diff options
Diffstat (limited to 'pkgs/applications/science')
23 files changed, 72 insertions, 165 deletions
diff --git a/pkgs/applications/science/astronomy/xearth/default.nix b/pkgs/applications/science/astronomy/xearth/default.nix index e9fc0607998..752e25b4d8d 100644 --- a/pkgs/applications/science/astronomy/xearth/default.nix +++ b/pkgs/applications/science/astronomy/xearth/default.nix @@ -12,8 +12,8 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ imake gccmakedep ]; buildInputs = [ libXt libXext ]; - installFlags=[ "DESTDIR=$(out)/" "BINDIR=bin" "MANDIR=man/man1"]; - installTargets="install install.man"; + installFlags = [ "DESTDIR=$(out)/" "BINDIR=bin" "MANDIR=man/man1"]; + installTargets = [ "install" "install.man" ]; meta = with stdenv.lib; { description = "sets the X root window to an image of the Earth"; diff --git a/pkgs/applications/science/biology/bcftools/default.nix b/pkgs/applications/science/biology/bcftools/default.nix index 33e4de0d95a..4a6a464de46 100644 --- a/pkgs/applications/science/biology/bcftools/default.nix +++ b/pkgs/applications/science/biology/bcftools/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "bcftools"; - version = "1.9"; + version = "1.10.2"; src = fetchurl { url = "https://github.com/samtools/bcftools/releases/download/${version}/${pname}-${version}.tar.bz2"; - sha256 = "1j3h638i8kgihzyrlnpj82xg1b23sijibys9hvwari3fy7kd0dkg"; + sha256 = "0b2f6lqhxdlrvfjqxv7a4nzqj68c1j4avn16iqxwwm80kn302wzm"; }; buildInputs = [ htslib zlib bzip2 lzma curl perl python ]; diff --git a/pkgs/applications/science/biology/megahit/default.nix b/pkgs/applications/science/biology/megahit/default.nix index 56bb35b64df..86414980177 100644 --- a/pkgs/applications/science/biology/megahit/default.nix +++ b/pkgs/applications/science/biology/megahit/default.nix @@ -1,23 +1,20 @@ -{ stdenv, fetchFromGitHub, zlib }: +{ stdenv, fetchFromGitHub, cmake, zlib }: stdenv.mkDerivation rec { pname = "megahit"; - version = "1.1.4"; + version = "1.2.9"; src = fetchFromGitHub { owner = "voutcn"; repo = "megahit"; rev = "v${version}"; - sha256 = "011k0776w76l03zmy70kfd3y9zjmdnspfbs9fcxmnl3bdwd36kcw"; + sha256 = "1r5d9nkdmgjsbrpj43q9hy3s8jwsabaz3ji561v18hy47v58923c"; }; + nativeBuildInputs = [ cmake ]; buildInputs = [ zlib ]; - installPhase = '' - for bin in megahit_sdbg_build megahit megahit_asm_core megahit_toolkit; do - install -vD $bin $out/bin/$bin - done - ''; + enableParallelBuilding = true; meta = with stdenv.lib; { description = "An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph"; diff --git a/pkgs/applications/science/biology/niftyreg/default.nix b/pkgs/applications/science/biology/niftyreg/default.nix index 6379f2c3282..48bd1b21ecd 100644 --- a/pkgs/applications/science/biology/niftyreg/default.nix +++ b/pkgs/applications/science/biology/niftyreg/default.nix @@ -9,6 +9,8 @@ stdenv.mkDerivation rec { sha256 = "07v9v9s41lvw72wpb1jgh2nzanyc994779bd35p76vg8mzifmprl"; }; + NIX_CFLAGS_COMPILE = [ "-Wno-error=narrowing" ]; + nativeBuildInputs = [ cmake ]; buildInputs = [ zlib ]; enableParallelBuilding = true; diff --git a/pkgs/applications/science/biology/strelka/default.nix