diff options
Diffstat (limited to 'pkgs/applications/science')
8 files changed, 58 insertions, 8 deletions
diff --git a/pkgs/applications/science/chemistry/apbs/default.nix b/pkgs/applications/science/chemistry/apbs/default.nix index f4a2bab4243..228c77ee5c0 100644 --- a/pkgs/applications/science/chemistry/apbs/default.nix +++ b/pkgs/applications/science/chemistry/apbs/default.nix @@ -33,6 +33,10 @@ let "-DBUILD_SUPERLU=OFF" ]; + env = lib.optionalAttrs stdenv.cc.isClang { + NIX_CFLAGS_COMPILE = "-Wno-error=implicit-int"; + }; + buildInputs = [ blas superlu @@ -92,6 +96,10 @@ stdenv.mkDerivation (finalAttrs: { "-DENABLE_TESTS=1" ]; + env = lib.optionalAttrs stdenv.cc.isClang { + NIX_CFLAGS_COMPILE = "-Wno-error=incompatible-function-pointer-types"; + }; + doCheck = true; meta = with lib; { diff --git a/pkgs/applications/science/chemistry/gwyddion/default.nix b/pkgs/applications/science/chemistry/gwyddion/default.nix index 89fb3534c60..5794d7077af 100644 --- a/pkgs/applications/science/chemistry/gwyddion/default.nix +++ b/pkgs/applications/science/chemistry/gwyddion/default.nix @@ -12,7 +12,7 @@ zlibSupport ? true, zlib, libuniqueSupport ? true, libunique, libpngSupport ? true, libpng, - openglSupport ? !stdenv.isDarwin + openglSupport ? !stdenv.isDarwin, libGL }: let @@ -31,7 +31,7 @@ stdenv.mkDerivation rec { buildInputs = with lib; [ gtk2 fftw ] ++ - optional openglSupport gnome2.gtkglext ++ + optionals openglSupport [ gnome2.gtkglext libGL ] ++ optional openexrSupport openexr ++ optional libXmuSupport xorg.libXmu ++ optional fitsSupport cfitsio ++ diff --git a/pkgs/applications/science/electronics/verilog/default.nix b/pkgs/applications/science/electronics/verilog/default.nix index 0a93759947d..06e8a94a4c5 100644 --- a/pkgs/applications/science/electronics/verilog/default.nix +++ b/pkgs/applications/science/electronics/verilog/default.nix @@ -44,6 +44,10 @@ stdenv.mkDerivation rec { enableParallelBuilding = true; + env = lib.optionalAttrs stdenv.isDarwin { + NIX_CFLAGS_COMPILE = "-Wno-error=implicit-function-declaration"; + }; + # NOTE(jleightcap): the `make check` target only runs a "Hello, World"-esque sanity check. # the tests in the doInstallCheck phase run a full regression test suite. # however, these tests currently fail upstream on aarch64 diff --git a/pkgs/applications/science/logic/aiger/default.nix b/pkgs/applications/science/logic/aiger/default.nix index 15c45466b13..972bea3fbc3 100644 --- a/pkgs/applications/science/logic/aiger/default.nix +++ b/pkgs/applications/science/logic/aiger/default.nix @@ -9,6 +9,11 @@ stdenv.mkDerivation rec { sha256 = "1ish0dw0nf9gyghxsdhpy1jjiy5wp54c993swp85xp7m6vdx6l0y"; }; + patches = [ + # Fix implicit declaration of `isatty`, which is an error with newer versions of clang. + ./fix-missing-header.patch + ]; + enableParallelBuilding = true; configurePhase = '' diff --git a/pkgs/applications/science/logic/aiger/fix-missing-header.patch b/pkgs/applications/science/logic/aiger/fix-missing-header.patch new file mode 100644 index 00000000000..5f0101bd7a0 --- /dev/null +++ b/pkgs/applications/science/logic/aiger/fix-missing-header.patch @@ -0,0 +1,11 @@ +diff -ur a/aigunconstraint.c b/aigunconstraint.c +--- a/aigunconstraint.c 2013-10-06 09:08:03.000000000 -0400 ++++ b/aigunconstraint.c 2023-10-27 08:55:01.678566389 -0400 +@@ -26,6 +26,7 @@ + #include <stdarg.h> + #include <stdlib.h> + #include <string.h> ++#include <unistd.h> + + static const char * USAGE = + "usage: aigunconstraint [-h][-v] [<input> [<output>]]\n" diff --git a/pkgs/applications/science/logic/vampire/default.nix b/pkgs/applications/science/logic/vampire/default.nix index 253c88705ae..a3c1aa3f131 100644 --- a/pkgs/applications/science/logic/vampire/default.nix +++ b/pkgs/applications/science/logic/vampire/default.nix @@ -19,13 +19,13 @@ stdenv.mkDerivation rec { # https://github.com/vprover/vampire/pull/54 (fetchpatch { name = "fix-apple-cygwin-defines.patch"; - url = "https://github.com/vprover/vampire/pull/54.patch"; + url = "https://github.com/vprover/vampire/commit/b4bddd3bcac6a7688742da75c369b7b3213f6d1c.patch"; sha256 = "0i6nrc50wlg1dqxq38lkpx4rmfb3lf7s8f95l4jkvqp0nxa20cza"; }) # https://github.com/vprover/vampire/pull/55 (fetchpatch { name = "fix-wait-any.patch"; - url = "https://github.com/vprover/vampire/pull/55.patch"; + url = "https://github.com/vprover/vampire/commit/6da10eabb333aec54cdf13833ea33cb851159543.patch"; sha256 = "1pwfpwpl23bqsgkmmvw6bnniyvp5j9v8l3z9s9pllfabnfcrcz9l"; }) ]; diff --git a/pkgs/applications/science/math/readstat/default.nix b/pkgs/applications/science/math/readstat/default.nix index efbf80ba16e..08555d12640 100644 --- a/pkgs/applications/science/math/readstat/default.nix +++ b/pkgs/applications/science/math/readstat/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchFromGitHub, autoreconfHook, pkg-config, libiconv }: +{ lib, stdenv, fetchFromGitHub, fetchpatch, autoreconfHook, pkg-config, libiconv }: stdenv.mkDerivation rec { pname = "readstat"; @@ -11,6 +11,13 @@ stdenv.mkDerivation rec { sha256 = "sha256-4lRJgZPB2gfaQ9fQKvDDpGhy1eDNT/nT1QmeZlCmCis="; }; + patches = [ + (fetchpatch { + url = "https://github.com/WizardMac/ReadStat/commit/211c342a1cfe46fb7fb984730dd7a29ff4752f35.patch"; + hash = "sha256-nkaEgusylVu7NtzSzBklBuOnqO9qJPovf0qn9tTE6ls="; + }) + ]; + nativeBuildInputs = [ pkg-config autoreconfHook ]; buildInputs = [ libiconv ]; @@ -22,5 +29,6 @@ stdenv.mkDerivation rec { description = "Command-line tool (+ C library) for converting SAS, Stata, and SPSS files"; license = lib.licenses.mit; maintainers = with lib.maintainers; [ swflint ]; + platforms = lib.platforms.all; }; } diff --git a/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix index 8064a965bd1..97754c04d95 100644 --- a/pkgs/applications/science/math/sage/sage-src.nix +++ b/pkgs/applications/science/math/sage/sage-src.nix @@ -104,11 +104,11 @@ stdenv.mkDerivation rec { sha256 = "sha256-GqMgoi0tsP7zcCcPumhdsbvhPB6fgw1ufx6gHlc6iSc="; }) - # https://github.com/sagemath/sage/pull/36006, positively reviewed + # https://github.com/sagemath/sage/pull/36006, landed in 10.2.beta2 (fetchpatch { name = "gmp-6.3-upgrade.patch"; - url = "https://github.com/sagemath/sage/commit/d88bc3815c0901bfdeaa3e4a31107c084199f614.diff"; - sha256 = "sha256-dXaEwk2wXxmx02sCw4Vu9mF0ZrydhFD4LRwNAiQsPgM="; + url = "https://github.com/sagemath/sage/commit/5e841de46c3baa99cd1145b36ff9163e9340a55c.diff"; + sha256 = "sha256-fJPDryLtGBQz9qHDiCkBwjiW2lN6v7HiHgxY7CTeHcs="; }) # https://github.com/sagemath/sage/pull/36279, landed in 10.2.beta4 @@ -117,6 +117,20 @@ stdenv.mkDerivation rec { url = "https://github.com/sagemath/sage/commit/0fcf88935908440930c5f79202155aca4ad57518.diff"; sha256 = "sha256-mvqAHaTCXsxPv901L8HSTnrfghfXYdq0wfLoP/cYQZI="; }) + + # https://github.com/sagemath/sage/pull/35658, landed in 10.1.beta2 + (fetchpatch { + name = "sphinx-7-upgrade.patch"; + url = "https://github.com/sagemath/sage/commit/cacd9a89b5c4fdcf84a8dd2b7d5bdc10cc78109a.diff"; + sha256 = "sha256-qJvliTJjR3XBc5pH6Q0jtm8c4bhtZcTcF3O04Ro1uaU="; + }) + + # https://github.com/sagemath/sage/pull/36296, landed in 10.2.beta4 + (fetchpatch { + name = "duplicate-args-region_plot.patch"; + url = "https://github.com/sagemath/sage/commit/461727b453712550a2c5dc0ae11933523255aaed.diff"; + sha256 = "sha256-mC8084VQoUBk4hocALF+Y9Cwb38Zt360eldi/SSjna8="; + }) ]; patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches; |