diff options
Diffstat (limited to 'pkgs/applications/science')
81 files changed, 1280 insertions, 211 deletions
diff --git a/pkgs/applications/science/astronomy/celestia/default.nix b/pkgs/applications/science/astronomy/celestia/default.nix index d7814aa5b78f..d4da5c113c99 100644 --- a/pkgs/applications/science/astronomy/celestia/default.nix +++ b/pkgs/applications/science/astronomy/celestia/default.nix @@ -65,6 +65,8 @@ stdenv.mkDerivation { ) ''; + installPhase = ''make MKDIR_P="mkdir -p" install''; + enableParallelBuilding = true; meta = { diff --git a/pkgs/applications/science/astronomy/gravit/default.nix b/pkgs/applications/science/astronomy/gravit/default.nix index a2cc07b0a61c..696890f95f1e 100644 --- a/pkgs/applications/science/astronomy/gravit/default.nix +++ b/pkgs/applications/science/astronomy/gravit/default.nix @@ -15,7 +15,7 @@ stdenv.mkDerivation rec { meta = { homepage = "http://gravit.slowchop.com"; description = "A beautiful OpenGL-based gravity simulator"; - license = "GPLv2"; + license = stdenv.lib.licenses.gpl2; longDescription = '' Gravit is a gravity simulator which runs under Linux, Windows and diff --git a/pkgs/applications/science/astronomy/stellarium/default.nix b/pkgs/applications/science/astronomy/stellarium/default.nix index 04c82b21e859..6b84143d0138 100644 --- a/pkgs/applications/science/astronomy/stellarium/default.nix +++ b/pkgs/applications/science/astronomy/stellarium/default.nix @@ -1,14 +1,11 @@ -{stdenv, fetchurl, cmake, freetype, libpng, mesa, gettext, openssl, qt4, perl, libiconv}: +{ stdenv, fetchurl, cmake, freetype, libpng, mesa, gettext, openssl, qt4, perl, libiconv }: -let - name = "stellarium-0.12.1"; -in -stdenv.mkDerivation { - inherit name; +stdenv.mkDerivation rec { + name = "stellarium-0.12.4"; src = fetchurl { url = "mirror://sourceforge/stellarium/${name}.tar.gz"; - sha256 = "02qfp56mkg3bqggv3ndx8v6zfswg51gkczwiqy5c9y4rw28hazla"; + sha256 = "11367hv9niyz9v47lf31vjsqkgc8da0vy2nhiyxgmk1i49p1pbhg"; }; buildInputs = [ cmake freetype libpng mesa gettext openssl qt4 perl libiconv ]; diff --git a/pkgs/applications/science/astronomy/xplanet/default.nix b/pkgs/applications/science/astronomy/xplanet/default.nix index 816119a3b925..bdb93c992262 100644 --- a/pkgs/applications/science/astronomy/xplanet/default.nix +++ b/pkgs/applications/science/astronomy/xplanet/default.nix @@ -2,15 +2,17 @@ , libjpeg, netpbm}: stdenv.mkDerivation rec { - name = "xplanet-1.2.2"; + name = "xplanet-1.3.0"; src = fetchurl { url = "mirror://sourceforge/xplanet/${name}.tar.gz"; - sha256 = "1jnkrly9njkibxqbg5im4pq9cqjzwmki6jzd318dvlfmnicqr3vg"; + sha256 = "0hml2v228wi2r61m1pgka7h96rl92b6apk0iigm62miyp4mp9ys4"; }; buildInputs = [ pkgconfig freetype pango libpng libtiff giflib libjpeg netpbm ]; + patches = [ ./giflib.patch ]; + meta = { description = "Renders an image of the earth or other planets into the X root window"; homepage = http://xplanet.sourceforge.net; diff --git a/pkgs/applications/science/astronomy/xplanet/giflib.patch b/pkgs/applications/science/astronomy/xplanet/giflib.patch new file mode 100644 index 000000000000..aaf024198fbc --- /dev/null +++ b/pkgs/applications/science/astronomy/xplanet/giflib.patch @@ -0,0 +1,130 @@ +diff -wbBur xplanet-1.3.0/src/libimage/gif.c /home/sergej/tmp/BUILD/staging-i686/sergej/build/xplanet/src/xplanet-1.3.0/src/libimage/gif.c +--- xplanet-1.3.0/src/libimage/gif.c 2006-03-26 01:50:51.000000000 +0300 ++++ /home/sergej/tmp/BUILD/staging-i686/sergej/build/xplanet/src/xplanet-1.3.0/src/libimage/gif.c 2013-07-30 18:21:17.412474692 +0400 +@@ -20,7 +20,7 @@ + + #include <stdio.h> + #include <stdlib.h> +- ++#define FALSE 0 + #include <gif_lib.h> + + /* +@@ -42,11 +42,11 @@ + int color_index; + unsigned char *ptr = NULL; + +- infile = DGifOpenFileName(filename); ++ infile = DGifOpenFileName(filename, NULL); + + if (infile == NULL) + { +- PrintGifError(); ++ printf("%s\n", GifErrorString(GIF_ERROR)); + return(0); + } + +@@ -54,7 +54,7 @@ + { + if (DGifGetRecordType(infile, &record_type) == GIF_ERROR) + { +- PrintGifError(); ++ printf("%s\n", GifErrorString(GIF_ERROR)); + return(0); + } + +@@ -63,7 +63,7 @@ + case IMAGE_DESC_RECORD_TYPE: + if (DGifGetImageDesc(infile) == GIF_ERROR) + { +- PrintGifError(); ++ printf("%s\n", GifErrorString(GIF_ERROR)); + return(0); + } + +@@ -107,14 +107,14 @@ + GifByteType *ext; + if (DGifGetExtension(infile, &ext_code, &ext) == GIF_ERROR) + { +- PrintGifError(); ++ printf("%s\n", GifErrorString(GIF_ERROR)); + return(0); + } + while (ext != NULL) + { + if (DGifGetExtensionNext(infile, &ext) == GIF_ERROR) + { +- PrintGifError(); ++ printf("%s\n", GifErrorString(GIF_ERROR)); + return(0); + } + } +@@ -178,7 +178,7 @@ + return(0); + } + +- colormap = MakeMapObject(colormap_size, NULL); ++ colormap = GifMakeMapObject(colormap_size, NULL); + + for (i = 0; i < width * height; i++) + { +@@ -187,10 +187,10 @@ + blue[i] = (GifByteType) rgb[3*i+2]; + } + +- if (QuantizeBuffer(width, height, &colormap_size, red, green, blue, ++ if (GifQuantizeBuffer(width, height, &colormap_size, red, green, blue, + buffer, colormap->Colors) == GIF_ERROR) + { +- PrintGifError(); ++ printf("%s\n", GifErrorString(GIF_ERROR)); + return(0); + } + +@@ -198,24 +198,24 @@ + free(green); + free(blue); + +- outfile = EGifOpenFileName((char *) filename, FALSE); ++ outfile = EGifOpenFileName((char *) filename, FALSE, NULL); + if (outfile == NULL) + { +- PrintGifError(); ++ printf("%s\n", GifErrorString(GIF_ERROR)); + return(0); + } + + if (EGifPutScreenDesc(outfile, width, height, colormap_size, 0, colormap) + == GIF_ERROR) + { +- PrintGifError(); ++ printf("%s\n", GifErrorString(GIF_ERROR)); + return(0); + } + + if (EGifPutImageDesc(outfile, 0, 0, width, height, FALSE, NULL) + == GIF_ERROR) + { +- PrintGifError(); ++ printf("%s\n", GifErrorString(GIF_ERROR)); + return(0); + } + +@@ -224,7 +224,7 @@ + { + if (EGifPutLine(outfile, ptr, width) == GIF_ERROR) + { +- PrintGifError(); ++ printf("%s\n", GifErrorString(GIF_ERROR)); + return(0); + } + ptr += width; +@@ -233,7 +233,7 @@ + EGifSpew(outfile); + + if (EGifCloseFile(outfile) == GIF_ERROR) +- PrintGifError(); ++ printf("%s\n", GifErrorString(GIF_ERROR)); + + free(buffer); + diff --git a/pkgs/applications/science/biology/arb/default.nix b/pkgs/applications/science/biology/arb/default.nix index 279091f21bd2..2f622e94057b 100644 --- a/pkgs/applications/science/biology/arb/default.nix +++ b/pkgs/applications/science/biology/arb/default.nix @@ -81,5 +81,6 @@ stdenv.mkDerivation { pkgMaintainer = "http://BioLib.open-bio.org/"; homepage = http://www.arb-home.de/; priority = "10"; # because it includes binaries of clustal etc. + broken = true; }; } diff --git a/pkgs/applications/science/biology/plink/default.nix b/pkgs/applications/science/biology/plink/default.nix index fa6dcaa82ede..009e12aa02f0 100644 --- a/pkgs/applications/science/biology/plink/default.nix +++ b/pkgs/applications/science/biology/plink/default.nix @@ -18,7 +18,8 @@ stdenv.mkDerivation { meta = { description = "Whole genome association toolkit"; homepage = "http://pngu.mgh.harvard.edu/~purcell/plink/"; - license = "GNUv2"; + license = stdenv.lib.licenses.gpl2; platforms = stdenv.lib.platforms.all; + broken = true; }; } diff --git a/pkgs/applications/science/chemistry/avogadro/default.nix b/pkgs/applications/science/chemistry/avogadro/default.nix index e45f5b645fd9..1e9f3ee521b1 100644 --- a/pkgs/applications/science/chemistry/avogadro/default.nix +++ b/pkgs/applications/science/chemistry/avogadro/default.nix @@ -1,16 +1,16 @@ -{ stdenv, fetchurl, cmake, qt4, zlib, eigen, openbabel, pkgconfig, mesa, libX11 }: +{ stdenv, fetchurl, cmake, qt4, zlib, eigen, openbabel, pkgconfig, mesa, libX11, doxygen }: stdenv.mkDerivation rec { - name = "avogadro-1.0.3"; + name = "avogadro-1.1.1"; src = fetchurl { url = "mirror://sourceforge/avogadro/${name}.tar.bz2"; - sha256 = "0s44r78vm7hf4cs13d2qki3gf178gjj1ihph6rs04g6s4figvdpg"; + sha256 = "050ag9p4vg7jg8hj1wqfv7lsm6ar2isxjw2vw85s49vsl7g7nvzy"; }; buildInputs = [ qt4 eigen zlib openbabel mesa libX11 ]; - nativeBuildInputs = [ cmake pkgconfig ]; + nativeBuildInputs = [ cmake pkgconfig doxygen ]; NIX_CFLAGS_COMPILE = "-include ${mesa}/include/GL/glu.h"; diff --git a/pkgs/applications/science/electronics/archimedes/default.nix b/pkgs/applications/science/electronics/archimedes/default.nix index f22ef09a9839..a6a5f68755a4 100644 --- a/pkgs/applications/science/electronics/archimedes/default.nix +++ b/pkgs/applications/science/electronics/archimedes/default.nix @@ -1,17 +1,17 @@ {stdenv, fetchurl}: stdenv.mkDerivation rec { - name = "archimedes-2.0.0"; + name = "archimedes-2.0.1"; src = fetchurl { url = "mirror://gnu/archimedes/${name}.tar.gz"; - sha256 = "1ajg4xvk5slv05fsbikrina9g4bmhx8gykk249yz21pir67sdk4x"; + sha256 = "0jfpnd3pns5wxcxbiw49v5sgpmm5b4v8s4q1a5292hxxk2hzmb3z"; }; meta = { description = "GNU package for semiconductor device simulations"; homepage = http://www.gnu.org/software/archimedes; - license = "GPLv2+"; + license = stdenv.lib.licenses.gpl2Plus; platforms = with stdenv.lib.platforms; linux; }; } diff --git a/pkgs/applications/science/electronics/caneda/default.nix b/pkgs/applications/science/electronics/caneda/default.nix index d135fb094345..404ffc5010b4 100644 --- a/pkgs/applications/science/electronics/caneda/default.nix +++ b/pkgs/applications/science/electronics/caneda/default.nix @@ -32,7 +32,7 @@ stdenv.mkDerivation rec { meta = { description = "Open source EDA software focused on easy of use and portability"; homepage = http://caneda.tuxfamily.org; - license = "GPLv2+"; + license = stdenv.lib.licenses.gpl2Plus; maintainers = with stdenv.lib.maintainers; [viric]; platforms = with stdenv.lib.platforms; linux; }; diff --git a/pkgs/applications/science/electronics/gtkwave/default.nix b/pkgs/applications/science/electronics/gtkwave/default.nix index bb4b969f0621..c761f6196424 100644 --- a/pkgs/applications/science/electronics/gtkwave/default.nix +++ b/pkgs/applications/science/electronics/gtkwave/default.nix @@ -1,10 +1,10 @@ {stdenv, fetchurl, gtk, gperf, pkgconfig, bzip2, tcl, tk, judy, xz}: stdenv.mkDerivation rec { - name = "gtkwave-3.3.39"; + name = "gtkwave-3.3.53"; src = fetchurl { url = "mirror://sourceforge/gtkwave/${name}.tar.gz"; - sha256 = "1va506anlbpbha7l6h94s44xjdy6ch22iv629swn4bh5m3qi33bg"; + sha256 = "1jmrk2p2azjca250h2bi4c8v0cp1gqd3c027dx18sxy3cgw1fsp1"; }; buildInputs = [ gtk gperf pkgconfig bzip2 tcl tk judy xz ]; @@ -14,7 +14,7 @@ stdenv.mkDerivation rec { meta = { description = "Wave viewer for Unix and Win32"; homepage = http://gtkwave.sourceforge.net; - license = "GPLv2+"; + license = stdenv.lib.licenses.gpl2Plus; maintainers = with stdenv.lib.maintainers; [viric]; platforms = with stdenv.lib.platforms; linux; }; diff --git a/pkgs/applications/science/electronics/kicad/default.nix b/pkgs/applications/science/electronics/kicad/default.nix index cc53611493d0..1fc97abef927 100644 --- a/pkgs/applications/science/electronics/kicad/default.nix +++ b/pkgs/applications/science/electronics/kicad/default.nix @@ -1,21 +1,21 @@ -{ stdenv, fetchurl, fetchbzr, unzip, cmake, mesa, gtk, wxGTK, zlib, libX11, -gettext, cups } : +{ stdenv, fetchurl, fetchbzr, cmake, mesa, wxGTK, zlib, libX11, gettext }: stdenv.mkDerivation rec { - name = "kicad-20130325"; + name = "kicad-20131025"; - src = fetchurl { - url = "http://iut-tice.ujf-grenoble.fr/cao/kicad-sources-stable_2013-03-25_BZR4005.zip"; - sha256 = "0hg2aiis14am7mmpimcxnxvhy7c7fr5rgzlk6rjv44d9m0f9957m"; + src = fetchbzr { + url = "https://code.launchpad.net/~kicad-stable-committers/kicad/stable"; + rev = 4024; + sha256 = "1sv1l2zpbn6439ccz50p05hvqg6j551aqra551wck9h3929ghly5"; }; srcLibrary = fetchbzr { url = "http://bazaar.launchpad.net/~kicad-lib-committers/kicad/library"; - revision = 220; - sha256 = "0l2lblgnm51n2w1p4ifpwdvq04rxgq73zrfxlhqa9zdlyh4rcddb"; + rev = 293; + sha256 = "1wn9a4nhqyjzzfkq6xm7ag8n5n10xy7gkq6i7yry7wxini7pzv1i"; }; - cmakeFlags = "-DKICAD_TESTING_VERSION=ON"; + cmakeFlags = "-DKICAD_STABLE_VERSION=ON"; # They say they only support installs to /usr or /usr/local, # so we have to handle this. @@ -23,9 +23,9 @@ stdenv.mkDerivation rec { sed -i -e 's,/usr/local/kicad,'$out,g common/gestfich.cpp ''; - enableParallelBuilding = true; + #enableParallelBuilding = true; # often fails on Hydra: fatal error: pcb_plot_params_lexer.h: No such file or directory - buildInputs = [ unzip cmake mesa wxGTK zlib libX11 gettext ]; + buildInputs = [ cmake mesa wxGTK zlib libX11 gettext ]; postInstall = '' mkdir library @@ -37,7 +37,7 @@ stdenv.mkDerivation rec { meta = { description = "Free Software EDA