b/pkgs/applications/science/biology/strelka/default.nix index cb83b19269b..184dcb48a0d 100644 --- a/pkgs/applications/science/biology/strelka/default.nix +++ b/pkgs/applications/science/biology/strelka/default.nix @@ -14,7 +14,10 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake ]; buildInputs = [ zlib python2 ]; - NIX_CFLAGS_COMPILE = [ "-Wno-error=maybe-uninitialized" ]; + NIX_CFLAGS_COMPILE = [ + "-Wno-error=maybe-uninitialized" + "-Wno-error=pessimizing-move" + ]; preConfigure = '' sed -i 's|/usr/bin/env python|${python2}/bin/python|' src/python/lib/makeRunScript.py diff --git a/pkgs/applications/science/biology/sumatools/default.nix b/pkgs/applications/science/biology/sumatools/default.nix index f9042f30011..5230fcd2eb6 100644 --- a/pkgs/applications/science/biology/sumatools/default.nix +++ b/pkgs/applications/science/biology/sumatools/default.nix @@ -22,7 +22,7 @@ in rec { rev = "sumalib_v${version}"; sha256 = "0hwkrxzfz7m5wdjvmrhkjg8kis378iaqr5n4nhdhkwwhn8x1jn5a"; }; - makeFlags = "PREFIX=$(out)"; + makeFlags = [ "PREFIX=$(out)" ]; inherit meta; }; diff --git a/pkgs/applications/science/logic/avy/default.nix b/pkgs/applications/science/logic/avy/default.nix index 9b59828ddab..b43e0c6fbf1 100644 --- a/pkgs/applications/science/logic/avy/default.nix +++ b/pkgs/applications/science/logic/avy/default.nix @@ -12,14 +12,14 @@ stdenv.mkDerivation { }; buildInputs = [ cmake zlib boost.out boost.dev ]; - NIX_CFLAGS_COMPILE = [ "-Wno-narrowing" ] + NIX_CFLAGS_COMPILE = toString ([ "-Wno-narrowing" ] # Squelch endless stream of warnings on same few things ++ stdenv.lib.optionals stdenv.cc.isClang [ "-Wno-empty-body" "-Wno-tautological-compare" "-Wc++11-compat-deprecated-writable-strings" "-Wno-deprecated" - ]; + ]); prePatch = '' sed -i -e '1i#include <stdint.h>' abc/src/bdd/dsd/dsd.h diff --git a/pkgs/applications/science/logic/coq/default.nix b/pkgs/applications/science/logic/coq/default.nix index 2378cb9408e..ac001540e09 100644 --- a/pkgs/applications/science/logic/coq/default.nix +++ b/pkgs/applications/science/logic/coq/default.nix @@ -143,7 +143,7 @@ self = stdenv.mkDerivation { prefixKey = "-prefix "; - buildFlags = "revision coq coqide bin/votour"; + buildFlags = [ "revision" "coq" "coqide" "bin/votour" ]; createFindlibDestdir = true; diff --git a/pkgs/applications/science/logic/minisat/clang.diff b/pkgs/applications/science/logic/minisat/clang.diff deleted file mode 100644 index 5b5072c71f3..00000000000 --- a/pkgs/applications/science/logic/minisat/clang.diff +++ /dev/null @@ -1,45 +0,0 @@ -diff -aur minisat/core/SolverTypes.h minisat.clang/core/SolverTypes.h ---- minisat/core/SolverTypes.h 2010-07-10 18:07:36.000000000 +0200 -+++ minisat.clang/core/SolverTypes.h 2016-05-13 12:14:50.759671959 +0200 -@@ -47,7 +47,7 @@ - int x; - - // Use this as a constructor: -- friend Lit mkLit(Var var, bool sign = false); -+ //friend Lit mkLit(Var var, bool sign = false); - - bool operator == (Lit p) const { return x == p.x; } - bool operator != (Lit p) const { return x != p.x; } -@@ -55,7 +55,7 @@ - }; - - --inline Lit mkLit (Var var, bool sign) { Lit p; p.x = var + var + (int)sign; return p; } -+inline Lit mkLit (Var var, bool sign = false) { Lit