From 95373d3634d6431037d8d752513392227c76c66b Mon Sep 17 00:00:00 2001 From: Matthew Bauer Date: Sun, 4 Nov 2018 20:12:55 -0600 Subject: atlas: remove atlas is broken and can apparently be removed. Fixes #49594 --- pkgs/applications/science/math/giac/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'pkgs/applications/science/math') diff --git a/pkgs/applications/science/math/giac/default.nix b/pkgs/applications/science/math/giac/default.nix index 6a0b686602f..2823165d022 100644 --- a/pkgs/applications/science/math/giac/default.nix +++ b/pkgs/applications/science/math/giac/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, fetchpatch, texlive, bison, flex, liblapackWithoutAtlas +{ stdenv, fetchurl, fetchpatch, texlive, bison, flex, liblapack , gmp, mpfr, pari, ntl, gsl, blas, mpfi , readline, gettext, libpng, libao, gfortran, perl , enableGUI ? false, libGLU_combined ? null, xorg ? null, fltk ? null @@ -42,7 +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) - liblapackWithoutAtlas + liblapack ] ++ stdenv.lib.optionals enableGUI [ libGLU_combined fltk xorg.libX11 ]; -- cgit 1.4.1 From 6f2bb3c275c4ffd04506c96c35efd9791a50782b Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Fri, 9 Nov 2018 17:41:49 -0800 Subject: gmsh: 4.0.2 -> 4.0.4 Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/gmsh/versions --- pkgs/applications/science/math/gmsh/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'pkgs/applications/science/math') diff --git a/pkgs/applications/science/math/gmsh/default.nix b/pkgs/applications/science/math/gmsh/default.nix index 525fc5f1dc2..4d0bb487c12 100644 --- a/pkgs/applications/science/math/gmsh/default.nix +++ b/pkgs/applications/science/math/gmsh/default.nix @@ -1,14 +1,14 @@ { stdenv, fetchurl, cmake, blas, liblapack, gfortran, gmm, fltk, libjpeg , zlib, libGLU_combined, libGLU, xorg }: -let version = "4.0.2"; in +let version = "4.0.4"; in stdenv.mkDerivation { name = "gmsh-${version}"; src = fetchurl { url = "http://gmsh.info/src/gmsh-${version}-source.tgz"; - sha256 = "03aw3sbz4x998rk29az7mgm0mrdb6614aqnppg81p5jkh5097jgk"; + sha256 = "1hvrls3xyxvn69kwicpvndrs0zhifcfkhfsxr8zkmhmn6fhnjhha"; }; # The original CMakeLists tries to use some version of the Lapack lib -- cgit 1.4.1 From f5b4eb63f330c6eeb19d15fb4e1ec31c49c21e7b Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Fri, 9 Nov 2018 17:56:17 -0800 Subject: gp2c: 0.0.11 -> 0.0.11pl1 Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/gp2c/versions --- pkgs/applications/science/math/pari/gp2c.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'pkgs/applications/science/math') diff --git a/pkgs/applications/science/math/pari/gp2c.nix b/pkgs/applications/science/math/pari/gp2c.nix index 42f35edb256..4915e42025b 100644 --- a/pkgs/applications/science/math/pari/gp2c.nix +++ b/pkgs/applications/science/math/pari/gp2c.nix @@ -4,11 +4,11 @@ stdenv.mkDerivation rec { name = "gp2c-${version}"; - version = "0.0.11"; + version = "0.0.11pl1"; src = fetchurl { url = "https://pari.math.u-bordeaux.fr/pub/pari/GP2C/${name}.tar.gz"; - sha256 = "1z69xj2dpd8yyi8108rz26c50xpv0k2j8qnk0bzy1c5lw3pd1adm"; + sha256 = "1c6f6vmncw032kfzrfyr8bynw6yd3faxpy2285r009fmr0zxfs5s"; }; buildInputs = [ pari perl ]; -- cgit 1.4.1 From 6533d7588d697568afccff398df5369e851ebc62 Mon Sep 17 00:00:00 2001 From: Markus Kowalewski Date: Sun, 11 Nov 2018 02:17:49 +0100 Subject: colpack: set platform to linux --- pkgs/applications/science/math/colpack/default.nix | 1 + 1 file changed, 1 insertion(+) (limited to 'pkgs/applications/science/math') diff --git a/pkgs/applications/science/math/colpack/default.nix b/pkgs/applications/science/math/colpack/default.nix index e62df7f11cc..94e0a44226d 