Suite"; homepage = "http://www.kicad-pcb.org/"; - license = "GPLv2"; + license = stdenv.lib.licenses.gpl2; maintainers = with stdenv.lib.maintainers; [viric]; platforms = with stdenv.lib.platforms; linux; }; diff --git a/pkgs/applications/science/electronics/ngspice/default.nix b/pkgs/applications/science/electronics/ngspice/default.nix index 579492248ea3..493af97d1567 100644 --- a/pkgs/applications/science/electronics/ngspice/default.nix +++ b/pkgs/applications/science/electronics/ngspice/default.nix @@ -1,11 +1,11 @@ {stdenv, fetchurl, readline, bison, libX11, libICE, libXaw, libXext}: stdenv.mkDerivation { - name = "ng-spice-rework-24"; + name = "ng-spice-rework-25"; src = fetchurl { - url = "mirror://sourceforge/ngspice/ngspice-24.tar.gz"; - sha256 = "0rgh75hbqrsljz767whbj65wi6369yc286v0qk8jxnv2da7p9ll6"; + url = "mirror://sourceforge/ngspice/ngspice-25.tar.gz"; + sha256 = "03hlxwvl2j1wlb5yg4swvmph9gja37c2gqvwvzv6z16vg2wvn06h"; }; buildInputs = [ readline libX11 bison libICE libXaw libXext ]; diff --git a/pkgs/applications/science/electronics/pulseview/default.nix b/pkgs/applications/science/electronics/pulseview/default.nix new file mode 100644 index 000000000000..07724d932541 --- /dev/null +++ b/pkgs/applications/science/electronics/pulseview/default.nix @@ -0,0 +1,24 @@ +{ stdenv, fetchurl, pkgconfig, cmake, glib, qt4, boost, libsigrok +, libsigrokdecode, libserialport, libzip, udev, libusb1, libftdi +}: + +stdenv.mkDerivation rec { + name = "pulseview-0.2.0"; + + src = fetchurl { + url = "http://sigrok.org/download/source/pulseview/${name}.tar.gz"; + sha256 = "1pf1dgwd9j586nqmni6gqf3qxrsmawcmi9wzqfzqkjci18xd7dgy"; + }; + + buildInputs = [ pkgconfig cmake glib qt4 boost libsigrok + libsigrokdecode libserialport libzip udev libusb1 libftdi + ]; + + meta = with stdenv.lib; { + description = "Qt-based LA/scope/MSO GUI for sigrok (a signal analysis software suite)"; + homepage = http://sigrok.org/; + license = licenses.gpl3Plus; + platforms = platforms.linux; + maintainers = [ maintainers.bjornfor ]; + }; +} diff --git a/pkgs/applications/science/electronics/qfsm/default.nix b/pkgs/applications/science/electronics/qfsm/default.nix index 0f24784e9e57..160c530e722e 100644 --- a/pkgs/applications/science/electronics/qfsm/default.nix +++ b/pkgs/applications/science/electronics/qfsm/default.nix @@ -18,7 +18,6 @@ stdenv.mkDerivation rec { description = "Graphical editor for finite state machines"; homepage = "http://qfsm.sourceforge.net/"; license = stdenv.lib.licenses.gpl3Plus; - maintainers = [ stdenv.lib.maintainers.simons ]; - platforms = stdenv.lib.platforms.linux; + broken = true; }; } diff --git a/pkgs/applications/science/electronics/qucs/default.nix b/pkgs/applications/science/electronics/qucs/default.nix index e434c97db2b0..dd3eaecc7441 100644 --- a/pkgs/applications/science/electronics/qucs/default.nix +++ b/pkgs/applications/science/electronics/qucs/default.nix @@ -16,7 +16,7 @@ stdenv.mkDerivation rec { meta = { description = "Integrated circuit simulator"; homepage = http://qucs.sourceforge.net; - license = "GPLv2+"; + license = stdenv.lib.licenses.gpl2Plus; maintainers = with stdenv.lib.maintainers; [viric]; platforms = with stdenv.lib.platforms; linux; }; diff --git a/pkgs/applications/science/electronics/tkgate/1.x.nix b/pkgs/applications/science/electronics/tkgate/1.x.nix index 7c04c85fdb7e..30e882a7f38e 100644 --- a/pkgs/applications/science/electronics/tkgate/1.x.nix +++ b/pkgs/applications/science/electronics/tkgate/1.x.nix @@ -1,7 +1,9 @@ -{ stdenv, fetchurl, tcl, tk, libX11, libiconvOrLibc, which, yacc, flex, imake, xproto, gccmakedep }: - -assert stdenv.system == "i686-linux" || stdenv.system == "x86_64-linux"; +{ stdenv, fetchurl, tcl, tk, libX11, glibc, which, yacc, flex, imake, xproto, gccmakedep }: +let + libiconvInc = stdenv.lib.optionalString stdenv.isLinux "${glibc}/include"; + libiconvLib = stdenv.lib.optionalString stdenv.isLinux "${glibc}/lib"; +in stdenv.mkDerivation rec { name = "tkgate-1.8.7"; @@ -10,13 +12,13 @@ stdenv.mkDerivation rec { sha256 = "1pqywkidfpdbj18i03h97f4cimld4fb3mqfy8jjsxs12kihm18fs"; }; - buildInputs = [ tcl tk libX11 libiconvOrLibc which yacc flex imake xproto gccmakedep ]; + buildInputs = [ tcl tk libX11 which yacc flex imake xproto gccmakedep ]; patchPhase = '' sed -i config.h \ -e 's|.