diff options
Diffstat (limited to 'pkgs/applications/science')
34 files changed, 270 insertions, 63 deletions
diff --git a/pkgs/applications/science/biology/minc-tools/default.nix b/pkgs/applications/science/biology/minc-tools/default.nix index 41813dcda149..aae0cf40cee3 100644 --- a/pkgs/applications/science/biology/minc-tools/default.nix +++ b/pkgs/applications/science/biology/minc-tools/default.nix @@ -15,7 +15,7 @@ stdenv.mkDerivation rec { cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" ]; checkPhase = "ctest"; - doCheck = true; + doCheck = false; meta = with stdenv.lib; { homepage = https://github.com/BIC-MNI/minc-tools; diff --git a/pkgs/applications/science/biology/neuron/default.nix b/pkgs/applications/science/biology/neuron/default.nix index 33f6d50d8ad8..5d69b1f29e73 100644 --- a/pkgs/applications/science/biology/neuron/default.nix +++ b/pkgs/applications/science/biology/neuron/default.nix @@ -1,33 +1,65 @@ { stdenv , fetchurl -, pkgconfig -, ncurses +, pkgconfig +, automake +, autoconf +, libtool +, ncurses +, readline +, which +, python ? null , mpi ? null }: stdenv.mkDerivation rec { - name = "neuron-7.4"; - buildInputs = [ stdenv pkgconfig ncurses mpi ]; + name = "neuron-${version}"; + version = "7.4"; + + nativeBuildInputs = [ which pkgconfig automake autoconf libtool ]; + buildInputs = [ ncurses readline python mpi ]; src = fetchurl { - url = "http://www.neuron.yale.edu/ftp/neuron/versions/v7.4/nrn-7.4.tar.gz"; + url = "http://www.neuron.yale.edu/ftp/neuron/versions/v${version}/nrn-${version}.tar.gz"; sha256 = "1rid8cmv5mca0vqkgwahm0prkwkbdvchgw2bdwvx4adkn8bbl0ql"; }; + patches = (stdenv.lib.optional (stdenv.isDarwin) [ ./neuron-carbon-disable.patch ]); enableParallelBuilding = true; - configureFlags = [ "--without-x" - "${if mpi != null then "--with-mpi" else "--without-mpi"}" ]; + ## neuron install by default everything under prefix/${host_arch}/* + ## override this to support nix standard file hierarchy + ## without issues: install everything under prefix/ + preConfigure = '' + ./build.sh + export prefix="''${prefix} --exec-prefix=''${out}" + ''; + + configureFlags = with stdenv.lib; + [ "--without-x" "--with-readline=${readline}" ] + ++ optionals (python != null) [ "--with-nrnpython=${python.interpreter}" ] + ++ (if mpi != null then ["--with-mpi" "--with-paranrn"] + else ["--without-mpi"]); + + + postInstall = stdenv.lib.optionals (python != null) [ '' + ## standardise python neuron install dir if any + if [[ -d $out/lib/python ]]; then + mkdir -p ''${out}/${python.sitePackages} + mv ''${out}/lib/python/* ''${out}/${python.sitePackages}/ + fi + '']; + + propagatedBuildInputs = [ readline ncurses which libtool ]; meta = with stdenv.lib; { description = "Simulation environment for empirically-based simulations of neurons and networks of neurons"; longDescription = "NEURON is a simulation environment for developing and exercising models of - neurons and networks of neurons. It is particularly well-suited to problems where - cable properties of cells play an important role, possibly including extracellular - potential close to the membrane), and where cell membrane properties are complex, - involving many ion-specific channels, ion accumulation, and second messengers"; + neurons and networks of neurons. It is particularly well-suited to problems where + cable properties of cells play an important role, possibly including extracellular + potential close to the membrane), and where cell membrane properties are complex, + involving many ion-specific channels, ion accumulation, and second messengers"; license = licenses.bsd3; homepage = http://www.neuron.yale.edu/neuron; diff --git a/pkgs/applications/science/biology/neuron/neuron-carbon-disable.patch b/pkgs/applications/science/biology/neuron/neuron-carbon-disable.patch new file mode 100644 index 000000000000..923bffb1c338 --- /dev/null +++ b/pkgs/applications/science/biology/neuron/neuron-carbon-disable.patch @@ -0,0 +1,21 @@ +--- nrn-7.4/src/mac/Makefile.am 2015-11-12 21:42:45.000000000 +0100 ++++ nrn-7.4.new/src/mac/Makefile.am 2016-08-24 17:43:39.000000000 +0200 +@@ -15,18 +15,8 @@ + host_cpu = @host_cpu@ + + if MAC_DARWIN +-carbon = @enable_carbon@ + bin_SCRIPTS = $(launch_scripts) + install: install-am +-if UniversalMacBinary +- $(CC) -arch ppc -o aoutppc -Dcpu="\"$(host_cpu)\"" -I. $(srcdir)/launch.c $(srcdir)/mac2uxarg.c -framework Carbon +- $(CC) -arch i386 -o aouti386 -Dcpu="\"$(host_cpu)\"" -I. $(srcdir)/launch.c $(srcdir)/mac2uxarg.c -framework Carbon +- lipo aouti386 aoutppc -create -output a.out +-else +- gcc -g -arch i386 -Dncpu="\"$(host_cpu)\"" -I. $(srcdir)/launch.c $(srcdir)/mac2uxarg.c -framework Carbon +- +-endif +- carbon=$(carbon) sh $(srcdir)/launch_inst.sh "$(host_cpu)" "$(DESTDIR)$(prefix)" "$(srcdir)" + for i in $(S) ; do \ + sed "s/^CPU.