diff options
Diffstat (limited to 'pkgs/applications/science')
31 files changed, 32 insertions, 32 deletions
diff --git a/pkgs/applications/science/astronomy/astrolog/default.nix b/pkgs/applications/science/astronomy/astrolog/default.nix index 26d0639ae67f2..743a58e9e053d 100644 --- a/pkgs/applications/science/astronomy/astrolog/default.nix +++ b/pkgs/applications/science/astronomy/astrolog/default.nix @@ -19,7 +19,7 @@ stdenv.mkDerivation rec { ''; buildInputs = [ xorg.libX11 ]; - NIX_CFLAGS_COMPILE = "-Wno-format-security"; + env.NIX_CFLAGS_COMPILE = "-Wno-format-security"; installPhase = let diff --git a/pkgs/applications/science/astronomy/gildas/default.nix b/pkgs/applications/science/astronomy/gildas/default.nix index 50eee7d3aa3f7..64e3f8713b2f8 100644 --- a/pkgs/applications/science/astronomy/gildas/default.nix +++ b/pkgs/applications/science/astronomy/gildas/default.nix @@ -26,7 +26,7 @@ stdenv.mkDerivation rec { patches = [ ./wrapper.patch ./clang.patch ./aarch64.patch ]; - NIX_CFLAGS_COMPILE = lib.optionalString stdenv.cc.isClang "-Wno-unused-command-line-argument"; + env.NIX_CFLAGS_COMPILE = lib.optionalString stdenv.cc.isClang "-Wno-unused-command-line-argument"; NIX_LDFLAGS = lib.optionalString stdenv.isDarwin (with darwin.apple_sdk.frameworks; "-F${CoreFoundation}/Library/Frameworks"); diff --git a/pkgs/applications/science/astronomy/xplanet/default.nix b/pkgs/applications/science/astronomy/xplanet/default.nix index d284171831b87..94aa92a1b713f 100644 --- a/pkgs/applications/science/astronomy/xplanet/default.nix +++ b/pkgs/applications/science/astronomy/xplanet/default.nix @@ -26,7 +26,7 @@ stdenv.mkDerivation rec { }) ]; - NIX_CFLAGS_COMPILE = lib.optionalString stdenv.cc.isClang "-Wno-error=c++11-narrowing"; + env.NIX_CFLAGS_COMPILE = lib.optionalString stdenv.cc.isClang "-Wno-error=c++11-narrowing"; meta = with lib; { description = "Renders an image of the earth or other planets into the X root window"; diff --git a/pkgs/applications/science/biology/bayescan/default.nix b/pkgs/applications/science/biology/bayescan/default.nix index cd5bb3210364e..e715ff4b45b06 100644 --- a/pkgs/applications/science/biology/bayescan/default.nix +++ b/pkgs/applications/science/biology/bayescan/default.nix @@ -29,7 +29,7 @@ stdenv.mkDerivation rec { cp -r ../*pdf ../input_examples ../"R functions" $out/share/doc/bayescan ''; - NIX_CFLAGS_COMPILE = [ "-std=c++14" ]; + env.NIX_CFLAGS_COMPILE = toString [ "-std=c++14" ]; meta = with lib; { description = "Detecting natural selection from population-based genetic data"; diff --git a/pkgs/applications/science/biology/cmtk/default.nix b/pkgs/applications/science/biology/cmtk/default.nix index 42ce5f934e826..3eef648372555 100644 --- a/pkgs/applications/science/biology/cmtk/default.nix +++ b/pkgs/applications/science/biology/cmtk/default.nix @@ -12,7 +12,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake ]; - NIX_CFLAGS_COMPILE = [ + env.NIX_CFLAGS_COMPILE = toString [ "-std=c++11" (lib.optional stdenv.cc.isClang "-Wno-error=c++11-narrowing") ]; diff --git a/pkgs/applications/science/biology/freebayes/default.nix