*#define.*TKGATE_TCLTK_VERSIONS.*|#define TKGATE_TCLTK_VERSIONS "8.5"|' \ - -e 's|.*#define.*TKGATE_INCDIRS.*|#define TKGATE_INCDIRS "${tcl}/include ${tk}/include ${libiconvOrLibc}/include ${libX11}/include"|' \ - -e 's|.*#define.*TKGATE_LIBDIRS.*|#define TKGATE_LIBDIRS "${tcl}/lib ${tk}/lib ${libiconvOrLibc}/lib ${libX11}/lib"|' \ + -e 's|.*#define.*TKGATE_INCDIRS.*|#define TKGATE_INCDIRS "${tcl}/include ${tk}/include ${libiconvInc} ${libX11}/include"|' \ + -e 's|.*#define.*TKGATE_LIBDIRS.*|#define TKGATE_LIBDIRS "${tcl}/lib ${tk}/lib ${libiconvLib} ${libX11}/lib"|' \ \ -e '20 i #define TCL_LIBRARY "${tcl}/lib"' \ -e '20 i #define TK_LIBRARY "${tk}/lib/${tk.libPrefix}"' \ @@ -31,8 +33,8 @@ stdenv.mkDerivation rec { meta = { description = "Event driven digital circuit simulator with a TCL/TK-based graphical editor"; homepage = "http://www.tkgate.org/"; - license = "GPLv2+"; + license = stdenv.lib.licenses.gpl2Plus; maintainers = [ stdenv.lib.maintainers.simons ]; - platforms = stdenv.lib.platforms.linux; + hydraPlatforms = stdenv.lib.platforms.linux; }; } diff --git a/pkgs/applications/science/electronics/tkgate/2.x.nix b/pkgs/applications/science/electronics/tkgate/2.x.nix index 756fe7052d83..108986ddefe4 100644 --- a/pkgs/applications/science/electronics/tkgate/2.x.nix +++ b/pkgs/applications/science/electronics/tkgate/2.x.nix @@ -1,7 +1,9 @@ -{ stdenv, fetchurl, tcl, tk, libX11, libiconvOrLibc }: - -assert stdenv.system == "i686-linux" || stdenv.system == "x86_64-linux"; +{ stdenv, fetchurl, tcl, tk, libX11, glibc }: +let + libiconvInc = stdenv.lib.optionalString stdenv.isLinux "${glibc}/include"; + libiconvLib = stdenv.lib.optionalString stdenv.isLinux "${glibc}/lib"; +in stdenv.mkDerivation rec { name = "tkgate-2.0-b10"; @@ -16,8 +18,8 @@ stdenv.mkDerivation rec { patchPhase = '' sed -i configure \ - -e 's|TKGATE_INCDIRS=.*|TKGATE_INCDIRS="${tcl}/include ${tk}/include ${libiconvOrLibc}/include"|' \ - -e 's|TKGATE_LIBDIRS=.*|TKGATE_LIBDIRS="${tcl}/lib ${tk}/lib ${libiconvOrLibc}/lib"|' + -e 's|TKGATE_INCDIRS=.*|TKGATE_INCDIRS="${tcl}/include ${tk}/include ${libiconvInc}"|' \ + -e 's|TKGATE_LIBDIRS=.*|TKGATE_LIBDIRS="${tcl}/lib ${tk}/lib ${libiconvLib}"|' sed -i options.h \ -e 's|.* #define TCL_LIBRARY .*|#define TCL_LIBRARY "${tcl}/${tcl.libdir}"|' \ -e 's|.* #define TK_LIBRARY .*|#define TK_LIBRARY "${tk}/lib/${tk.libPrefix}"|' @@ -26,8 +28,7 @@ stdenv.mkDerivation rec { meta = { description = "Event driven digital circuit simulator with a TCL/TK-based graphical editor"; homepage = "http://www.tkgate.org/"; - license = "GPLv2+"; - maintainers = [ stdenv.lib.maintainers.simons ]; - platforms = stdenv.lib.platforms.linux; + license = stdenv.lib.licenses.gpl2Plus; + broken = true; }; } diff --git a/pkgs/applications/science/electronics/verilog/default.nix b/pkgs/applications/science/electronics/verilog/default.nix index a4c803e2952c..e68d2a4ab91a 100644 --- a/pkgs/applications/science/electronics/verilog/default.nix +++ b/pkgs/applications/science/electronics/verilog/default.nix @@ -1,19 +1,20 @@ {stdenv, fetchurl, gperf, flex, bison}: stdenv.mkDerivation rec { - name = "verilog-0.9.3"; + name = "verilog-0.9.7"; src = fetchurl { url = "mirror://sourceforge/iverilog/${name}.tar.gz"; - sha256 = "dd68c8ab874a93805d1e93fa76ee1e91fc0c7b20822ded3e57b6536cd8c0d1ba"; + sha256 = "0m3liqw7kq24vn7k8wvi630ljz0awz23r3sd4rcklk7vgghp4pks"; }; buildInputs = [ gperf flex bison ]; meta = { description = "Icarus Verilog compiler"; + repositories.git = https://github.com/steveicarus/iverilog.git; homepage = http://www.icarus.com; - license = "GPLv2+"; + license = stdenv.lib.licenses.gpl2Plus; maintainers = with stdenv.lib.maintainers; [winden]; platforms = with stdenv.lib.platforms; linux; }; diff --git a/pkgs/applications/science/electronics/xoscope/default.nix b/pkgs/applications/science/electronics/xoscope/default.nix index 54aae9e7d3bf..df7d053d93bd 100644 --- a/pkgs/applications/science/electronics/xoscope/default.nix +++ b/pkgs/applications/science/electronics/xoscope/default.nix @@ -16,7 +16,7 @@ stdenv.mkDerivation rec { meta = { description = "Oscilloscope through the sound card"; homepage = http://xoscope.sourceforge.net; - license = "GPLv2+"; + license = stdenv.lib.licenses.gpl2Plus; maintainers = with stdenv.lib.maintainers; [viric]; platforms = with stdenv.lib.platforms; linux; }; diff --git a/pkgs/applications/science/geometry/tetgen/default.nix b/pkgs/applications/science/geometry/tetgen/default.nix index a43ec3b0eb9f..ddfb92def958 100644 --- a/pkgs/applications/science/geometry/tetgen/default.nix +++ b/pkgs/applications/science/geometry/tetgen/default.nix @@ -4,8 +4,8 @@ stdenv.mkDerivation rec { name = "tetgen-1.4.3"; src = fetchurl { - url = http://tetgen.berlios.de/files/tetgen1.4.3.tar.gz; - sha256 = "159i0vdjz7abb8bycz47ax4fqlzc82kv19sygqnrkr86qm4g43wy"; + url = "${meta.homepage}/files/tetgen1.4.3.tar.gz"; + sha256 = "0d70vjqdapmy1ghlsxjlvl5z9yp310zw697bapc4zxmp0sxi29wm"; }; installPhase = '' @@ -15,7 +15,7 @@ stdenv.mkDerivation rec { meta = { description = "Quality Tetrahedral Mesh Generator and 3D Delaunay Triangulator"; - homepage = "http://tetgen.berlios.de/"; - license = "MIT"; + homepage = "http://tetgen.org/"; + license = stdenv.lib.licenses.mit; }; } diff --git a/pkgs/applications/science/logic/abc/default.nix b/pkgs/applications/science/logic/abc/default.nix new file mode 100644 index 000000000000..30c36ae29dc8 --- /dev/null +++ b/pkgs/applications/science/logic/abc/default.nix @@ -0,0 +1,27 @@ +{ fetchhg, stdenv, readline }: + +stdenv.mkDerivation rec { + name = "abc-verifier-${version}"; + version = "140509"; # YYMMDD + + src = fetchhg { + url = "https://bitbucket.org/alanmi/abc"; + rev = "03e221443d71e49e56cbc37f1907ee3b0ff3e7c9"; + sha256 = "0ahrqg718y7xpv939f6x8w1kqh7wsja4pw8hca7j67j0qjdgb4lm"; + }; + + buildInputs = [ readline ]; + enableParallelBuilding = true; + installPhase = '' + mkdir -p $out/bin + mv abc $out/bin + ''; + + meta = { + description = "Sequential Logic Synthesis and Formal Verification"; + homepage = "www.eecs.berkeley.edu/~alanmi/abc/abc.htm"; + license = stdenv.lib.licenses.mit; + platforms = stdenv.lib.platforms.unix; + maintainers = [ stdenv.lib.maintainers.thoughtpolice ]; + }; +} diff --git a/pkgs/applications/science/logic/alt-ergo/default.nix b/pkgs/applications/science/logic/alt-ergo/default.nix new file mode 100644 index 000000000000..2a95d0cd65bb --- /dev/null +++ b/pkgs/applications/science/logic/alt-ergo/default.nix @@ -0,0 +1,23 @@ +{ fetchurl, stdenv, ocaml, ocamlPackages, gmp }: + +stdenv.mkDerivation rec { + name = "alt-ergo-${version}"; + version = "0.95.2"; + + src = fetchurl { + url = "http://alt-ergo.ocamlpro.com/download_manager.php?target=${name}.tar.gz"; + name = "${name}.tar.gz"; + sha256 = "1b7f0rh3jgm67g0x2m3wv7gnnqmz9cjlrfm136z56ihlkhsd8v2s"; + }; + + buildInputs = with ocamlPackages; + [ ocaml findlib ocamlgraph zarith lablgtk gmp ]; + + meta = { + description = "Alt-Ergo is a high-performance theorem prover and SMT solver"; + homepage = "http://alt-ergo.ocamlpro.com/"; + license = stdenv.lib.licenses.cecill-c; # LGPL-2 compatible + platforms = stdenv.lib.platforms.linux; + maintainers = [ stdenv.lib.maintainers.thoughtpolice ]; + }; +} diff --git a/pkgs/applications/science/logic/boolector/default.nix b/pkgs/applications/science/logic/boolector/default.nix new file mode 100644 index 000000000000..3879ee8ef470 --- /dev/null +++ b/pkgs/applications/science/logic/boolector/default.nix @@ -0,0 +1,47 @@ +{ stdenv, fetchurl, zlib, useV16 ? false }: + +let + v15 = rec { + name = "boolector-${version}"; + version = "1.5.118"; + src = fetchurl { + url = "http://fmv.jku.at/boolector/${name}-with-sat-solvers.tar.gz"; + sha256 = "17j7q02rryvfwgvglxnhx0kv8hxwy8wbhzawn48lw05i98vxlmk9"; + }; + }; + + v16 = rec { + name = "boolector-${version}"; + version = "1.6.0"; + src = fetchurl { + url = "http://fmv.jku.at/boolector/${name}-with-sat-solvers.tar.gz"; + sha256 = "0jka4r6bc3i24axgdp6qbq6gjadwz9kvi11s2c5sbwmdnjd7cp85"; + }; + }; + + boolectorPkg = if useV16 then v16 else v15; + license = with stdenv.lib.licenses; if useV16 then unfreeRedistributable else gpl3; +in +stdenv.mkDerivation (boolectorPkg // { + buildInputs = [ zlib ]; + enableParallelBuilding = false; + + buildPhase = "./build.sh"; + + installPhase = '' + mkdir -p $out/bin $out/lib $out/include + cp boolector/boolector $out/bin + cp boolector/deltabtor $out/bin + cp boolector/synthebtor $out/bin + cp boolector/libboolector.a $out/lib + cp boolector/boolector.h $out/include + ''; + + meta = { + inherit license; + description = "An extremely fast SMT solver for bit-vectors and arrays"; + homepage = "http://fmv.jku.at/boolector"; + platforms = stdenv.lib.platforms.linux; + maintainers = [ stdenv.lib.maintainers.thoughtpolice ]; + }; +}) diff --git a/pkgs/applications/science/logic/coq/HEAD.nix b/pkgs/applications/science/logic/coq/HEAD.nix new file mode 100644 index 000000000000..8e6fde6bc240 --- /dev/null +++ b/pkgs/applications/science/logic/coq/HEAD.nix @@ -0,0 +1,57 @@ +# - coqide compilation can be disabled by setting lablgtk to null; + +{stdenv, fetchgit, pkgconfig, ocaml, findlib, camlp5, ncurses, lablgtk ? null}: + +let + version = "8.5pre-8bc01590"; + buildIde = lablgtk != null; + ideFlags = if buildIde then "-lablgtkdir ${lablgtk}/lib/ocaml/*/site-lib/lablgtk2 -coqide opt" else ""; + idePath = if buildIde then '' + CAML_LD_LIBRARY_PATH=${lablgtk}/lib/ocaml/3.12.1/site-lib/stublibs + '' else ""; +in + +stdenv.mkDerivation { + name = "coq-${version}"; + + src = fetchgit { + url = git://scm.gforge.inria.fr/coq/coq.git; + rev = "8bc0159095cb0230a50c55a1611c8b77134a6060"; + sha256 = "1cp4hbk9jw78y03vwz099yvixax161h60hsbyvwiwz2z5czjxzcv"; + }; + + buildInputs = [ pkgconfig ocaml findlib camlp5 ncurses lablgtk ]; + + postPatch = '' + UNAME=$(type -tp uname) + RM=$(type -tp rm) + substituteInPlace configure --replace "/bin/uname" "$UNAME" + substituteInPlace tools/beautify-archive --replace "/bin/rm" "$RM" + ''; + + preConfigure = '' + buildFlagsArray=(${idePath}) + configureFlagsArray=( + -opt + ${ideFlags} + ) + ''; + + prefixKey = "-prefix "; + + buildFlags = "revision coq coqide"; + + meta = { + description = "Coq proof assistant"; + longDescription = '' + Coq is a formal proof management system. It provides a formal language + to write mathematical definitions, executable algorithms and theorems + together with an environment for semi-interactive development of + machine-checked proofs. + ''; + homepage = "http://coq.inria.fr"; + license = "LGPL"; + maintainers = with stdenv.lib.maintainers; [ roconnor thoughtpolice ]; + platforms = stdenv.lib.platforms.unix; + }; +} diff --git a/pkgs/applications/science/logic/coq/default.nix b/pkgs/applications/science/logic/coq/default.nix index b4a7a203a3c4..678ec6a4b049 100644 --- a/pkgs/applications/science/logic/coq/default.nix +++ b/pkgs/applications/science/logic/coq/default.nix @@ -3,7 +3,7 @@ {stdenv, fetchurl, pkgconfig, ocaml, findlib, camlp5, ncurses, lablgtk ? null}: let - version = "8.4pl2"; + version = "8.4pl4"; buildIde = lablgtk != null; ideFlags = if buildIde then "-lablgtkdir ${lablgtk}/lib/ocaml/*/site-lib/lablgtk2 -coqide opt" else ""; idePath = if buildIde then '' @@ -16,7 +16,7 @@ stdenv.mkDerivation { src = fetchurl { url = "http://coq.inria.fr/distrib/V${version}/files/coq-${version}.tar.gz"; - sha256 = "1n52pky7bb45irk2jw6f4rd3kvy8lm2yfldjwdhiic0kyqw9lwgv"; + sha256 = "00bzf4kfbd0g279jrr8ynzvb9wqcly3wi577bkrxivhrg2msxhq6"; }; buildInputs = [ pkgconfig ocaml findlib camlp5 ncurses lablgtk ]; @@ -54,7 +54,7 @@ stdenv.mkDerivation { ''; homepage = "http://coq.inria.fr"; license = "LGPL"; - maintainers = [ stdenv.lib.maintainers.roconnor ]; - platforms = stdenv.lib.platforms.linux; + maintainers = with stdenv.lib.maintainers; [ roconnor thoughtpolice ]; + platforms = stdenv.lib.platforms.unix; }; } diff --git a/pkgs/applications/science/logic/cvc3/default.nix b/pkgs/applications/science/logic/cvc3/default.nix index 9bb8f8cde4ca..07b87e3cf073 100644 --- a/pkgs/applications/science/logic/cvc3/default.nix +++ b/pkgs/applications/science/logic/cvc3/default.nix @@ -12,10 +12,10 @@ let ++ [(a.lib.overrideDerivation x.gmp (y: {dontDisableStatic=true;}))]; sourceInfo = rec { baseName="cvc3"; - version="2.2"; + version="2.4.1"; name="${baseName}-${version}"; url="http://www.cs.nyu.edu/acsys/cvc3/releases/${version}/${name}.tar.gz"; - hash="1dw12d5vrixfr6l9j6j7026vrr22zb433xyl6n5yxx4hgfywi0ji"; + hash="1xxcwhz3y6djrycw8sm6xz83wb4hb12rd1n0skvc7fng0rh1snym"; }; in