100644 --- a/pkgs/applications/science/math/colpack/default.nix +++ b/pkgs/applications/science/math/colpack/default.nix @@ -25,6 +25,7 @@ stdenv.mkDerivation rec { vertex coloring and derivative computation"; homepage = "http://cscapes.cs.purdue.edu/coloringpage/software.htm#functionalities"; license = licenses.lgpl3; + platforms = platforms.linux; maintainers = with maintainers; [ edwtjo ]; }; -- cgit 1.4.1 From ced40eabfdb14b21a14e36ce1874b3090794fb3d Mon Sep 17 00:00:00 2001 From: Markus Kowalewski Date: Wed, 14 Nov 2018 11:41:46 +0100 Subject: gmsh: use openblas instead of atlas/lapack * openblas is properly recognized by cmake * the cmake patch is no longer neccessary --- .../science/math/gmsh/CMakeLists.txt.patch | 37 ---------------------- pkgs/applications/science/math/gmsh/default.nix | 8 ++--- 2 files changed, 2 insertions(+), 43 deletions(-) delete mode 100644 pkgs/applications/science/math/gmsh/CMakeLists.txt.patch (limited to 'pkgs/applications/science/math') diff --git a/pkgs/applications/science/math/gmsh/CMakeLists.txt.patch b/pkgs/applications/science/math/gmsh/CMakeLists.txt.patch deleted file mode 100644 index 0326a8d296a..00000000000 --- a/pkgs/applications/science/math/gmsh/CMakeLists.txt.patch +++ /dev/null @@ -1,37 +0,0 @@ ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -324,25 +324,16 @@ - set_config_option(HAVE_BLAS "Blas(IntelMKL)") - set_config_option(HAVE_LAPACK "Lapack(IntelMKL)") - else(LAPACK_LIBRARIES) -- # on Linux also try to find ATLAS without a Fortran compiler, because -- # cmake ships with a buggy FindBLAS e.g. on Ubuntu Lucid Lynx -- set(ATLAS_LIBS_REQUIRED lapack f77blas cblas atlas) -- find_all_libraries(LAPACK_LIBRARIES ATLAS_LIBS_REQUIRED "" "") -+ # try with generic names -+ set(GENERIC_LIBS_REQUIRED lapack blas pthread) -+ find_all_libraries(LAPACK_LIBRARIES GENERIC_LIBS_REQUIRED "" "") - if(LAPACK_LIBRARIES) -- set_config_option(HAVE_BLAS "Blas(ATLAS)") -- set_config_option(HAVE_LAPACK "Lapack(ATLAS)") -- else(LAPACK_LIBRARIES) -- # try with generic names -- set(GENERIC_LIBS_REQUIRED lapack blas pthread) -- find_all_libraries(LAPACK_LIBRARIES GENERIC_LIBS_REQUIRED "" "") -- if(LAPACK_LIBRARIES) -- set_config_option(HAVE_BLAS "Blas(Generic)") -- set_config_option(HAVE_LAPACK "Lapack(Generic)") -- find_library(GFORTRAN_LIB gfortran) -- if(GFORTRAN_LIB) -- list(APPEND LAPACK_LIBRARIES ${GFORTRAN_LIB}) -- endif(GFORTRAN_LIB) -- endif(LAPACK_LIBRARIES) -+ set_config_option(HAVE_BLAS "Blas(Generic)") -+ set_config_option(HAVE_LAPACK "Lapack(Generic)") -+ find_library(GFORTRAN_LIB gfortran) -+ if(GFORTRAN_LIB) -+ list(APPEND LAPACK_LIBRARIES ${GFORTRAN_LIB}) -+ endif(GFORTRAN_LIB) - endif(LAPACK_LIBRARIES) - endif(LAPACK_LIBRARIES) - elseif(${CMAKE_SYSTEM_NAME} MATCHES "SunOS") diff --git a/pkgs/applications/science/math/gmsh/default.nix b/pkgs/applications/science/math/gmsh/default.nix index 4d0bb487c12..de4bd270d68 100644 --- a/pkgs/applications/science/math/gmsh/default.nix +++ b/pkgs/applications/science/math/gmsh/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, cmake, blas, liblapack, gfortran, gmm, fltk, libjpeg +{ stdenv, fetchurl, cmake, openblasCompat, gfortran, gmm, fltk, libjpeg , zlib, libGLU_combined, libGLU, xorg }: let version = "4.0.4"; in @@ -11,11 +11,7 @@ stdenv.mkDerivation { sha256 = "1hvrls3xyxvn69kwicpvndrs0zhifcfkhfsxr8zkmhmn6fhnjhha"; }; - # The original CMakeLists tries to use some version of the Lapack lib - # that is supposed to work without Fortran but didn't for me. - patches = [ ./CMakeLists.txt.patch ]; - - buildInputs = [ cmake blas liblapack gmm fltk libjpeg zlib libGLU_combined + buildInputs = [ cmake openblasCompat gmm fltk libjpeg