*/CPU=\"$(host_cpu)\"/" < $(DESTDIR)$(bindir)/$$i > temp; \ + mv temp $(DESTDIR)$(bindir)/$$i; \ diff --git a/pkgs/applications/science/electronics/caneda/default.nix b/pkgs/applications/science/electronics/caneda/default.nix index 404ffc5010b4..dc00cef88982 100644 --- a/pkgs/applications/science/electronics/caneda/default.nix +++ b/pkgs/applications/science/electronics/caneda/default.nix @@ -19,7 +19,7 @@ stdenv.mkDerivation rec { sha256 = "dfbcac97f5a1b41ad9a63392394f37fb294cbf78c576673c9bc4a5370957b2c8"; }; - cmakeFlags = [ "-DCMAKE_BUILD_TYPE=Release" ]; + hardeningDisable = [ "format" ]; buildInputs = [ cmake qt4 libxml2 libxslt ]; diff --git a/pkgs/applications/science/electronics/geda/default.nix b/pkgs/applications/science/electronics/geda/default.nix index 25934c71e8eb..b8406c3255cc 100644 --- a/pkgs/applications/science/electronics/geda/default.nix +++ b/pkgs/applications/science/electronics/geda/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, pkgconfig, guile, gtk, flex, gawk, perl }: +{ stdenv, fetchurl, pkgconfig, guile, gtk2, flex, gawk, perl }: stdenv.mkDerivation rec { name = "geda-${version}"; @@ -10,7 +10,7 @@ stdenv.mkDerivation rec { }; configureFlags = "--disable-update-xdg-database"; - buildInputs = [ pkgconfig guile gtk flex gawk perl ]; + buildInputs = [ pkgconfig guile gtk2 flex gawk perl ]; meta = with stdenv.lib; { description = "Full GPL'd suite of Electronic Design Automation tools"; diff --git a/pkgs/applications/science/electronics/gerbv/default.nix b/pkgs/applications/science/electronics/gerbv/default.nix index 92d0ceba1cfe..7cdcbb7fd197 100644 --- a/pkgs/applications/science/electronics/gerbv/default.nix +++ b/pkgs/applications/science/electronics/gerbv/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchgit, pkgconfig, gettext, libtool, automake, autoconf, cairo, gtk, autoreconfHook }: +{ stdenv, fetchgit, pkgconfig, gettext, libtool, automake, autoconf, cairo, gtk2, autoreconfHook }: stdenv.mkDerivation rec { name = "gerbv-${version}"; @@ -10,7 +10,7 @@ stdenv.mkDerivation rec { sha256 = "00jn1xhf6kblxc5gac1wvk8zm12fy6sk81nj3jwdag0z6wk3z446"; }; - buildInputs = [ pkgconfig gettext libtool automake autoconf cairo gtk autoreconfHook ]; + buildInputs = [ pkgconfig gettext libtool automake autoconf cairo gtk2 autoreconfHook ]; configureFlags = ["--disable-update-desktop-database"]; diff --git a/pkgs/applications/science/electronics/gtkwave/default.nix b/pkgs/applications/science/electronics/gtkwave/default.nix index 32d39d8a609d..657d20553b7f 100644 --- a/pkgs/applications/science/electronics/gtkwave/default.nix +++ b/pkgs/applications/science/electronics/gtkwave/default.nix @@ -1,4 +1,4 @@ -{stdenv, fetchurl, gtk, gperf, pkgconfig, bzip2, tcl, tk, judy, xz}: +{stdenv, fetchurl, gtk2, gperf, pkgconfig, bzip2, tcl, tk, judy, xz}: stdenv.mkDerivation rec { name = "gtkwave-3.3.70"; @@ -7,7 +7,7 @@ stdenv.mkDerivation rec { sha256 = "1akzf1sq8mwarrbrbz5chrvgwlsp444h5za8rg1dfyqk733s7piz"; }; - buildInputs = [ gtk gperf pkgconfig bzip2 tcl tk judy xz ]; + buildInputs = [ gtk2 gperf pkgconfig bzip2 tcl tk judy xz ]; configureFlags = [ "--with-tcl=${tcl}/lib" "--with-tk=${tk}/lib" "--enable-judy" ]; diff --git a/pkgs/applications/science/electronics/pcb/default.nix b/pkgs/applications/science/electronics/pcb/default.nix index 257d6993ff59..1f5109434000 100644 --- a/pkgs/applications/science/electronics/pcb/default.nix +++ b/pkgs/applications/science/electronics/pcb/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, pkgconfig, gtk, bison, intltool, flex, netpbm, imagemagick, dbus, xlibsWrapper, mesa, shared_mime_info, tcl, tk, gnome, pangox_compat, gd, xorg }: +{ stdenv, fetchurl, pkgconfig, gtk2, bison, intltool, flex, netpbm, imagemagick, dbus, xlibsWrapper, mesa, shared_mime_info, tcl, tk, gnome2, pangox_compat, gd, xorg }: stdenv.mkDerivation rec { name = "pcb-${version}"; @@ -9,7 +9,7 @@ stdenv.mkDerivation rec { sha256 = "0l6944hq79qsyp60i5ai02xwyp8l47q7xdm3js0jfkpf72ag7i42"; }; - buildInputs = [ pkgconfig gtk bison intltool flex netpbm imagemagick dbus xlibsWrapper mesa tcl shared_mime_info tk gnome.gtkglext pangox_compat gd xorg.libXmu ]; + buildInputs = [ pkgconfig gtk2 bison intltool flex netpbm imagemagick dbus xlibsWrapper mesa tcl shared_mime_info tk gnome2.gtkglext pangox_compat gd xorg.libXmu ]; configureFlags = ["--disable-update-desktop-database"]; diff --git a/pkgs/applications/science/electronics/qfsm/default.nix b/pkgs/applications/science/electronics/qfsm/default.nix index 95b312a44389..4b4d21aca006 100644 --- a/pkgs/applications/science/electronics/qfsm/default.nix +++ b/pkgs/applications/science/electronics/qfsm/default.nix @@ -12,6 +12,8 @@ stdenv.mkDerivation rec { patches = [ ./drop-hardcoded-prefix.patch ]; + hardeningDisable = [ "format" ]; + enableParallelBuilding = true; meta = { diff --git a/pkgs/applications/science/electronics/tkgate/1.x.nix b/pkgs/applications/science/electronics/tkgate/1.x.nix index 61d03173e0ba..2a3f17b670b4 100644 --- a/pkgs/applications/science/electronics/tkgate/1.x.nix +++ b/pkgs/applications/science/electronics/tkgate/1.x.nix @@ -17,8 +17,8 @@ stdenv.mkDerivation rec { patchPhase = '' sed -i config.h \ -e 's|.*#define.*TKGATE_TCLTK_VERSIONS.*|#define TKGATE_TCLTK_VERSIONS "${tcl.release}"|' \ - -e 's|.*#define.*TKGATE_INCDIRS.*|#define TKGATE_INCDIRS "${tcl}/include ${tk}/include ${libiconvInc} ${libX11}/include"|' \ - -e 's|.*#define.*TKGATE_LIBDIRS.*|#define TKGATE_LIBDIRS "${tcl}/lib ${tk}/lib ${libiconvLib} ${libX11}/lib"|' \ + -e 's|.*#define.*TKGATE_INCDIRS.*|#define TKGATE_INCDIRS "${tcl}/include ${tk}/include ${libiconvInc} ${libX11.dev}/include"|' \ + -e 's|.*#define.*TKGATE_LIBDIRS.*|#define TKGATE_LIBDIRS "${tcl}/lib ${tk}/lib ${libiconvLib} ${libX11.out}/lib"|' \ \ -e '20 i #define TCL_LIBRARY "${tcl}/lib"' \ -e '20 i #define TK_LIBRARY "${tk}/lib/${tk.libPrefix}"' \ diff --git a/pkgs/applications/science/electronics/xoscope/default.nix b/pkgs/applications/science/electronics/xoscope/default.nix index df7d053d93bd..f26b13c5e32c 100644 --- a/pkgs/applications/science/electronics/xoscope/default.nix +++ b/pkgs/applications/science/electronics/xoscope/default.nix @@ -1,4 +1,4 @@ -{stdenv, fetchurl, gtk, pkgconfig}: +{stdenv, fetchurl, gtk2, pkgconfig}: stdenv.mkDerivation rec { name = "xoscope-2.0"; @@ -8,7 +8,7 @@ stdenv.mkDerivation rec { sha256 = "00xlvvqyw6l1ljbsx1vgx2v1jfh0xacz1a0yhq1dj6yxf5wh58x8"; }; - buildInputs = [ gtk pkgconfig ]; + buildInputs = [ gtk2 pkgconfig ]; # from: https://aur.archlinux.org/packages.php?ID=12140&detail=1 patches = [ ./gtkdepre.diff ]; diff --git a/pkgs/applications/science/geometry/drgeo/default.nix b/pkgs/applications/science/geometry/drgeo/default.nix index 048f34d7abfa..8db1beedebbb 100644 --- a/pkgs/applications/science/geometry/drgeo/default.nix +++ b/pkgs/applications/science/geometry/drgeo/default.nix @@ -1,17 +1,19 @@ -{ stdenv, fetchurl, libglade, gtk, guile, libxml2, perl +{ stdenv, fetchurl, libglade, gtk2, guile, libxml2, perl , intltool, libtool, pkgconfig }: stdenv.mkDerivation rec { name = "drgeo-${version}"; version = "1.1.0"; + hardeningDisable = [ "format" ]; + src = fetchurl { url = "mirror://sourceforge/ofset/${name}.tar.gz"; sha256 = "05i2czgzhpzi80xxghinvkyqx4ym0gm9f38fz53idjhigiivp4wc"; }; patches = [ ./struct.patch ]; - buildInputs = [libglade gtk guile libxml2 + buildInputs = [libglade gtk2 guile libxml2 perl intltool libtool pkgconfig]; prebuild = '' diff --git a/pkgs/applications/science/logic/boolector/default.nix b/pkgs/applications/science/logic/boolector/default.nix index 3879ee8ef470..37d25c9e9477 100644 --- a/pkgs/applications/science/logic/boolector/default.nix +++ b/pkgs/applications/science/logic/boolector/default.nix @@ -23,10 +23,11 @@ let license = with stdenv.lib.licenses; if useV16 then unfreeRedistributable else gpl3; in stdenv.mkDerivation (boolectorPkg // { - buildInputs = [ zlib ]; - enableParallelBuilding = false; + buildInputs = [ + zlib zlib.static (stdenv.lib.getOutput "static" stdenv.cc.libc) + ]; - buildPhase = "./build.sh"; + enableParallelBuilding = false; installPhase = '' mkdir -p $out/bin $out/lib $out/include diff --git a/pkgs/applications/science/logic/ltl2ba/default.nix b/pkgs/applications/science/logic/ltl2ba/default.nix index 59c6461f5b6c..f0947fa0ed6e 100644 --- a/pkgs/applications/science/logic/ltl2ba/default.nix +++ b/pkgs/applications/science/logic/ltl2ba/default.nix @@ -9,6 +9,8 @@ stdenv.mkDerivation rec { sha256 = "16z0gc7a9dkarwn0l6rvg5jdhw1q4qyn4501zlchy0zxqddz0sx6"; }; + hardeningDisable = [ "format" ]; + preConfigure = '' substituteInPlace Makefile \ --replace "CC=gcc" "" diff --git a/pkgs/applications/science/logic/otter/default.nix b/pkgs/applications/science/logic/otter/default.nix index 08d19c143eed..b19650eb8630 100644 --- a/pkgs/applications/science/logic/otter/default.nix +++ b/pkgs/applications/science/logic/otter/default.nix @@ -17,6 +17,9 @@ stdenv.mkDerivation { src = fetchurl { inherit (s) url sha256; }; + + hardeningDisable = [ "format" ]; + buildPhase = '' find . -name Makefile | xargs sed -i -e "s@/bin/rm@$(type -P rm)@g" find . -name Makefile | xargs sed -i -e "s@/bin/mv@$(type -P mv)@g" @@ -32,11 +35,13 @@ stdenv.mkDerivation { make -C source/formed realclean make -C source/formed formed ''; + installPhase = '' mkdir -p "$out"/{bin,share/otter} cp bin/* source/formed/formed "$out/bin/" cp -r examples examples-mace2 documents README* Legal Changelog Contents index.html "$out/share/otter/" ''; + meta = { inherit (s) version; description = "A reliable first-order theorem prover"; diff --git a/pkgs/applications/science/logic/prover9/default.nix b/pkgs/applications/science/logic/prover9/default.nix index d92c7887210e..43c2ae141b7a 100644 --- a/pkgs/applications/science/logic/prover9/default.nix +++ b/pkgs/applications/science/logic/prover9/default.nix @@ -8,7 +8,7 @@ stdenv.mkDerivation { sha256 = "1l2i3d3h5z7nnbzilb6z92r0rbx0kh6yaxn2c5qhn3000xcfsay3"; }; - phases = "unpackPhase patchPhase buildPhase installPhase"; + hardeningDisable = [ "format" ]; patchPhase = '' RM=$(type -tp rm) @@ -23,6 +23,8 @@ stdenv.mkDerivation { buildFlags = "all"; + checkPhase = "make test1"; + installPhase = '' mkdir -p $out/bin cp bin/* $out/bin @@ -37,7 +39,7 @@ stdenv.mkDerivation { for first-order and equational logic. Prover9 is a successor of the Otter Prover. This is the LADR command-line version. ''; - platforms = stdenv.lib.platforms.unix; + platforms = stdenv.lib.platforms.linux; maintainers = []; }; } diff --git a/pkgs/applications/science/logic/tptp/default.nix b/pkgs/applications/science/logic/tptp/default.nix index 32906b88d590..db7e0c0c9382 100644 --- a/pkgs/applications/science/logic/tptp/default.nix +++ b/pkgs/applications/science/logic/tptp/default.nix @@ -9,7 +9,7 @@ stdenv.mkDerivation rec { "http://www.cs.miami.edu/~tptp/TPTP/Distribution/TPTP-v${version}.tgz" "http://www.cs.miami.edu/~tptp/TPTP/Archive/TPTP-v${version}/TPTP-v${version}.tgz" ]; - sha256 = "1i5hi8grfl5zyh8py63zn39rg019bd90h2l312iswbgai6nyfdw0"; + sha256 = "17mnqxnyibmzf5vvbnyhsd010zykqw8ikx4pvyj0x9sfyhpvgfix"; }; buildInputs = [ tcsh yap perl patchelf ]; diff --git a/pkgs/applications/science/logic/twelf/default.nix b/pkgs/applications/science/logic/twelf/default.nix index 7d5724967c17..ca2422558e9a 100644 --- a/pkgs/applications/science/logic/twelf/default.nix +++ b/pkgs/applications/science/logic/twelf/default.nix @@ -21,6 +21,9 @@ stdenv.mkDerivation rec { rsync -av bin/{*,.heap} $out/bin/ bin/.mkexec ${smlnj}/bin/sml $out/ twelf-server twelf-server + substituteInPlace emacs/twelf-init.el \ + --replace '(concat twelf-root "emacs")' '(concat twelf-root "share/emacs/site-lisp/twelf")' + mkdir -p $out/share/emacs/site-lisp/twelf/ rsync -av emacs/ $out/share/emacs/site-lisp/twelf/ diff --git a/pkgs/applications/science/logic/verifast/default.nix b/pkgs/applications/science/logic/verifast/default.nix index d7c593b736e4..ada586fc4e6d 100644 --- a/pkgs/applications/science/logic/verifast/default.nix +++ b/pkgs/applications/science/logic/verifast/default.nix @@ -1,11 +1,11 @@ -{ stdenv, fetchurl, gtk, gdk_pixbuf, atk, pango, glib, cairo, freetype +{ stdenv, fetchurl, gtk2, gdk_pixbuf, atk, pango, glib, cairo, freetype , fontconfig, libxml2, gnome2 }: assert stdenv.isLinux; let libPath = stdenv.lib.makeLibraryPath - [ stdenv.cc.libc stdenv.cc.cc gtk gdk_pixbuf atk pango glib cairo + [ stdenv.cc.libc stdenv.cc.cc gtk2 gdk_pixbuf atk pango glib cairo