b/pkgs/applications/science/biology/freebayes/default.nix index 5c2f09a4faefa..0ceaab4ab46be 100644 --- a/pkgs/applications/science/biology/freebayes/default.nix +++ b/pkgs/applications/science/biology/freebayes/default.nix @@ -19,7 +19,7 @@ stdenv.mkDerivation rec { # gcc-10. Otherwise build fails as: # ld: foomatic_rip-options.o:/build/foomatic-filters-4.0.17/options.c:49: multiple definition of `cupsfilter'; # foomatic_rip-foomaticrip.o:/build/foomatic-filters-4.0.17/foomaticrip.c:158: first defined here - NIX_CFLAGS_COMPILE = "-fcommon"; + env.NIX_CFLAGS_COMPILE = "-fcommon"; installPhase = '' install -vD bin/freebayes bin/bamleftalign scripts/* -t $out/bin diff --git a/pkgs/applications/science/biology/minia/default.nix b/pkgs/applications/science/biology/minia/default.nix index 6b6bc300e0d9f..023a05d7504f9 100644 --- a/pkgs/applications/science/biology/minia/default.nix +++ b/pkgs/applications/science/biology/minia/default.nix @@ -14,7 +14,7 @@ stdenv.mkDerivation rec { patches = [ ./no-bundle.patch ]; - NIX_CFLAGS_COMPILE = [ "-Wformat" ]; + env.NIX_CFLAGS_COMPILE = toString [ "-Wformat" ]; nativeBuildInputs = [ cmake ]; buildInputs = [ hdf5 boost ]; diff --git a/pkgs/applications/science/biology/niftyreg/default.nix b/pkgs/applications/science/biology/niftyreg/default.nix index d5f625893e925..0be59bcd726a0 100644 --- a/pkgs/applications/science/biology/niftyreg/default.nix +++ b/pkgs/applications/science/biology/niftyreg/default.nix @@ -9,7 +9,7 @@ stdenv.mkDerivation rec { sha256 = "07v9v9s41lvw72wpb1jgh2nzanyc994779bd35p76vg8mzifmprl"; }; - NIX_CFLAGS_COMPILE = [ "-Wno-error=narrowing" ]; + env.NIX_CFLAGS_COMPILE = toString [ "-Wno-error=narrowing" ]; nativeBuildInputs = [ cmake ]; buildInputs = [ zlib ]; diff --git a/pkgs/applications/science/biology/octopus/default.nix b/pkgs/applications/science/biology/octopus/default.nix index b7c8c138cb82b..c2948087d8ed7 100644 --- a/pkgs/applications/science/biology/octopus/default.nix +++ b/pkgs/applications/science/biology/octopus/default.nix @@ -19,7 +19,7 @@ stdenv.mkDerivation rec { sha256 = "sha256-VaUr63v7mzhh4VBghH7a7qrqOYwl6vucmmKzTi9yAjY="; }) ]; - NIX_CFLAGS_COMPILE = [ + env.NIX_CFLAGS_COMPILE = toString [ # Needed with GCC 12 "-Wno-error=deprecated-declarations" ]; diff --git a/pkgs/applications/science/biology/paml/default.nix b/pkgs/applications/science/biology/paml/default.nix index 66ba244cacd68..871c76dc6e31b 100644 --- a/pkgs/applications/science/biology/paml/default.nix +++ b/pkgs/applications/science/biology/paml/default.nix @@ -12,7 +12,7 @@ stdenv.mkDerivation rec { # gcc-10. Otherwise build fails as: # ld: /build/ccKomtcd.o:(.bss+0x4544): multiple definition of `SeqTypes'; # /build/ccx7EsgU.o:(.bss+0x2a0dfdc): first defined here - NIX_CFLAGS_COMPILE = "-fcommon"; + env.NIX_CFLAGS_COMPILE = "-fcommon"; preBuild = '' cd ./src/ diff --git a/pkgs/applications/science/biology/strelka/default.nix b/pkgs/applications/science/biology/strelka/default.nix index 8585f3770fbcd..9730601e4e7d1 100644 --- a/pkgs/applications/science/biology/strelka/default.nix +++ b/pkgs/applications/science/biology/strelka/default.nix @@ -14,7 +14,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake ]; buildInputs = [ zlib python2 ]; - NIX_CFLAGS_COMPILE = [ + env.NIX_CFLAGS_COMPILE = toString [ "-Wno-error=maybe-uninitialized" "-Wno-error=pessimizing-move" ]; diff --git a/pkgs/applications/science/biology/svaba/default.nix b/pkgs/applications/science/biology/svaba/default.nix index b1a174aaf882d..441c7ed6dcc3d 100644 --- a/pkgs/applications/science/biology/svaba/default.nix +++ b/pkgs/applications/science/biology/svaba/default.nix @@ -18,7 +18,7 @@ stdenv.mkDerivation rec { # gcc-10. Otherwise build fails as: # ld: ./libfml.a(rle.o):/build/source/SeqLib/fermi-lite/rle.h:33: multiple definition of # `rle_auxtab'; ./libfml.a(misc.o):/build/source/SeqLib/fermi-lite/rle.h:33: first defined here - NIX_CFLAGS_COMPILE = "-fcommon"; + env.NIX_CFLAGS_COMPILE = "-fcommon"; installPhase = '' runHook preInstall diff --git a/pkgs/applications/science/chemistry/avogadro/default.nix b/pkgs/applications/science/chemistry/avogadro/default.nix index c6339bab1228e..547123b67957c 100644 --- a/pkgs/applications/science/chemistry/avogadro/default.nix +++ b/pkgs/applications/science/chemistry/avogadro/default.nix @@ -13,7 +13,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake pkg-config doxygen ]; - NIX_CFLAGS_COMPILE = "-include ${libGLU.dev}/include/GL/glu.h"; + env.NIX_CFLAGS_COMPILE = "-include ${libGLU.dev}/include/GL/glu.h"; patches = [ (fetchurl { diff --git a/pkgs/applications/science/chemistry/chemtool/default.nix b/pkgs/applications/science/chemistry/chemtool/default.nix index 37057e1c604a4..fe2d658b5a44f 100644 --- a/pkgs/applications/science/chemistry/chemtool/default.nix +++ b/pkgs/applications/science/chemistry/chemtool/default.nix @@ -28,7 +28,7 @@ stdenv.mkDerivation rec { # Otherwise built fails as: # ld: inout.o:/build/chemtool-1.6.14/ct1.h:279: multiple definition of # `outtype'; draw.o:/build/chemtool-1.6.14/ct1.h:279: first defined here - NIX_CFLAGS_COMPILE = "-fcommon"; + env.NIX_CFLAGS_COMPILE = "-fcommon"; preFixup = '' gappsWrapperArgs+=(--prefix PATH : "${lib.makeBinPath [ fig2dev ]}") diff --git a/pkgs/applications/science/chemistry/pymol/default.nix b/pkgs/applications/science/chemistry/pymol/default.nix index 4ad0380ef1e31..15a1e3158233f 100644 --- a/pkgs/applications/science/chemistry/pymol/default.nix +++ b/pkgs/applications/science/chemistry/pymol/default.nix @@ -48,7 +48,7 @@ python3Packages.buildPythonApplication rec { nativeBuildInputs = [ qt5.wrapQtAppsHook ]; buildInputs = [ python3Packages.numpy python3Packages.pyqt5 glew glm libpng libxml2 freetype msgpack netcdf ]; - NIX_CFLAGS_COMPILE = "-I ${libxml2.dev}/include/libxml2"; + env.NIX_CFLAGS_COMPILE = "-I ${libxml2.dev}/include/libxml2"; hardeningDisable = [ "format" ]; installPhase = '' diff --git a/pkgs/applications/science/computer-architecture/timeloop/default.nix b/pkgs/applications/science/computer-architecture/timeloop/default.nix index 9b277ac650b74..4e794aaa29e24 100644 --- a/pkgs/applications/science/computer-architecture/timeloop/default.nix +++ b/pkgs/applications/science/computer-architecture/timeloop/default.nix @@ -43,7 +43,7 @@ stdenv.mkDerivation rec { #link-time optimization fails on darwin #see https://github.com/NixOS/nixpkgs/issues/19098 - NIX_CFLAGS_COMPILE = lib.optional stdenv.isDarwin "-fno-lto"; + env.NIX_CFLAGS_COMPILE = lib.optionalString stdenv.isDarwin "-fno-lto"; postPatch = '' # use nix ar/ranlib diff --git a/pkgs/applications/science/electronics/fped/default.nix b/pkgs/applications/science/electronics/fped/default.nix index b1244b79a89f8..138d45c787cdd 100644 --- a/pkgs/applications/science/electronics/fped/default.nix +++ b/pkgs/applications/science/electronics/fped/default.nix @@ -17,7 +17,7 @@ stdenv.mkDerivation { # Workaround build failure on -fno-common toolchains: # ld: postscript.o:postscript.h:29: multiple definition of # `postscript_params'; fped.o:postscript.h:29: first defined here - NIX_CFLAGS_COMPILE = "-fcommon"; + env.NIX_CFLAGS_COMPILE = "-fcommon"; # This uses '/bin/bash', '/usr/local' and 'lex' by default makeFlags = [ diff --git a/pkgs/applications/science/electronics/fritzing/default.nix b/pkgs/applications/science/electronics/fritzing/default.nix index 22b65f2da313a..fdda4b2b0af2c 100644 --- a/pkgs/applications/science/electronics/fritzing/default.nix +++ b/pkgs/applications/science/electronics/fritzing/default.nix @@ -61,7 +61,7 @@ stdenv.mkDerivation rec { cp -a ${parts}/* parts/ ''; - NIX_CFLAGS_COMPILE = "-I${lib.getDev quazip}/include/QuaZip-Qt${lib.versions.major qtbase.version}-${quazip.version}/quazip"; + env.NIX_CFLAGS_COMPILE = "-I${lib.getDev quazip}/include/QuaZip-Qt${lib.versions.major qtbase.version}-${quazip.version}/quazip"; qmakeFlags = [ "phoenix.pro" diff --git a/pkgs/applications/science/electronics/magic-vlsi/default.nix b/pkgs/applications/science/electronics/magic-vlsi/default.nix index edee5946d9460..fc68969bd498a 100644 --- a/pkgs/applications/science/electronics/magic-vlsi/default.nix +++ b/pkgs/applications/science/electronics/magic-vlsi/default.nix @@ -44,7 +44,7 @@ stdenv.mkDerivation rec { patchShebangs scripts/* ''; - NIX_CFLAGS_COMPILE = "-Wno-implicit-function-declaration"; + env.NIX_CFLAGS_COMPILE = "-Wno-implicit-function-declaration"; patches = [ ./0001-strip-bin-prefix.patch diff --git a/pkgs/applications/science/logic/avy/default.nix b/pkgs/applications/science/logic/avy/default.nix index f6f43f1b0bb30..38fef51c56e6d 100644 --- a/pkgs/applications/science/logic/avy/default.nix +++ b/pkgs/applications/science/logic/avy/default.nix @@ -13,7 +13,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake ]; buildInputs = [ zlib boost.out boost.dev ]; - NIX_CFLAGS_COMPILE = toString ([ "-Wno-narrowing" ] + env.NIX_CFLAGS_COMPILE = toString ([ "-Wno-narrowing" ] # Squelch endless stream of warnings on same few things ++ lib.optionals stdenv.cc.isClang [ "-Wno-empty-body" diff --git a/pkgs/applications/science/logic/cbmc/default.nix b/pkgs/applications/science/logic/cbmc/default.nix index d61a9893942f8..ddfa999fcc7e3 100644 --- a/pkgs/applications/science/logic/cbmc/default.nix +++ b/pkgs/applications/science/logic/cbmc/default.nix @@ -60,13 +60,13 @@ stdenv.mkDerivation rec { --prefix PATH : "$out/share/cbmc" \ ''; - NIX_CFLAGS_COMPILE = lib.optionals stdenv.cc.isGNU [ + env.NIX_CFLAGS_COMPILE = toString (lib.optionals stdenv.cc.isGNU [ # Needed with GCC 12 but breaks on darwin (with clang) "-Wno-error=maybe-uninitialized" ] ++ lib.optionals stdenv.cc.isClang [ # fix "argument unused during compilation" "-Wno-unused-command-line-argument" - ]; + ]); # TODO: add jbmc support cmakeFlags = [ "-DWITH_JBMC=OFF" "-Dsat_impl=cadical" "-Dcadical_INCLUDE_DIR=${cadical.dev}/include" ]; diff --git a/pkgs/applications/science/logic/klee/default.nix b/pkgs/applications/science/logic/klee/default.nix index 024e6e526c4e4..898e344f2a453 100644 --- a/pkgs/applications/science/logic/klee/default.nix +++ b/pkgs/applications/science/logic/klee/default.nix @@ -96,7 +96,7 @@ in stdenv.mkDerivation rec { ]; # Silence various warnings during the compilation of fortified bitcode. - NIX_CFLAGS_COMPILE = ["-Wno-macro-redefined"]; + env.NIX_CFLAGS_COMPILE = toString ["-Wno-macro-redefined"]; prePatch = '' patchShebangs . diff --git a/pkgs/applications/science/logic/satallax/default.nix b/pkgs/applications/science/logic/satallax/default.nix index 5e5fe9925376b..af11cd0d6d8f9 100644 --- a/pkgs/applications/science/logic/satallax/default.nix +++ b/pkgs/applications/science/logic/satallax/default.nix @@ -49,7 +49,7 @@ stdenv.mkDerivation rec { ''; # error: invalid suffix on literal; C++11 requires a space between literal and identifier - NIX_CFLAGS_COMPILE = lib.optionalString stdenv.isDarwin "-Wno-reserved-user-defined-literal"; + env.NIX_CFLAGS_COMPILE = lib.optionalString stdenv.isDarwin "-Wno-reserved-user-defined-literal"; installPhase = '' mkdir -p "$out/share/doc/satallax" "$out/bin" "$out/lib" "$out/lib/satallax" diff --git a/pkgs/applications/science/math/calculix/default.nix b/pkgs/applications/science/math/calculix/default.nix index 4b0ae6f8ac9d9..7a89fdd73c848 100644 --- a/pkgs/applications/science/math/calculix/default.nix +++ b/pkgs/applications/science/math/calculix/default.nix @@ -17,7 +17,7 @@ stdenv.mkDerivation rec { buildInputs = [ arpack spooles blas lapack ]; - NIX_CFLAGS_COMPILE = [ + env.NIX_CFLAGS_COMPILE = toString [ "-I${spooles}/include/spooles" "-std=legacy" ]; diff --git a/pkgs/applications/science/math/cntk/default.nix b/pkgs/applications/science/math/cntk/default.nix index bffd208f9ef61..f885dae444ba6 100644 --- a/pkgs/applications/science/math/cntk/default.nix +++ b/pkgs/applications/science/math/cntk/default.nix @@ -60,7 +60,7 @@ in stdenv.mkDerivation rec { OMPI_CXX = "g++"; # Uses some deprecated tensorflow functions - NIX_CFLAGS_COMPILE = "-Wno-error=deprecated-declarations"; + env.NIX_CFLAGS_COMPILE = "-Wno-error=deprecated-declarations"; buildInputs = [ openblas opencv3 libzip boost protobuf mpi ] ++ lib.optional cudaSupport cudatoolkit diff --git a/pkgs/applications/science/math/eukleides/default.nix b/pkgs/applications/science/math/eukleides/default.nix index 507fa0815298b..42e17c70673e6 