p; p.x = var + var + (int)sign; return p; } - inline Lit operator ~(Lit p) { Lit q; q.x = p.x ^ 1; return q; } - inline Lit operator ^(Lit p, bool b) { Lit q; q.x = p.x ^ (unsigned int)b; return q; } - inline bool sign (Lit p) { return p.x & 1; } -diff -aur minisat/utils/Options.h minisat.clang/utils/Options.h ---- minisat/utils/Options.h 2010-07-10 18:07:36.000000000 +0200 -+++ minisat.clang/utils/Options.h 2016-05-13 12:14:50.759671959 +0200 -@@ -282,15 +282,15 @@ - if (range.begin == INT64_MIN) - fprintf(stderr, "imin"); - else -- fprintf(stderr, "%4"PRIi64, range.begin); -+ fprintf(stderr, "%4" PRIi64, range.begin); - - fprintf(stderr, " .. "); - if (range.end == INT64_MAX) - fprintf(stderr, "imax"); - else -- fprintf(stderr, "%4"PRIi64, range.end); -+ fprintf(stderr, "%4" PRIi64, range.end); - -- fprintf(stderr, "] (default: %"PRIi64")\n", value); -+ fprintf(stderr, "] (default: %" PRIi64 ")\n", value); - if (verbose){ - fprintf(stderr, "\n %s\n", description); - fprintf(stderr, "\n"); -Only in minisat.clang/utils: Options.o -Only in minisat.clang/utils: System.o diff --git a/pkgs/applications/science/logic/minisat/darwin.patch b/pkgs/applications/science/logic/minisat/darwin.patch deleted file mode 100644 index f2b618d6bb3..00000000000 --- a/pkgs/applications/science/logic/minisat/darwin.patch +++ /dev/null @@ -1,26 +0,0 @@ -https://github.com/fasterthanlime/homebrew-mingw/blob/master/Library/Formula/minisat.rb - -diff --git a/utils/System.cc b/utils/System.cc -index a7cf53f..feeaf3c 100644 ---- a/utils/System.cc -+++ b/utils/System.cc -@@ -78,16 +78,17 @@ double Minisat::memUsed(void) { - struct rusage ru; - getrusage(RUSAGE_SELF, &ru); - return (double)ru.ru_maxrss / 1024; } --double MiniSat::memUsedPeak(void) { return memUsed(); } -+double Minisat::memUsedPeak(void) { return memUsed(); } - - - #elif defined(__APPLE__) - #include <malloc/malloc.h> - --double Minisat::memUsed(void) { -+double Minisat::memUsed() { - malloc_statistics_t t; - malloc_zone_statistics(NULL, &t); - return (double)t.max_size_in_use / (1024*1024); } -+double Minisat::memUsedPeak() { return memUsed(); } - - #else - double Minisat::memUsed() { diff --git a/pkgs/applications/science/logic/minisat/default.nix b/pkgs/applications/science/logic/minisat/default.nix index 34051a1da40..6b642832b83 100644 --- a/pkgs/applications/science/logic/minisat/default.nix +++ b/pkgs/applications/science/logic/minisat/default.nix @@ -1,27 +1,19 @@ -{ stdenv, fetchurl, zlib }: +{ stdenv, fetchFromGitHub, cmake, zlib }: stdenv.mkDerivation rec { pname = "minisat"; - version = "2.2.0"; + version = "2.2.1"; - src = fetchurl { - url = "http://minisat.se/downloads/${pname}-${version}.tar.gz"; - sha256 = "023qdnsb6i18yrrawlhckm47q8x0sl7chpvvw3gssfyw3j2pv5cj"; + src = fetchFromGitHub { + owner = "stp"; + repo = pname; + rev = "releases/${version}"; + sha256 = "14vcbjnlia00lpyv2fhbmw3wbc9bk9h7bln9zpyc3nwiz5cbjz4a"; }; - patches = - [ ./darwin.patch ] - ++ stdenv.lib.optionals stdenv.cc.isClang [ ./clang.diff ]; - + nativeBuildInputs = [ cmake ]; buildInputs = [ zlib ]; - preBuild = "cd simp"; - makeFlags = [ "r" "MROOT=.." ]; - installPhase = '' - mkdir -p $out/bin - cp minisat_release $out/bin/minisat - ''; - meta = with stdenv.lib; { description = "Compact and readable SAT solver"; maintainers = with maintainers; [ gebner raskin ]; diff --git a/pkgs/applications/science/logic/minisat/unstable.nix b/pkgs/applications/science/logic/minisat/unstable.nix deleted file mode 100644 index ef46c694acb..00000000000 --- a/pkgs/applications/science/logic/minisat/unstable.nix +++ /dev/null @@ -1,23 +0,0 @@ -{ stdenv, fetchFromGitHub, zlib, cmake }: - -stdenv.mkDerivation { - name = "minisat-unstable-2013-09-25"; - - src = fetchFromGitHub { - owner = "niklasso"; - repo = "minisat"; - rev = "37dc6c67e2af26379d88ce349eb9c4c6160e8543"; - sha256 = "091hf3qkm197s5r7xcr3m07xsdwyz2rqk1hc9kj0hn13imz09irq"; - }; - - buildInputs = [ zlib ]; - nativeBuildInputs = [ cmake ]; - - meta = with stdenv.lib; { - description = "Compact and readable SAT solver"; - maintainers = with maintainers; [ mic92 ]; - platforms = platforms.unix; - license = licenses.mit; - homepage = http://minisat.se/; - }; -} diff --git a/pkgs/applications/science/logic/prover9/default.nix b/pkgs/applications/science/logic/prover9/default.nix index a4538e1070a..9528a5942a4 100644 --- a/pkgs/applications/science/logic/prover9/default.nix +++ b/pkgs/applications/science/logic/prover9/default.nix @@ -21,7 +21,7 @@ stdenv.mkDerivation { done ''; - buildFlags = "all"; + buildFlags = [ "all" ]; checkPhase = "make test1"; diff --git a/pkgs/applications/science/logic/stp/default.nix b/pkgs/applications/science/logic/stp/default.nix index 0ea659d1927..dd00eda1b57 100644 --- a/pkgs/applications/science/logic/stp/default.nix +++ b/pkgs/applications/science/logic/stp/default.nix @@ -1,4 +1,5 @@ -{ stdenv, cmake, boost, bison, flex, fetchFromGitHub, perl, python3, python3Packages, zlib, minisatUnstable, cryptominisat }: +{ stdenv, cmake, boost, bison, flex, fetchFromGitHub, perl +, python3, python3Packages, zlib, minisat, cryptominisat }: stdenv.mkDerivation rec { pname = "stp"; @@ -11,7 +12,7 @@ stdenv.mkDerivation rec { sha256 = "1yg2v4wmswh1sigk47drwsxyayr472mf4i47lqmlcgn9hhbx1q87"; }; - buildInputs = [ boost zlib minisatUnstable cryptominisat python3 ]; + buildInputs = [ boost zlib minisat cryptominisat python3 ]; nativeBuildInputs = [ cmake bison flex perl ]; preConfigure = '' python_install_dir=$out/${python3Packages.python.sitePackages} diff --git a/pkgs/applications/science/math/calculix/default.nix b/pkgs/applications/science/math/calculix/default.nix index 24d5f99ec32..6f2d61cd80f 100644 --- a/pkgs/applications/science/math/calculix/default.nix +++ b/pkgs/applications/science/math/calculix/default.nix @@ -13,9 +13,7 @@ stdenv.mkDerivation rec { buildInputs = [ arpack spooles openblas ]; - NIX_CFLAGS_COMPILE = [ - "-I${spooles}/include/spooles" - ]; + NIX_CFLAGS_COMPILE = "-I${spooles}/include/spooles"; patches = [ ./calculix.patch diff --git a/pkgs/applications/science/math/msieve/default.nix b/pkgs/applications/science/math/msieve/default.nix index 6e1926810df..643d990feb8 100644 --- a/pkgs/applications/science/math/msieve/default.nix +++ b/pkgs/applications/science/math/msieve/default.nix @@ -13,7 +13,7 @@ stdenv.mkDerivation { ECM = if ecm == null then "0" else "1"; # Doesn't hurt Linux but lets clang-based platforms like Darwin work fine too - makeFlags = "CC=cc all"; + makeFlags = [ "CC=cc" "all" ]; installPhase = '' mkdir -p $out/bin/ diff --git a/pkgs/applications/science/math/polymake/default.nix b/pkgs/applications/science/math/polymake/default.nix index fdc4de7b028..d4f13f84f81 100644 --- a/pkgs/applications/science/math/polymake/default.nix +++ b/pkgs/applications/science/math/polymake/default.nix @@ -28,7 +28,7 @@ stdenv.mkDerivation rec { makeWrapper ninja ant perl ]; - ninjaFlags = "-C build/Opt"; + ninjaFlags = [ "-C" "build/Opt" ]; postInstall = '' for i in "$out"/bin/*; do diff --git a/pkgs/applications/science/math/ries/default.nix b/pkgs/applications/science/math/ries/default.nix index 4b237a01a3e..b244ee75b30 100644 --- a/pkgs/applications/science/math/ries/default.nix +++ b/pkgs/applications/science/math/ries/default.nix @@ -8,7 +8,7 @@ stdenv.mkDerivation { sha256 = "1h2wvd4k7f0l0i1vm9niz453xdbcs3nxccmri50qyrzzzc1b0842"; }; - makeFlags = "PREFIX=$(out)"; + makeFlags = [ "PREFIX=$(out)" ]; meta = with stdenv.lib; { homepage = https://mrob.com/pub/ries/; diff --git a/pkgs/applications/science/math/scilab/default.nix b/pkgs/applications/science/math/scilab/default.nix index 432280a18fb..02f1f4e58a9 100644 --- a/pkgs/applications/science/math/scilab/default.nix +++ b/pkgs/applications/science/math/scilab/default.nix @@ -54,7 +54,7 @@ stdenv.mkDerivation rec { ++ lib.optional (!withXaw3d) "--with-local-xaw" ; - makeFlags = "all"; + makeFlags = [ "all" ]; meta = { homepage = http://www.scilab.org/; diff --git a/pkgs/applications/science/misc/colmap/default.nix b/pkgs/applications/science/misc/colmap/default.nix index 672569ed100..da118f6bca5 100644 --- a/pkgs/applications/science/misc/colmap/default.nix +++ b/pkgs/applications/science/misc/colmap/default.nix @@ -1,11 +1,11 @@ -{ mkDerivation, lib, fetchFromGitHub, cmake, boost, ceres-solver, eigen, +{ mkDerivation, lib, fetchpatch, fetchFromGitHub, cmake, boost, ceres-solver, eigen, freeimage, glog, libGLU, glew, qtbase, cudaSupport ? false, cudatoolkit ? null }: assert !cudaSupport || cudatoolkit != null; let boost_static = boost.override { enableStatic = true; }; -in +in mkDerivation rec { version = "3.5"; pname = "colmap"; @@ -15,7 +15,14 @@ mkDerivation rec { rev = version; sha256 = "1vnb62p0y2bnga173wmjs0lnyqdjikv0fkcxjzxm8187khk2lly8"; }; - + + patches = [ + (fetchpatch { + url = "https://github.com/colmap/colmap/commit/6af3d8b0048cecc3b9fc6f4e78c3214dd038180b.patch"; + sha256 = "1zv5girmv4hv78w1xn131v8njwhpbyylc1m15731lnhrs8bri0jq"; + }) + ]; + buildInputs = [ boost_static ceres-solver eigen freeimage glog libGLU glew qtbase diff --git a/pkgs/applications/science/misc/megam/default.nix b/pkgs/applications/science/misc/megam/default.nix index f86bed854a2..6cdc86d20eb 100644 --- a/pkgs/applications/science/misc/megam/default.nix +++ b/pkgs/applications/science/misc/megam/default.nix @@ -16,7 +16,7 @@ stdenv.mkDerivation { nativeBuildInputs = [ makeWrapper ]; - makeFlags = "CAML_INCLUDES=${ocaml}/lib/ocaml/caml"; + makeFlags = [ "CAML_INCLUDES=${ocaml}/lib/ocaml/caml" ]; # see