diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science/math')
25 files changed, 108 insertions, 85 deletions
diff --git a/nixpkgs/pkgs/applications/science/math/R/0001-Disable-test-pending-upstream-fix.patch b/nixpkgs/pkgs/applications/science/math/R/0001-Disable-test-pending-upstream-fix.patch deleted file mode 100644 index 7bf32df0b7a..00000000000 --- a/nixpkgs/pkgs/applications/science/math/R/0001-Disable-test-pending-upstream-fix.patch +++ /dev/null @@ -1,26 +0,0 @@ -From 85ede2cf452800710de136f4f864921d3bb9773c Mon Sep 17 00:00:00 2001 -From: Tom Hall <tahall256@protonmail.ch> -Date: Fri, 21 Feb 2020 22:56:06 +0000 -Subject: [PATCH] Disable test pending upstream fix - -See https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17718 ---- - tests/reg-tests-1d.R | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/tests/reg-tests-1d.R b/tests/reg-tests-1d.R -index 9b551a1fc8..18ce6027ed 100644 ---- a/tests/reg-tests-1d.R -+++ b/tests/reg-tests-1d.R -@@ -3079,7 +3079,7 @@ stopifnot(exprs = { - x[1:52] %% 3 == 2:1 - -x[1:52] %% 3 == 1:2 - }) # larger x suffer from cancellation (well, warning too early now): --tools::assertWarning(x[60:68] %% 3) -+#tools::assertWarning(x[60:68] %% 3) - - - ## Hilmar Berger's on R-devel list: 'data.frame() == NULL' etc --- -2.24.1 - diff --git a/nixpkgs/pkgs/applications/science/math/R/default.nix b/nixpkgs/pkgs/applications/science/math/R/default.nix index 3ee62fad44d..52da3b4a1ac 100644 --- a/nixpkgs/pkgs/applications/science/math/R/default.nix +++ b/nixpkgs/pkgs/applications/science/math/R/default.nix @@ -1,6 +1,6 @@ { stdenv, fetchurl, bzip2, gfortran, libX11, libXmu, libXt, libjpeg, libpng -, libtiff, ncurses, pango, pcre, perl, readline, tcl, texLive, tk, xz, zlib -, less, texinfo, graphviz, icu, pkgconfig, bison, imake, which, jdk, openblas +, libtiff, ncurses, pango, pcre2, perl, readline, tcl, texLive, tk, xz, zlib +, less, texinfo, graphviz, icu, pkgconfig, bison, imake, which, jdk, blas, lapack , curl, Cocoa, Foundation, libobjc, libcxx, tzdata, fetchpatch , withRecommendedPackages ? true , enableStrictBarrier ? false @@ -9,28 +9,27 @@ , static ? false }: +assert (!blas.isILP64) && (!lapack.isILP64); + stdenv.mkDerivation rec { - name = "R-3.6.3"; + name = "R-4.0.0"; src = fetchurl { - url = "https://cran.r-project.org/src/base/R-3/${name}.tar.gz"; - sha256 = "13xaxwfbzj0bd6rn2n27z0n04lb93mcyq991w4vdbbg8v282jc49"; + url = "https://cran.r-project.org/src/base/R-4/${name}.tar.gz"; + sha256 = "0h1995smlyiyhx7gpg9paxsfqrcn6g9bbp5h9r47i6an3clv1gh6"; }; dontUseImakeConfigure = true; buildInputs = [ bzip2 gfortran libX11 libXmu libXt libXt libjpeg libpng libtiff ncurses - pango pcre perl readline texLive xz zlib less texinfo graphviz icu - pkgconfig bison imake which openblas curl tcl tk jdk + pango pcre2 perl readline texLive xz zlib less texinfo graphviz icu + pkgconfig bison imake which blas lapack curl tcl tk jdk ] ++ stdenv.lib.optionals stdenv.isDarwin [ Cocoa Foundation libobjc libcxx ]; patches = [ ./no-usr-local-search-paths.patch - ] ++ stdenv.lib.optionals stdenv.hostPlatform.isAarch64 [ - # Remove a test which fails on aarch64. - # See https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17718 - ./0001-Disable-test-pending-upstream-fix.patch + ./fix-failing-test.patch ]; prePatch = stdenv.lib.optionalString stdenv.isDarwin '' @@ -43,8 +42,8 @@ stdenv.mkDerivation rec { configureFlagsArray=( --disable-lto --with${stdenv.lib.optionalString (!withRecommendedPackages) "out"}-recommended-packages - --with-blas="-L${openblas}/lib -lopenblas" - --with-lapack="-L${openblas}/lib -lopenblas" + --with-blas="-L${blas}/lib -lblas" + --with-lapack="-L${lapack}/lib -llapack" --with-readline --with-tcltk --with-tcl-config="${tcl}/lib/tclConfig.sh" --with-tk-config="${tk}/lib/tkConfig.sh" --with-cairo diff --git a/nixpkgs/pkgs/applications/science/math/R/fix-failing-test.patch b/nixpkgs/pkgs/applications/science/math/R/fix-failing-test.patch new file mode 100644 index 00000000000..5fb3b3b9c31 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/R/fix-failing-test.patch @@ -0,0 +1,25 @@ +From e8f54bc562eb301d204b5f880614be58a2b39a2b Mon Sep 17 00:00:00 2001 +From: maechler <maechler@00db46b3-68df-0310-9c12-caf00c1e9a41> +Date: Mon, 30 Mar 2020 19:15:59 +0000 +Subject: [PATCH] no longer fail in norm() check for broken OpenBLAS Lapack + 3.9.0 + +git-svn-id: https://svn.r-project.org/R/trunk@78112 00db46b3-68df-0310-9c12-caf00c1e9a41 +--- + tests/reg-tests-1d.R | 3 ++- + 1 file changed, 2 insertions(+), 1 deletion(-) + +diff --git a/tests/reg-tests-1d.R b/tests/reg-tests-1d.R +index 6b7de765a95..fafd6911e7a 100644 +--- a/tests/reg-tests-1d.R ++++ b/tests/reg-tests-1d.R +@@ -3836,7 +3836,8 @@ stopifnot(is.na( norm(diag(c(1, NA)), "2") )) + ## norm(<matrix-w-NA>, "F") + (m <- cbind(0, c(NA, 0), 0:-1)) + nTypes <- eval(formals(base::norm)$type) # "O" "I" "F" "M" "2" +-stopifnot(is.na( print(vapply(nTypes, norm, 0., x = m)) )) # print(): show NA *or* NaN ++print( # stopifnot( -- for now, as Lapack is still broken in some OpenBLAS -- FIXME ++ is.na( print(vapply(nTypes, norm, 0., x = m)) )) # print(): show NA *or* NaN + ## "F" gave non-NA with LAPACK 3.9.0, before our patch in R-devel and R-patched + + diff --git a/nixpkgs/pkgs/applications/science/math/caffe/default.nix b/nixpkgs/pkgs/applications/science/math/caffe/default.nix index ea87c4953ee..4a6a2dc6c7e 100644 --- a/nixpkgs/pkgs/applications/science/math/caffe/default.nix +++ b/nixpkgs/pkgs/applications/science/math/caffe/default.nix @@ -9,7 +9,7 @@ , opencv3 , protobuf , doxygen -, openblas +, blas , Accelerate, CoreGraphics, CoreVideo , lmdbSupport ? true, lmdb , leveldbSupport ? true, leveldb, snappy @@ -63,7 +63,7 @@ stdenv.mkDerivation rec { ++ ["-DUSE_LEVELDB=${toggle leveldbSupport}"] ++ ["-DUSE_LMDB=${toggle lmdbSupport}"]; - buildInputs = [ boost gflags glog protobuf hdf5-cpp opencv3 openblas ] + buildInputs = [ boost gflags glog protobuf hdf5-cpp opencv3 blas ] ++ lib.optional cudaSupport cudatoolkit ++ lib.optional cudnnSupport cudnn ++ lib.optional lmdbSupport lmdb diff --git a/nixpkgs/pkgs/applications/science/math/calculix/calculix.patch b/nixpkgs/pkgs/applications/science/math/calculix/calculix.patch index 311421f2ef5..5b8f492a8e7 100644 --- a/nixpkgs/pkgs/applications/science/math/calculix/calculix.patch +++ b/nixpkgs/pkgs/applications/science/math/calculix/calculix.patch @@ -15,7 +15,7 @@ index 9cab2fc..6e977b8 100755 OCCXMAIN = $(SCCXMAIN:.c=.o) -DIR=../../../SPOOLES.2.2 -+LIBS = -lpthread -lm -lc -lspooles -larpack -lopenblas ++LIBS = -lpthread -lm -lc -lspooles -larpack -lblas -llapack -LIBS = \ - $(DIR)/spooles.a \ diff --git a/nixpkgs/pkgs/applications/science/math/calculix/default.nix b/nixpkgs/pkgs/applications/science/math/calculix/default.nix index 6f2d61cd80f..44882594550 100644 --- a/nixpkgs/pkgs/applications/science/math/calculix/default.nix +++ b/nixpkgs/pkgs/applications/science/math/calculix/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, gfortran, arpack, spooles, openblas }: +{ stdenv, fetchurl, gfortran, arpack, spooles, blas, lapack }: stdenv.mkDerivation rec { pname = "calculix"; @@ -11,7 +11,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ gfortran ]; - buildInputs = [ arpack spooles openblas ]; + buildInputs = [ arpack spooles blas lapack ]; NIX_CFLAGS_COMPILE = "-I${spooles}/include/spooles"; diff --git a/nixpkgs/pkgs/applications/science/math/cemu/default.nix b/nixpkgs/pkgs/applications/science/math/cemu/default.nix index f91e5be5170..b41135229dd 100644 --- a/nixpkgs/pkgs/applications/science/math/cemu/default.nix +++ b/nixpkgs/pkgs/applications/science/math/cemu/default.nix @@ -4,7 +4,7 @@ , SDL2 , libGL , libarchive -, libusb +, libusb-compat-0_1 , qtbase , qmake , git @@ -33,7 +33,7 @@ mkDerivation rec { SDL2 libGL libarchive - libusb + libusb-compat-0_1 qtbase libpng_apng ]; diff --git a/nixpkgs/pkgs/applications/science/math/cntk/default.nix b/nixpkgs/pkgs/applications/science/math/cntk/default.nix index e2db40a402e..401454a6b69 100644 --- a/nixpkgs/pkgs/applications/science/math/cntk/default.nix +++ b/nixpkgs/pkgs/applications/science/math/cntk/default.nix @@ -1,11 +1,12 @@ { lib, stdenv, fetchgit, fetchFromGitHub, cmake -, openblas, opencv3, libzip, boost, protobuf, openmpi +, openblas, blas, lapack, opencv3, libzip, boost, protobuf, openmpi , onebitSGDSupport ? false , cudaSupport ? false, addOpenGLRunpath, cudatoolkit, nvidia_x11 , cudnnSupport ? cudaSupport, cudnn }: assert cudnnSupport -> cudaSupport; +assert blas.implementation == "openblas" && lapack.implementation == "openblas"; let # Old specific version required for CNTK. diff --git a/nixpkgs/pkgs/applications/science/math/csdp/default.nix b/nixpkgs/pkgs/applications/science/math/csdp/default.nix index eef60829f8e..ef9d5e733ca 100644 --- a/nixpkgs/pkgs/applications/science/math/csdp/default.nix +++ b/nixpkgs/pkgs/applications/science/math/csdp/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchurl, blas, gfortran, liblapack }: +{ lib, stdenv, fetchurl, blas, gfortran, lapack }: stdenv.mkDerivation { name = "csdp-6.1.1"; @@ -8,7 +8,7 @@ stdenv.mkDerivation { sha256 = "1f9ql6cjy2gwiyc51ylfan24v1ca9sjajxkbhszlds1lqmma8n05"; }; - buildInputs = [ blas gfortran.cc.lib liblapack ]; + buildInputs = [ blas gfortran.cc.lib lapack ]; postPatch = '' substituteInPlace Makefile --replace /usr/local/bin $out/bin diff --git a/nixpkgs/pkgs/applications/science/math/getdp/default.nix b/nixpkgs/pkgs/applications/science/math/getdp/default.nix index 0ac2ea7d1b3..ae93e89f141 100644 --- a/nixpkgs/pkgs/applications/science/math/getdp/default.nix +++ b/nixpkgs/pkgs/applications/science/math/getdp/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, cmake, gfortran, openblas, openmpi, petsc, python3 }: +{ stdenv, fetchurl, cmake, gfortran, blas, lapack, openmpi, petsc, python3 }: stdenv.mkDerivation rec { name = "getdp-${version}"; @@ -9,7 +9,7 @@ stdenv.mkDerivation rec { }; nativeBuildInputs = [ cmake gfortran ]; - buildInputs = [ openblas openmpi petsc python3 ]; + buildInputs = [ blas lapack openmpi petsc python3 ]; meta = with stdenv.lib; { description = "A General Environment for the Treatment of Discrete Problems"; diff --git a/nixpkgs/pkgs/applications/science/math/giac/default.nix b/nixpkgs/pkgs/applications/science/math/giac/default.nix index b3777528ecd..ea9c921f19e 100644 --- a/nixpkgs/pkgs/applications/science/math/giac/default.nix +++ b/nixpkgs/pkgs/applications/science/math/giac/default.nix @@ -1,10 +1,11 @@ -{ stdenv, lib, fetchurl, fetchpatch, texlive, bison, flex, liblapack -, gmp, mpfr, pari, ntl, gsl, blas, mpfi, ecm, glpk, nauty +{ stdenv, lib, fetchurl, fetchpatch, texlive, bison, flex, lapack, blas +, gmp, mpfr, pari, ntl, gsl, mpfi, ecm, glpk, nauty , readline, gettext, libpng, libao, gfortran, perl , enableGUI ? false, libGL ? null, libGLU ? null, xorg ? null, fltk ? null }: assert enableGUI -> libGLU != null && libGL != null && xorg != null && fltk != null; +assert (!blas.isILP64) && (!lapack.isILP64); stdenv.mkDerivation rec { pname = "giac${lib.optionalString enableGUI "-with-xcas"}"; @@ -41,7 +42,7 @@ stdenv.mkDerivation rec { # gfortran.cc default output contains static libraries compiled without -fPIC # we want libgfortran.so.3 instead (stdenv.lib.getLib gfortran.cc) - liblapack + lapack blas ] ++ stdenv.lib.optionals enableGUI [ libGL libGLU fltk xorg.libX11 ]; diff --git a/nixpkgs/pkgs/applications/science/math/gmsh/default.nix b/nixpkgs/pkgs/applications/science/math/gmsh/default.nix index 2c4d5f254da..946beff8003 100644 --- a/nixpkgs/pkgs/applications/science/math/gmsh/default.nix +++ b/nixpkgs/pkgs/applications/science/math/gmsh/default.nix @@ -1,6 +1,8 @@ -{ stdenv, fetchurl, cmake, openblasCompat, gfortran, gmm, fltk, libjpeg +{ stdenv, fetchurl, cmake, blas, lapack, gfortran, gmm, fltk, libjpeg , zlib, libGL, libGLU, xorg, opencascade-occt }: +assert (!blas.isILP64) && (!lapack.isILP64); + stdenv.mkDerivation rec { pname = "gmsh"; version = "4.5.6"; @@ -10,7 +12,7 @@ stdenv.mkDerivation rec { sha256 = "0gs65bgr1ph5lz7r6manqj8cra30s7c94pxilkd2z0p5vq6fpsj6"; }; - buildInputs = [ openblasCompat gmm fltk libjpeg zlib libGLU libGL + buildInputs = [ blas lapack gmm fltk libjpeg zlib libGLU libGL libGLU xorg.libXrender xorg.libXcursor xorg.libXfixes xorg.libXext xorg.libXft xorg.libXinerama xorg.libX11 xorg.libSM xorg.libICE opencascade-occt diff --git a/nixpkgs/pkgs/applications/science/math/jags/default.nix b/nixpkgs/pkgs/applications/science/math/jags/default.nix index 5ac1594e19a..122c6288847 100644 --- a/nixpkgs/pkgs/applications/science/math/jags/default.nix +++ b/nixpkgs/pkgs/applications/science/math/jags/default.nix @@ -1,4 +1,4 @@ -{stdenv, fetchurl, gfortran, openblas}: +{stdenv, fetchurl, gfortran, blas, lapack}: stdenv.mkDerivation rec { name = "JAGS-4.3.0"; @@ -6,8 +6,8 @@ stdenv.mkDerivation rec { url = "mirror://sourceforge/mcmc-jags/${name}.tar.gz"; sha256 = "1z3icccg2ic56vmhyrpinlsvpq7kcaflk1731rgpvz9bk1bxvica"; }; - buildInputs = [gfortran openblas]; - configureFlags = [ "--with-blas=-lopenblas" "--with-lapack=-lopenblas" ]; + buildInputs = [gfortran blas lapack]; + configureFlags = [ "--with-blas=-lblas" "--with-lapack=-llapack" ]; meta = with stdenv.lib; { description = "Just Another Gibbs Sampler"; diff --git a/nixpkgs/pkgs/applications/science/math/mathematica/10.nix b/nixpkgs/pkgs/applications/science/math/mathematica/10.nix index c7da7b16da8..277fb1984c4 100644 --- a/nixpkgs/pkgs/applications/science/math/mathematica/10.nix +++ b/nixpkgs/pkgs/applications/science/math/mathematica/10.nix @@ -8,7 +8,7 @@ , gcc , glib , ncurses -, opencv +, opencv2 , openssl , unixODBC , xorg @@ -49,7 +49,7 @@ stdenv.mkDerivation rec { gcc.libc glib ncurses - opencv + opencv2 openssl unixODBC libxml2 diff --git a/nixpkgs/pkgs/applications/science/math/mathematica/11.nix b/nixpkgs/pkgs/applications/science/math/mathematica/11.nix index 898d6a48635..1c698a5e542 100644 --- a/nixpkgs/pkgs/applications/science/math/mathematica/11.nix +++ b/nixpkgs/pkgs/applications/science/math/mathematica/11.nix @@ -10,7 +10,7 @@ , gcc , glib , ncurses -, opencv +, opencv2 , openssl , unixODBC , xkeyboard_config @@ -46,7 +46,7 @@ stdenv.mkDerivation rec { gcc.libc glib ncurses - opencv + opencv2 openssl unixODBC xkeyboard_config diff --git a/nixpkgs/pkgs/applications/science/math/mathematica/9.nix b/nixpkgs/pkgs/applications/science/math/mathematica/9.nix index 617ac865713..d0967485c01 100644 --- a/nixpkgs/pkgs/applications/science/math/mathematica/9.nix +++ b/nixpkgs/pkgs/applications/science/math/mathematica/9.nix @@ -8,7 +8,7 @@ , gcc , glib , ncurses -, opencv +, opencv2 , openssl , unixODBC , xorg @@ -46,7 +46,7 @@ stdenv.mkDerivation rec { gcc.libc glib ncurses - opencv + opencv2 openssl unixODBC ] ++ (with xorg; [ diff --git a/nixpkgs/pkgs/applications/science/math/mathematica/default.nix b/nixpkgs/pkgs/applications/science/math/mathematica/default.nix index 7831640b124..94d72eec6ae 100644 --- a/nixpkgs/pkgs/applications/science/math/mathematica/default.nix +++ b/nixpkgs/pkgs/applications/science/math/mathematica/default.nix @@ -11,7 +11,7 @@ , glib , libssh2 , ncurses -, opencv +, opencv2 , openssl , unixODBC , xkeyboard_config @@ -47,7 +47,7 @@ stdenv.mkDerivation rec { glib libssh2 ncurses - opencv + opencv2 openssl stdenv.cc.cc.lib unixODBC diff --git a/nixpkgs/pkgs/applications/science/math/mxnet/default.nix b/nixpkgs/pkgs/applications/science/math/mxnet/default.nix index 5b7688f6051..b006a9dd18d 100644 --- a/nixpkgs/pkgs/applications/science/math/mxnet/default.nix +++ b/nixpkgs/pkgs/applications/science/math/mxnet/default.nix @@ -1,5 +1,5 @@ { config, stdenv, lib, fetchurl, bash, cmake -, opencv3, gtest, openblas, liblapack, perl +, opencv3, gtest, blas, perl , cudaSupport ? config.cudaSupport or false, cudatoolkit, nvidia_x11 , cudnnSupport ? cudaSupport, cudnn }: @@ -8,16 +8,16 @@ assert cudnnSupport -> cudaSupport; stdenv.mkDerivation rec { pname = "mxnet"; - version = "1.4.1"; + version = "1.6.0"; src = fetchurl { url = "https://github.com/apache/incubator-mxnet/releases/download/${version}/apache-mxnet-src-${version}-incubating.tar.gz"; - sha256 = "1d0lhlpdaxycjzpwwrpgjd3v2q2ka89v5rr13ddxayy7ld2hxiaj"; + sha256 = "1vvdb7pfh63kb9fzs6gqp95q550a3ck4cj9mqxlk9wwhkh30dsq1"; }; nativeBuildInputs = [ cmake perl ]; - buildInputs = [ opencv3 gtest openblas liblapack ] + buildInputs = [ opencv3 gtest blas ] ++ lib.optionals cudaSupport [ cudatoolkit