zlib libGLU_combined libGLU xorg.libXrender xorg.libXcursor xorg.libXfixes xorg.libXext xorg.libXft xorg.libXinerama xorg.libX11 xorg.libSM xorg.libICE ]; -- cgit 1.4.1 From 644ab709e70fe7631a8c2c77380fce9bcf562842 Mon Sep 17 00:00:00 2001 From: Markus Kowalewski Date: Wed, 14 Nov 2018 12:33:37 +0100 Subject: gmsh: restrict platform to x86_64-linux --- pkgs/applications/science/math/gmsh/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'pkgs/applications/science/math') diff --git a/pkgs/applications/science/math/gmsh/default.nix b/pkgs/applications/science/math/gmsh/default.nix index de4bd270d68..7c8e62cc97c 100644 --- a/pkgs/applications/science/math/gmsh/default.nix +++ b/pkgs/applications/science/math/gmsh/default.nix @@ -23,7 +23,7 @@ stdenv.mkDerivation { meta = { description = "A three-dimensional finite element mesh generator"; homepage = http://gmsh.info/; - platforms = stdenv.lib.platforms.all; + platforms = [ "x86_64-linux" ]; license = stdenv.lib.licenses.gpl2Plus; }; } -- cgit 1.4.1 From b4e13e62572691805872f3ddb466af81b043d140 Mon Sep 17 00:00:00 2001 From: Johannes Frankenau Date: Wed, 14 Nov 2018 19:38:18 +0100 Subject: gurobi: install Java library files --- pkgs/applications/science/math/gurobi/default.nix | 6 ++++++ 1 file changed, 6 insertions(+) (limited to 'pkgs/applications/science/math') diff --git a/pkgs/applications/science/math/gurobi/default.nix b/pkgs/applications/science/math/gurobi/default.nix index 06d448f6252..d4a4133d06e 100644 --- a/pkgs/applications/science/math/gurobi/default.nix +++ b/pkgs/applications/science/math/gurobi/default.nix @@ -33,9 +33,15 @@ stdenv.mkDerivation rec { cp include/gurobi*.h $out/include/ mkdir -p $out/lib + cp lib/*.jar $out/lib/ + cp lib/libGurobiJni*.so $out/lib/ cp lib/libgurobi*.so* $out/lib/ cp lib/libgurobi*.a $out/lib/ cp src/build/*.a $out/lib/ + + mkdir -p $out/share/java + ln -s $out/lib/gurobi.jar $out/share/java/ + ln -s $out/lib/gurobi-javadoc.jar $out/share/java/ ''; meta = with stdenv.lib; { -- cgit 1.4.1 From 131f2e93b6c3bf0cfa6280e84ee0f50f1bd1bdd9 Mon Sep 17 00:00:00 2001 From: Jörg Thalheim Date: Fri, 16 Nov 2018 15:32:39 +0000 Subject: sage: unpin nodePackage version --- pkgs/applications/science/math/sage/default.nix | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) (limited to 'pkgs/applications/science/math') diff --git a/pkgs/applications/science/math/sage/default.nix b/pkgs/applications/science/math/sage/default.nix index 7e62f0cf75e..cf8515283cd 100644 --- a/pkgs/applications/science/math/sage/default.nix +++ b/pkgs/applications/science/math/sage/default.nix @@ -3,7 +3,7 @@ }: let - inherit (nixpkgs) fetchpatch fetchurl symlinkJoin callPackage nodePackages_8_x; + inherit (nixpkgs) fetchpatch fetchurl symlinkJoin callPackage nodePackages; # https://trac.sagemath.org/ticket/15980 for tracking of python3 support python = nixpkgs.python2.override { @@ -26,7 +26,7 @@ let }; sagenb = self.callPackage ./sagenb.nix { - mathjax = nodePackages_8_x.mathjax; + mathjax = nodePackages.mathjax; }; sagedoc = self.callPackage ./sagedoc.nix { @@ -36,8 +36,8 @@ let env-locations = self.callPackage ./env-locations.nix { inherit pari_data ecl; inherit singular; - three = nodePackages_8_x.three; - mathjax = nodePackages_8_x.mathjax; + three = nodePackages.three; + mathjax = nodePackages.mathjax; }; sage-env = self.callPackage ./sage-env.nix { @@ -49,7 +49,7 @@ let inherit pythonEnv; inherit sage-src openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular; pkg-config = nixpkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig - three = nodePackages_8_x.three; + three = nodePackages.three; }; sage = self.callPackage ./sage.nix { }; -- cgit 1.4.1