https://bugzilla.redhat.com/show_bug.cgi?id=435559 dontStrip = true; diff --git a/pkgs/applications/science/misc/simgrid/default.nix b/pkgs/applications/science/misc/simgrid/default.nix index 58f464575b0..44b0f5d84b6 100644 --- a/pkgs/applications/science/misc/simgrid/default.nix +++ b/pkgs/applications/science/misc/simgrid/default.nix @@ -54,28 +54,28 @@ stdenv.mkDerivation rec { # # For more information see: # https://simgrid.org/doc/3.22/Installing_SimGrid.html#simgrid-compilation-options) - cmakeFlags= '' - -Denable_documentation=${optionOnOff buildDocumentation} - -Denable_java=${optionOnOff buildJavaBindings} - -Denable_fortran=${optionOnOff fortranSupport} - -Denable_model-checking=${optionOnOff modelCheckingSupport} - -Denable_ns3=off - -Denable_lua=off - -Denable_lib_in_jar=off - -Denable_maintainer_mode=off - -Denable_mallocators=on - -Denable_debug=on - -Denable_smpi=on - -Denable_smpi_ISP_testsuite=${optionOnOff moreTests} - -Denable_smpi_MPICH3_testsuite=${optionOnOff moreTests} - -Denable_compile_warnings=${optionOnOff debug} - -Denable_compile_optimizations=${optionOnOff (!debug)} - -Denable_lto=${optionOnOff (!debug)} - ''; - # -Denable_lua=${optionOnOff luaSupport} - # -Denable_smpi_papi=${optionOnOff moreTests} + cmakeFlags = [ + "-Denable_documentation=${optionOnOff buildDocumentation}" + "-Denable_java=${optionOnOff buildJavaBindings}" + "-Denable_fortran=${optionOnOff fortranSupport}" + "-Denable_model-checking=${optionOnOff modelCheckingSupport}" + "-Denable_ns3=off" + "-Denable_lua=off" + "-Denable_lib_in_jar=off" + "-Denable_maintainer_mode=off" + "-Denable_mallocators=on" + "-Denable_debug=on" + "-Denable_smpi=on" + "-Denable_smpi_ISP_testsuite=${optionOnOff moreTests}" + "-Denable_smpi_MPICH3_testsuite=${optionOnOff moreTests}" + "-Denable_compile_warnings=${optionOnOff debug}" + "-Denable_compile_optimizations=${optionOnOff (!debug)}" + "-Denable_lto=${optionOnOff (!debug)}" + # "-Denable_lua=${optionOnOff luaSupport}" + # "-Denable_smpi_papi=${optionOnOff moreTests}" + ]; - makeFlags = optionalString debug "VERBOSE=1"; + makeFlags = optional debug "VERBOSE=1"; # Some Perl scripts are called to generate test during build which # is before the fixupPhase, so do this manualy here: diff --git a/pkgs/applications/science/physics/xfitter/default.nix b/pkgs/applications/science/physics/xfitter/default.nix index 2af93961e02..818bea7d0ff 100644 --- a/pkgs/applications/science/physics/xfitter/default.nix +++ b/pkgs/applications/science/physics/xfitter/default.nix @@ -2,19 +2,20 @@ stdenv.mkDerivation rec { pname = "xfitter"; - version = "2.0.0"; + version = "2.0.1"; src = fetchurl { name = "${pname}-${version}.tgz"; url = "https://www.xfitter.org/xFitter/xFitter/DownloadPage?action=AttachFile&do=get&target=${pname}-${version}.tgz"; - sha256 = "0j47s8laq3aqjlgp769yicvgyzqjb738a3rqss51d9fjrihi2515"; + sha256 = "0kmgc67nw5flp92yw5x6l2vsnhwsfi5z2a20404anisdgdjs8zc6"; }; patches = [ ./undefined_behavior.patch ]; - CXXFLAGS = "-Werror=return-type"; + # patch needs to updated due to version bump + #CXXFLAGS = "-Werror=return-type"; preConfigure = # Fix F77LD to workaround for a following build error: |