nvidia_x11 ] ++ lib.optional cudnnSupport cudnn; @@ -34,7 +34,7 @@ stdenv.mkDerivation rec { substituteInPlace 3rdparty/mkldnn/tests/CMakeLists.txt \ --replace "/bin/bash" "${bash}/bin/bash" - # Build against the system version of OpenMP. + # Build against the system version of OpenMP. # https://github.com/apache/incubator-mxnet/pull/12160 rm -rf 3rdparty/openmp ''; diff --git a/nixpkgs/pkgs/applications/science/math/palp/default.nix b/nixpkgs/pkgs/applications/science/math/palp/default.nix index 4912b82d158..42259a2c689 100644 --- a/nixpkgs/pkgs/applications/science/math/palp/default.nix +++ b/nixpkgs/pkgs/applications/science/math/palp/default.nix @@ -9,16 +9,15 @@ let in stdenv.mkDerivation rec { pname = "palp"; - version = "2.1"; + version = "2.11"; src = fetchurl { url = "http://hep.itp.tuwien.ac.at/~kreuzer/CY/palp/palp-${version}.tar.gz"; - sha256 = "1s7s2lc5f0ig1yy7ygsh3sddm3sbq4mxwybqsj8lp9wjdxs7qfrs"; + sha256 = "09l4ysrdkqs91igg1faah75ay6ii684634ggvcxbkjsck65378l4"; }; hardeningDisable = [ "format" - "strictoverflow" # causes runtime failure (tested in checkPhase) ]; patchPhase = stdenv.lib.optionalString stdenv.isDarwin '' @@ -78,6 +77,9 @@ stdenv.mkDerivation rec { facet enumeration compares well with existing packages. ''; homepage = "http://hep.itp.tuwien.ac.at/~kreuzer/CY/CYpalp.html"; + # Not really a changelog, but a one-line summary of each update that should + # be reviewed on update. + changelog = "http://hep.itp.tuwien.ac.at/~kreuzer/CY/CYpalp.html"; # Just a link on the website pointing to gpl -- now gplv3. When the last # version was released that pointed to gplv2 however, so thats probably # the right license. diff --git a/nixpkgs/pkgs/applications/science/math/rofi-calc/default.nix b/nixpkgs/pkgs/applications/science/math/rofi-calc/default.nix index 842265cf3d5..84adb2358d2 100644 --- a/nixpkgs/pkgs/applications/science/math/rofi-calc/default.nix +++ b/nixpkgs/pkgs/applications/science/math/rofi-calc/default.nix @@ -12,13 +12,13 @@ stdenv.mkDerivation rec { pname = "rofi-calc"; - version = "1.6"; + version = "1.7"; src = fetchFromGitHub { owner = "svenstaro"; repo = pname; rev = "v${version}"; - sha256 = "00pz0s99pihjdjy8pl4ckg2qciyp32k439lmjb5iazwck512ar92"; + sha256 = "046x2zpvza7n0m81s75qkvmnpkvsvvyqqqjxcqzj7by0llpqs7wa"; }; nativeBuildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage-env.nix b/nixpkgs/pkgs/applications/science/math/sage/sage-env.nix index 68e0d134ace..626e1bf1ea9 100644 --- a/nixpkgs/pkgs/applications/science/math/sage/sage-env.nix +++ b/nixpkgs/pkgs/applications/science/math/sage/sage-env.nix @@ -41,7 +41,8 @@ , lcalc , rubiks , flintqs -, openblasCompat +, blas +, lapack , flint , gmp , mpfr @@ -53,6 +54,8 @@ , less }: +assert (!blas.isILP64) && (!lapack.isILP64); + # This generates a `sage-env` shell file that will be sourced by sage on startup. # It sets up various environment variables, telling sage where to find its # dependencies. @@ -114,7 +117,7 @@ writeTextFile rec { # testsuite instead, but since all the packages are also runtime # dependencies it doesn't really hurt to include them here. singular - openblasCompat + blas lapack fflas-ffpack givaro gd libpng zlib diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix index cd465a8c413..4791d12450a 100644 --- a/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix +++ b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix @@ -29,6 +29,14 @@ stdenv.mkDerivation rec { url = "https://git.sagemath.org/sage.git/patch?id2=8bdc326ba57d1bb9664f63cf165a9e9920cc1afc&id=dc673c17555efca611f68398d5013b66e9825463"; sha256 = "1hhannz7xzprijakn2w2d0rhd5zv2zikik9p51i87bas3nc658f7"; }) + + # `is_unitary` test in `matrix_double_dense.pyx` fails with some BLAS implementations + # https://trac.sagemath.org/ticket/29297 should be included in 9.1 + (fetchpatch { + name = "is_unitary-special-case.patch"; + url = "https://git.sagemath.org/sage.git/patch?id=cc3eb9ffa991e328b09028d32aab7e7cc2ddbb6a"; + sha256 = "0jq4w8hnp5c9q99011ldr4n3knvm1rx2g85z0hidv3i9x868p0ay"; + }) # Unfortunately inclusion in upstream sage was rejected. Instead the bug was # fixed in python, but of course not backported to 2.7. So we'll probably diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage-with-env.nix b/nixpkgs/pkgs/applications/science/math/sage/sage-with-env.nix index 524085e8c01..87c1e07f530 100644 --- a/nixpkgs/pkgs/applications/science/math/sage/sage-with-env.nix +++ b/nixpkgs/pkgs/applications/science/math/sage/sage-with-env.nix @@ -2,7 +2,8 @@ , lib , makeWrapper , sage-env -, openblasCompat +, blas +, lapack , pkg-config , three , singular @@ -21,6 +22,9 @@ , pythonEnv }: +# lots of segfaults with (64 bit) blas +assert (!blas.isILP64) && (!lapack.isILP64); + # Wrapper that combined `sagelib` with `sage-env` to produce an actually # executable sage. No tests are run yet and no documentation is built. @@ -29,7 +33,7 @@ let pythonEnv # for patchShebangs makeWrapper pkg-config - openblasCompat # lots of segfaults with regular (64 bit) openblas + blas lapack singular three pynac diff --git a/nixpkgs/pkgs/applications/science/math/sage/sagelib.nix b/nixpkgs/pkgs/applications/science/math/sage/sagelib.nix index 69f7624078e..830d806a8bc 100644 --- a/nixpkgs/pkgs/applications/science/math/sage/sagelib.nix +++ b/nixpkgs/pkgs/applications/science/math/sage/sagelib.nix @@ -3,7 +3,8 @@ , perl , buildPythonPackage , arb -, openblasCompat +, blas +, lapack , brial , cliquer , cypari2 @@ -52,6 +53,8 @@ , pplpy }: +assert (!blas.isILP64) && (!lapack.isILP64); + # This is the core sage python package. Everything else is just wrappers gluing # stuff together. It is not very useful on its own though, since it will not # find many of its dependencies without `sage-env`, will not be tested without @@ -103,7 +106,8 @@ buildPythonPackage rec { m4rie mpfi ntl - openblasCompat + blas + lapack pari planarity ppl diff --git a/nixpkgs/pkgs/applications/science/math/wxmaxima/default.nix b/nixpkgs/pkgs/applications/science/math/wxmaxima/default.nix index 4d6e4bea34e..a6afc95ac09 100644 --- a/nixpkgs/pkgs/applications/science/math/wxmaxima/default.nix +++ b/nixpkgs/pkgs/applications/science/math/wxmaxima/default.nix @@ -4,13 +4,13 @@ stdenv.mkDerivation rec { pname = "wxmaxima"; - version = "20.02.4"; + version = "20.04.0"; src = fetchFromGitHub { owner = "wxMaxima-developers"; repo = "wxmaxima"; rev = "Version-${version}"; - sha256 = "106a7jrjwfmymzj70nsv44fm3jbxngr8pmkaghhpwy0ln38lhf54"; + sha256 = "0vrjxzfgmjdzm1rgl0crz4b4badl14jwh032y3xkcdvjl5j67lp3"; }; buildInputs = [ wxGTK maxima gnome3.adwaita-icon-theme ]; |