfitter/default.nix index 1852ef3ff1c8e..77b57e08e2bbe 100644 --- a/pkgs/applications/science/physics/xfitter/default.nix +++ b/pkgs/applications/science/physics/xfitter/default.nix @@ -47,6 +47,8 @@ stdenv.mkDerivation rec { env.NIX_CFLAGS_COMPILE = lib.optionalString (stdenv.hostPlatform.libc == "glibc") "-I${libtirpc.dev}/include/tirpc"; NIX_LDFLAGS = lib.optional (stdenv.hostPlatform.libc == "glibc") "-ltirpc"; + hardeningDisable = [ "format" ]; + # workaround wrong library IDs postInstall = lib.optionalString stdenv.isDarwin '' ln -sv "$out/lib/xfitter/"* "$out/lib/" |