100644 --- a/pkgs/applications/science/math/eukleides/default.nix +++ b/pkgs/applications/science/math/eukleides/default.nix @@ -36,7 +36,7 @@ lib.fix (eukleides: stdenv.mkDerivation rec { # gcc-10. Otherwise build fails as: # ld: eukleides_build/triangle.o:(.bss+0x28): multiple definition of `A'; # eukleides_build/quadrilateral.o:(.bss+0x18): first defined here - NIX_CFLAGS_COMPILE = "-fcommon"; + env.NIX_CFLAGS_COMPILE = "-fcommon"; preInstall = '' mkdir -p $out/bin diff --git a/pkgs/applications/science/math/mxnet/default.nix b/pkgs/applications/science/math/mxnet/default.nix index 021593124a37d..a5c0ebc85b13b 100644 --- a/pkgs/applications/science/math/mxnet/default.nix +++ b/pkgs/applications/science/math/mxnet/default.nix @@ -54,7 +54,7 @@ stdenv.mkDerivation rec { ] else [ "-DUSE_CUDA=OFF" ]) ++ lib.optional (!cudnnSupport) "-DUSE_CUDNN=OFF"; - NIX_CFLAGS_COMPILE = [ + env.NIX_CFLAGS_COMPILE = toString [ # Needed with GCC 12 "-Wno-error=maybe-uninitialized" "-Wno-error=uninitialized" diff --git a/pkgs/applications/science/math/perseus/default.nix b/pkgs/applications/science/math/perseus/default.nix index d9921e68edb11..bbfc8aed44284 100644 --- a/pkgs/applications/science/math/perseus/default.nix +++ b/pkgs/applications/science/math/perseus/default.nix @@ -13,7 +13,7 @@ stdenv.mkDerivation { }; sourceRoot = "."; - NIX_CFLAGS_COMPILE = [ "-std=c++14" ]; + env.NIX_CFLAGS_COMPILE = toString [ "-std=c++14" ]; buildPhase = '' g++ Pers.cpp -O3 -fpermissive -o perseus ''; diff --git a/pkgs/applications/science/misc/fityk/default.nix b/pkgs/applications/science/misc/fityk/default.nix index a4aa6457d608d..5ec7973065d2f 100644 --- a/pkgs/applications/science/misc/fityk/default.nix +++ b/pkgs/applications/science/misc/fityk/default.nix @@ -37,7 +37,7 @@ stdenv.mkDerivation rec { swig3 ]; - NIX_CFLAGS_COMPILE = [ + env.NIX_CFLAGS_COMPILE = toString [ "-std=c++11" ]; diff --git a/pkgs/applications/science/physics/dawncut/default.nix b/pkgs/applications/science/physics/dawncut/default.nix index 8c0bc1ae6394a..5c17837d2e952 100644 --- a/pkgs/applications/science/physics/dawncut/default.nix +++ b/pkgs/applications/science/physics/dawncut/default.nix @@ -20,7 +20,7 @@ stdenv.mkDerivation rec { dontConfigure = true; - NIX_CFLAGS_COMPILE="-std=c++98"; + env.NIX_CFLAGS_COMPILE = "-std=c++98"; installPhase = '' runHook preInstall diff --git a/pkgs/applications/science/physics/xfitter/default.nix b/pkgs/applications/science/physics/xfitter/default.nix index 31df19b539a3f..1852ef3ff1c8e 100644 --- a/pkgs/applications/science/physics/xfitter/default.nix +++ b/pkgs/applications/science/physics/xfitter/default.nix @@ -44,7 +44,7 @@ stdenv.mkDerivation rec { ++ lib.optional (stdenv.hostPlatform.libc == "glibc") libtirpc ; - NIX_CFLAGS_COMPILE = lib.optional (stdenv.hostPlatform.libc == "glibc") "-I${libtirpc.dev}/include/tirpc"; + env.NIX_CFLAGS_COMPILE = lib.optionalString (stdenv.hostPlatform.libc == "glibc") "-I${libtirpc.dev}/include/tirpc"; NIX_LDFLAGS = lib.optional (stdenv.hostPlatform.libc == "glibc") "-ltirpc"; # workaround wrong library IDs |