freetype fontconfig libxml2 gnome2.gtksourceview ] + ":${stdenv.cc.cc.lib}/lib64"; diff --git a/pkgs/applications/science/math/calc/default.nix b/pkgs/applications/science/math/calc/default.nix index 8673d7debd9d..b9db4174c094 100644 --- a/pkgs/applications/science/math/calc/default.nix +++ b/pkgs/applications/science/math/calc/default.nix @@ -3,7 +3,7 @@ with stdenv.lib; let makeFlags = '' - INCDIR=${glibc}/include \ + INCDIR=${glibc.dev}/include \ BINDIR=$out/bin LIBDIR=$out/lib CALC_INCDIR=$out/include/calc CALC_SHAREDIR=$out/share/calc MANDIR=$out/share/man/man1 \ USE_READLINE=-DUSE_READLINE READLINE_LIB=-lreadline READLINE_EXTRAS='-lhistory -lncurses' \ TERMCONTROL=-DUSE_TERMIOS \ diff --git a/pkgs/applications/science/math/cbc/default.nix b/pkgs/applications/science/math/cbc/default.nix index 0d1ef26092e2..7643c912db4b 100644 --- a/pkgs/applications/science/math/cbc/default.nix +++ b/pkgs/applications/science/math/cbc/default.nix @@ -12,6 +12,8 @@ stdenv.mkDerivation { enableParallelBuilding = true; + hardeningDisable = [ "format" ]; + buildInputs = [ zlib bzip2 ]; # FIXME: move share/coin/Data to a separate output? diff --git a/pkgs/applications/science/math/geogebra/default.nix b/pkgs/applications/science/math/geogebra/default.nix index fcbd13566657..0e16e1fb3050 100644 --- a/pkgs/applications/science/math/geogebra/default.nix +++ b/pkgs/applications/science/math/geogebra/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { name = "geogebra-${version}"; - version = "5.0.265.0"; + version = "5.0.271.0"; preferLocalBuild = true; src = fetchurl { url = "http://download.geogebra.org/installers/5.0/GeoGebra-Linux-Portable-${version}.tar.bz2"; - sha256 = "74e5abfa098ee0fc464cd391cd3ef6db474ff25e8ea4fbcd82c4b4b5d3d5c459"; + sha256 = "5dd5be1cde27c9b567f79c38048045864064b69c0d2b469ae93e1fca5f543475"; }; srcIcon = fetchurl { diff --git a/pkgs/applications/science/math/maxima/default.nix b/pkgs/applications/science/math/maxima/default.nix index 21d3c656d304..4981767f21f2 100644 --- a/pkgs/applications/science/math/maxima/default.nix +++ b/pkgs/applications/science/math/maxima/default.nix @@ -1,8 +1,8 @@ -{ stdenv, fetchurl, sbcl, texinfo, perl, makeWrapper, rlwrap ? null, tk ? null, gnuplot ? null }: +{ stdenv, fetchurl, sbcl, texinfo, perl, python, makeWrapper, rlwrap ? null, tk ? null, gnuplot ? null }: let name = "maxima"; - version = "5.36.1"; + version = "5.38.1"; searchPath = stdenv.lib.makeBinPath @@ -13,10 +13,10 @@ stdenv.mkDerivation { src = fetchurl { url = "mirror://sourceforge/${name}/${name}-${version}.tar.gz"; - sha256 = "0x1rk659sn3cq0n5c90848ilzr1gb1wf0072fl6jhkdq00qgh2s0"; + sha256 = "1p6646rvq43hk09msyp0dk50cqpkh07mf4x0bc2fqisqmcv6b1hf"; }; - buildInputs = [sbcl texinfo perl makeWrapper]; + buildInputs = [sbcl texinfo perl python makeWrapper]; postInstall = '' # Make sure that maxima can find its runtime dependencies. diff --git a/pkgs/applications/science/math/perseus/default.nix b/pkgs/applications/science/math/perseus/default.nix index 15a1de5f0c5f..55293e6c8a79 100644 --- a/pkgs/applications/science/math/perseus/default.nix +++ b/pkgs/applications/science/math/perseus/default.nix @@ -5,6 +5,8 @@ stdenv.mkDerivation { version = "4-beta"; buildInputs = [ unzip ]; + hardeningDisable = [ "stackprotector" ]; + src = fetchurl { url = "http://www.sas.upenn.edu/~vnanda/source/perseus_4_beta.zip"; sha256 = "09brijnqabhgfjlj5wny0bqm5dwqcfkp1x5wif6yzdmqh080jybj"; @@ -30,7 +32,7 @@ stdenv.mkDerivation { around datasets arising from point samples, images, distance matrices and so forth. ''; - homepage = "www.sas.upenn.edu/~vnanda/perseus/index.html"; + homepage = "http://www.sas.upenn.edu/~vnanda/perseus/index.html"; license = stdenv.lib.licenses.gpl3; maintainers = with stdenv.lib.maintainers; [erikryb]; platforms = stdenv.lib.platforms.linux; diff --git a/pkgs/applications/science/math/pssp/default.nix b/pkgs/applications/science/math/pssp/default.nix index 6ced805b3115..e74e17fa44f5 100644 --- a/pkgs/applications/science/math/pssp/default.nix +++ b/pkgs/applications/science/math/pssp/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, libxml2, readline, zlib, perl, cairo, gtk, gsl +{ stdenv, fetchurl, libxml2, readline, zlib, perl, cairo, gtk2, gsl , pkgconfig, gtksourceview, pango, gettext, libglade }: @@ -10,7 +10,7 @@ stdenv.mkDerivation rec { sha256 = "0vri2pzvmm38qaihfvwlry30f40lcnps4blg59ixic4q20ldxf5d"; }; - buildInputs = [ libxml2 readline zlib perl cairo gtk gsl pkgconfig + buildInputs = [ libxml2 readline zlib perl cairo gtk2 gsl pkgconfig gtksourceview pango gettext libglade ]; doCheck = false; diff --git a/pkgs/applications/science/math/qalculate-gtk/default.nix b/pkgs/applications/science/math/qalculate-gtk/default.nix index f825e798a065..5f49b240fc06 100644 --- a/pkgs/applications/science/math/qalculate-gtk/default.nix +++ b/pkgs/applications/science/math/qalculate-gtk/default.nix @@ -1,4 +1,5 @@ { stdenv, fetchurl, intltool, autoreconfHook, pkgconfig, libqalculate, gtk3, wrapGAppsHook }: + stdenv.mkDerivation rec { name = "qalculate-gtk-${version}"; version = "0.9.9"; @@ -8,6 +9,8 @@ stdenv.mkDerivation rec { sha256 = "0v9ibycilygmi9zzi7cxif7si56c85lfzdvbqnbf32whg8ydqqkg"; }; + hardeningDisable = [ "format" ]; + nativeBuildInputs = [ intltool pkgconfig autoreconfHook wrapGAppsHook ]; buildInputs = [ libqalculate gtk3 ]; diff --git a/pkgs/applications/science/math/sage/default.nix b/pkgs/applications/science/math/sage/default.nix index 6e0b4313b47d..9e17fe60c295 100644 --- a/pkgs/applications/science/math/sage/default.nix +++ b/pkgs/applications/science/math/sage/default.nix @@ -7,7 +7,7 @@ stdenv.mkDerivation rec { name = "sage-6.8"; src = fetchurl { - url = "mirror://sagemath/${name}.tar.gz"; + url = "http://old.files.sagemath.org/src-old/${name}.tar.gz"; sha256 = "102mrzzi215g1xn5zgcv501x9sghwg758jagx2jixvg1rj2jijj9"; }; @@ -18,11 +18,14 @@ stdenv.mkDerivation rec { enableParallelBuilding = true; + hardeningDisable = [ "format" ]; + preConfigure = '' export SAGE_NUM_THREADS=$NIX_BUILD_CORES export SAGE_ATLAS_ARCH=fast mkdir -p $out/sageHome export HOME=$out/sageHome + export CPPFLAGS="-P" ''; preBuild = "patchShebangs build"; @@ -30,7 +33,6 @@ stdenv.mkDerivation rec { installPhase = ''DESTDIR=$out make install''; meta = { - broken = true; homepage = "http://www.sagemath.org"; description = "A free open source mathematics software system"; license = stdenv.lib.licenses.gpl2Plus; diff --git a/pkgs/applications/science/math/scilab/default.nix b/pkgs/applications/science/math/scilab/default.nix index 8482bd6fe94b..4e30814ff7df 100644 --- a/pkgs/applications/science/math/scilab/default.nix +++ b/pkgs/applications/science/math/scilab/default.nix @@ -3,7 +3,7 @@ , Xaw3d, withXaw3d ? false #, withPVMlib ? false , tcl, tk, withTk ? false -, gtk, withGtk ? false # working ? +, gtk2, withGtk ? false # working ? #, withF2c ? false , ocaml, withOCaml ? false #, withJava ? false @@ -16,12 +16,11 @@ stdenv.mkDerivation rec { name = "scilab-${version}"; src = fetchurl { url = "http://www.scilab.org/download/${version}/${name}-src.tar.gz"; - # md5 coming from http://www.scilab.org/download/index_download.php - md5 = "17a7a6aa52918f33d96777a0dc423658"; + sha256 = "1adk6jqlj7i3gjklvlf1j3il1nb22axnp4rvwl314an62siih0sc"; }; buildInputs = [gfortran ncurses] - ++ lib.optionals withGtk [gtk] + ++ lib.optionals withGtk [gtk2] ++ lib.optionals withOCaml [ocaml] ++ lib.optional withX xlibsWrapper ; diff --git a/pkgs/applications/science/math/singular/default.nix b/pkgs/applications/science/math/singular/default.nix index 8bae1d6206d0..a0fdf7c82395 100644 --- a/pkgs/applications/science/math/singular/default.nix +++ b/pkgs/applications/science/math/singular/default.nix @@ -16,6 +16,8 @@ stdenv.mkDerivation rec { find . -exec sed -e 's@/bin/uname@${coreutils}&@g' -i '{}' ';' ''; + hardeningDisable = stdenv.lib.optional stdenv.isi686 "stackprotector"; + postInstall = '' rm -rf "$out/LIB" cp -r Singular/LIB "$out" diff --git a/pkgs/applications/science/math/yacas/default.nix b/pkgs/applications/science/math/yacas/default.nix index 2c9d63be1b4d..0f6dc35fe0cb 100644 --- a/pkgs/applications/science/math/yacas/default.nix +++ b/pkgs/applications/science/math/yacas/default.nix @@ -8,6 +8,8 @@ stdenv.mkDerivation rec { sha256 = "1dmafm3w0lm5w211nwkfzaid1rvvmgskz7k4500pjhgdczi5sd78"; }; + hardeningDisable = [ "format" ]; + # Perl is only for the documentation nativeBuildInputs = [ perl ]; @@ -32,11 +34,11 @@ stdenv.mkDerivation rec { ''; }; - meta = { + meta = { description = "Easy to use, general purpose Computer Algebra System"; homepage = http://yacas.sourceforge.net/; license = stdenv.lib.licenses.gpl2Plus; maintainers = with stdenv.lib.maintainers; [viric]; - platforms = with stdenv.lib.platforms; all; + platforms = with stdenv.lib.platforms; linux; }; } diff --git a/pkgs/applications/science/misc/boinc/default.nix b/pkgs/applications/science/misc/boinc/default.nix index d45f4a2b2102..53ea9ce72125 100644 --- a/pkgs/applications/science/misc/boinc/default.nix +++ b/pkgs/applications/science/misc/boinc/default.nix @@ -1,6 +1,6 @@ { fetchFromGitHub, stdenv, autoconf, automake, pkgconfig, m4, curl, mesa, libXmu, libXi, freeglut, libjpeg, libtool, wxGTK, xcbutil, -sqlite, gtk, patchelf, libXScrnSaver, libnotify, libX11, libxcb }: +sqlite, gtk2, patchelf, libXScrnSaver, libnotify, libX11, libxcb }: stdenv.mkDerivation rec { version = "7.4.42"; @@ -14,7 +14,7 @@ stdenv.mkDerivation rec { }; buildInputs = [ libtool automake autoconf m4 pkgconfig curl mesa libXmu libXi - freeglut libjpeg wxGTK sqlite gtk libXScrnSaver libnotify patchelf libX11 + freeglut libjpeg wxGTK sqlite gtk2 libXScrnSaver libnotify patchelf libX11 libxcb xcbutil ]; diff --git a/pkgs/applications/science/misc/openmodelica/default.nix b/pkgs/applications/science/misc/openmodelica/default.nix index 8ea670c38189..8d673a15fa8e 100644 --- a/pkgs/applications/science/misc/openmodelica/default.nix +++ b/pkgs/applications/science/misc/openmodelica/default.nix @@ -1,7 +1,7 @@ {stdenv, fetchgit, fetchsvn, autoconf, automake, libtool, gfortran, clang, cmake, gnumake, hwloc, jre, liblapack, blas, hdf5, expat, ncurses, readline, qt4, webkit, which, lp_solve, omniorb, sqlite, libatomic_ops, pkgconfig, file, gettext, flex, bison, -doxygen, boost, openscenegraph, gnome, pangox_compat, xorg, git, bash, gtk, makeWrapper }: +doxygen, boost, openscenegraph, gnome2, pangox_compat, xorg, git, bash, gtk2, makeWrapper }: let @@ -17,8 +17,12 @@ stdenv.mkDerivation { buildInputs = [autoconf cmake automake libtool gfortran clang gnumake hwloc jre liblapack blas hdf5 expat ncurses readline qt4 webkit which lp_solve omniorb sqlite libatomic_ops pkgconfig file gettext flex bison - doxygen boost openscenegraph gnome.gtkglext pangox_compat xorg.libXmu - git gtk makeWrapper]; + doxygen boost openscenegraph gnome2.gtkglext pangox_compat xorg.libXmu + git gtk2 makeWrapper]; + + hardeningDisable = [ "format" ]; + + enableParallelBuilding = true; patchPhase = '' cp -fv ${fakegit}/bin/checkout-git.sh libraries/checkout-git.sh diff --git a/pkgs/applications/science/misc/root/default.nix b/pkgs/applications/science/misc/root/default.nix index 855766cace7c..a736bdad2ea1 100644 --- a/pkgs/applications/science/misc/root/default.nix +++ b/pkgs/applications/science/misc/root/default.nix @@ -1,5 +1,5 @@ -{ stdenv, fetchurl, fetchpatch, cmake, pkgconfig, python -, libX11, libXpm, libXft, libXext, zlib, lzma, gsl }: +{ stdenv, fetchurl, fetchpatch, cmake, pcre, pkgconfig, python +, libX11, libXpm, libXft, libXext, zlib, lzma, gsl, Cocoa }: stdenv.mkDerivation rec { name = "root-${version}"; @@ -10,13 +10,17 @@ stdenv.mkDerivation rec { sha256 = "00f3v3l8nimfkcxpn9qpyh3h23na0mi4wkds2y5gwqh8wh3jryq9"; }; - buildInputs = [ cmake pkgconfig python libX11 libXpm libXft libXext zlib lzma gsl ]; + buildInputs = [ cmake pcre pkgconfig python zlib lzma gsl ] + ++ stdenv.lib.optionals (!stdenv.isDarwin) [ libX11 libXpm libXft libXext ] + ++ stdenv.lib.optionals (stdenv.isDarwin) [ Cocoa ] + ; patches = [ (fetchpatch { url = "https://github.com/root-mirror/root/commit/ee9964210c56e7c1868618a4434c5340fef38fe4.patch"; sha256 = "186i7ni75yvjydy6lpmaplqxfb5z2019bgpbhff1n6zn2qlrff2r"; }) + ./sw_vers.patch ]; preConfigure = '' @@ -27,14 +31,41 @@ stdenv.mkDerivation rec { "-Drpath=ON" "-DCMAKE_INSTALL_LIBDIR=lib" "-DCMAKE_INSTALL_INCLUDEDIR=include" + "-Dalien=OFF" + "-Dbonjour=OFF" + "-Dcastor=OFF" + "-Dchirp=OFF" + "-Ddavix=OFF" + "-Ddcache=OFF" + "-Dfftw3=OFF" + "-Dfitsio=OFF" + "-Dfortran=OFF" + "-Dgfal=OFF" + "-Dgviz=OFF" + "-Dhdfs=OFF" + "-Dkrb5=OFF" + "-Dldap=OFF" + "-Dmonalisa=OFF" + "-Dmysql=OFF" + "-Dodbc=OFF" + "-Dopengl=OFF" + "-Doracle=OFF" + "-Dpgsql=OFF" + "-Dpythia6=OFF" + "-Dpythia8=OFF" + "-Drfio=OFF" + "-Dsqlite=OFF" + "-Dssl=OFF" + "-Dxml=OFF" + "-Dxrootd=OFF" ] - ++ stdenv.lib.optional (stdenv.cc.libc != null) "-DC_INCLUDE_DIRS=${stdenv.cc.libc}/include"; + ++ stdenv.lib.optional (stdenv.cc.libc != null) "-DC_INCLUDE_DIRS=${stdenv.lib.getDev stdenv.cc.libc}/include"; enableParallelBuilding = true; meta = { homepage = "https://root.cern.ch/"; description = "A data analysis framework"; - platforms = stdenv.lib.platforms.linux; + platforms = stdenv.lib.platforms.unix; }; } diff --git a/pkgs/applications/science/misc/root/sw_vers.patch b/pkgs/applications/science/misc/root/sw_vers.patch new file mode 100644 index 000000000000..3de2b839bf4b --- /dev/null +++ b/pkgs/applications/science/misc/root/sw_vers.patch @@ -0,0 +1,90 @@ +diff --git a/build/unix/compiledata.sh b/build/unix/compiledata.sh +--- a/build/unix/compiledata.sh ++++ b/build/unix/compiledata.sh +@@ -49,7 +49,7 @@ fi + + if [ "$ARCH" = "macosx" ] || [ "$ARCH" = "macosx64" ] || \ + [ "$ARCH" = "macosxicc" ]; then +- macosx_minor=`sw_vers | sed -n 's/ProductVersion://p' | cut -d . -f 2` ++ macosx_minor=7 + SOEXT="so" + if [ $macosx_minor -ge 5 ]; then + if [ "x`echo $SOFLAGS | grep -- '-install_name'`" != "x" ]; then +diff --git a/cmake/modules/SetUpMacOS.cmake b/cmake/modules/SetUpMacOS.cmake +--- a/cmake/modules/SetUpMacOS.cmake ++++ b/cmake/modules/SetUpMacOS.cmake +@@ -12,25 +12,11 @@ set(CMAKE_PREFIX_PATH ${CMAKE_PREFIX_PATH} /usr/X11R6) + #--------------------------------------------------------------------------------------------------------- + + if (CMAKE_SYSTEM_NAME MATCHES Darwin) +- EXECUTE_PROCESS(COMMAND sw_vers "-productVersion" +- COMMAND cut -d . -f 1-2 +- OUTPUT_VARIABLE MACOSX_VERSION OUTPUT_STRIP_TRAILING_WHITESPACE) +- MESSAGE(STATUS "Found a Mac OS X System ${MACOSX_VERSION}") +- EXECUTE_PROCESS(COMMAND sw_vers "-productVersion" +- COMMAND cut -d . -f 2 +- OUTPUT_VARIABLE MACOSX_MINOR OUTPUT_STRIP_TRAILING_WHITESPACE) +- +- if(MACOSX_VERSION VERSION_GREATER 10.7 AND ${CMAKE_CXX_COMPILER_ID} STREQUAL Clang) + set(libcxx ON CACHE BOOL "Build using libc++" FORCE) +- endif() + +- if(${MACOSX_MINOR} GREATER 4) + #TODO: check haveconfig and rpath -> set rpath true + #TODO: check Thread, define link command + #TODO: more stuff check configure script +- execute_process(COMMAND /usr/sbin/sysctl machdep.cpu.extfeatures OUTPUT_VARIABLE SYSCTL_OUTPUT) +- if(${SYSCTL_OUTPUT} MATCHES 64) +- MESSAGE(STATUS "Found a 64bit system") + set(ROOT_ARCHITECTURE macosx64) + SET(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS}") + SET(CMAKE_SHARED_LIBRARY_CREATE_C_FLAGS "${CMAKE_SHARED_LIBRARY_CREATE_C_FLAGS} -m64") +@@ -38,27 +24,6 @@ if (CMAKE_SYSTEM_NAME MATCHES Darwin) + SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -m64") + SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -m64") + SET(CMAKE_FORTRAN_FLAGS "${CMAKE_FORTRAN_FLAGS} -m64") +- else(${SYSCTL_OUTPUT} MATCHES 64) +- MESSAGE(STATUS "Found a 32bit system") +- SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -m32") +- SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -m32") +- SET(CMAKE_FORTRAN_FLAGS "${CMAKE_FORTRAN_FLAGS} -m32") +- endif(${SYSCTL_OUTPUT} MATCHES 64) +- endif() +- +- if(MACOSX_VERSION VERSION_GREATER 10.6) +- set(MACOSX_SSL_DEPRECATED ON) +- endif() +- if(MACOSX_VERSION VERSION_GREATER 10.7) +- set(MACOSX_ODBC_DEPRECATED ON) +- endif() +- if(MACOSX_VERSION VERSION_GREATER 10.8) +- set(MACOSX_GLU_DEPRECATED ON) +- set(MACOSX_KRB5_DEPRECATED ON) +- endif() +- if(MACOSX_VERSION VERSION_GREATER 10.9) +- set(MACOSX_LDAP_DEPRECATED ON) +- endif() + + if (CMAKE_COMPILER_IS_GNUCXX) + message(STATUS "Found GNU compiler collection") +@@ -135,7 +100,7 @@ if (CMAKE_SYSTEM_NAME MATCHES Darwin) + endif() + + #---Set Linker flags---------------------------------------------------------------------- +- set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -mmacosx-version-min=${MACOSX_VERSION} -Wl,-rpath,@loader_path/../lib") ++ set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Wl,-rpath,@loader_path/../lib") + + + else (CMAKE_SYSTEM_NAME MATCHES Darwin) +diff --git a/config/root-config.in b/config/root-config.in +--- a/config/root-config.in ++++ b/config/root-config.in +@@ -304,7 +304,7 @@ macosxicc) + ;; + macosx64) + # MacOS X with gcc (GNU cc v4.x) in 64 bit mode +- macosx_minor=`sw_vers | sed -n 's/ProductVersion://p' | cut -d . -f 2` ++ macosx_minor=7 + # cannot find the one linked to libGraf if relocated after built + if [ $macosx_minor -le 4 ]; then + rootlibs="$rootlibs -lfreetype" |