rec { diff --git a/pkgs/applications/science/logic/ekrhyper/default.nix b/pkgs/applications/science/logic/ekrhyper/default.nix index c90099f495a2..e1eb9a2dcc3b 100644 --- a/pkgs/applications/science/logic/ekrhyper/default.nix +++ b/pkgs/applications/science/logic/ekrhyper/default.nix @@ -3,11 +3,11 @@ let s = # Generated upstream information rec { baseName="ekrhyper"; - version="1_4_30072013"; + version="1_4_21022014"; name="${baseName}-${version}"; - hash="0ashsblm477r7dmq9f33wajkbr29rbyyc919mifdgrrdy6zlc663"; - url="http://userpages.uni-koblenz.de/~bpelzer/ekrhyper/ekrh_1_4_30072013.tar.gz"; - sha256="0ashsblm477r7dmq9f33wajkbr29rbyyc919mifdgrrdy6zlc663"; + hash="14xaaxyvfli1nd4vd9fp4j1s8k76z2bhazxzzc7br3q6hc6b8ivw"; + url="http://userpages.uni-koblenz.de/~bpelzer/ekrhyper/ekrh_1_4_21022014.tar.gz"; + sha256="14xaaxyvfli1nd4vd9fp4j1s8k76z2bhazxzzc7br3q6hc6b8ivw"; }; buildInputs = [ ocaml perl diff --git a/pkgs/applications/science/logic/hol/default.nix b/pkgs/applications/science/logic/hol/default.nix index 2e1647b6c71d..dc8e975ce1d1 100644 --- a/pkgs/applications/science/logic/hol/default.nix +++ b/pkgs/applications/science/logic/hol/default.nix @@ -46,11 +46,11 @@ stdenv.mkDerivation { #sed -ie "/compute/,999 d" tools/build-sequence # for testing poly < tools/smart-configure.sml - + bin/build ${kernelFlag} -symlink mkdir -p "$out/bin" - ln -st $out/bin "$out/src/${holsubdir}/bin/"* + ln -st $out/bin $out/src/${holsubdir}/bin/* # ln -s $out/src/hol4.${version}/bin $out/bin ''; diff --git a/pkgs/applications/science/logic/hol_light/default.nix b/pkgs/applications/science/logic/hol_light/default.nix index d6c1c0c18781..3e6440ea9773 100644 --- a/pkgs/applications/science/logic/hol_light/default.nix +++ b/pkgs/applications/science/logic/hol_light/default.nix @@ -1,19 +1,20 @@ -{stdenv, fetchsvn, writeScript, ocaml, findlib, camlp5}: +{ stdenv, fetchsvn, writeScript, ocaml, findlib, camlp5 }: let start_script = '' #!/bin/sh cd "$out/lib/hol_light" - exec ${ocaml}/bin/ocaml -I "camlp5 -where" -init make.ml + exec ${ocaml}/bin/ocaml -I \`${camlp5}/bin/camlp5 -where\` -init make.ml ''; in +stdenv.mkDerivation rec { + name = "hol_light-${version}"; + version = "189"; -stdenv.mkDerivation { - name = "hol_light-20130324"; src = fetchsvn { url = http://hol-light.googlecode.com/svn/trunk; - rev = "157"; - sha256 = "0d0pbnkw2gb11dn30ggfl91lhdxv86kd1fyiqn170w08n0gi805f"; + rev = version; + sha256 = "1v10l64rs7da2kag3wlb651i09pn83icy9n5z84j8h1iwlxzajdh"; }; buildInputs = [ ocaml findlib camlp5 ]; @@ -27,16 +28,9 @@ stdenv.mkDerivation { meta = { description = "Interactive theorem prover based on Higher-Order Logic"; - longDescription = '' - HOL Light is a computer program to help users prove interesting - mathematical theorems completely formally in Higher-Order Logic. It sets - a very exacting standard of correctness, but provides a number of - automated tools and pre-proved mathematical theorems (e.g., about - arithmetic, basic set theory and real analysis) to save the user work. - It is also fully programmable, so users can extend it with new theorems - and inference rules without compromising its soundness. - ''; - homepage = http://www.cl.cam.ac.uk/~jrh13/hol-light/; - license = stdenv.lib.licenses.bsd2; + homepage = http://www.cl.cam.ac.uk/~jrh13/hol-light/; + license = stdenv.lib.licenses.bsd2; + platforms = stdenv.lib.platforms.unix; + maintainers = [ stdenv.lib.maintainers.thoughtpolice ]; }; } diff --git a/pkgs/applications/science/logic/iprover/default.nix b/pkgs/applications/science/logic/iprover/default.nix index 2fb9678b8329..e03b33fa43cc 100644 --- a/pkgs/applications/science/logic/iprover/default.nix +++ b/pkgs/applications/science/logic/iprover/default.nix @@ -2,9 +2,9 @@ x@{builderDefsPackage , ocaml, eprover , ...}: builderDefsPackage -(a : -let - helperArgNames = ["stdenv" "fetchurl" "builderDefsPackage"] ++ +(a : +let + helperArgNames = ["stdenv" "fetchurl" "builderDefsPackage"] ++ []; buildInputs = map (n: builtins.getAttr n x) @@ -38,7 +38,7 @@ rec { echo -e "#! /bin/sh\\n$out/bin/iproveropt --clausifier \"${eprover}/bin/eprover\" --clausifier_options \" --tstp-format --silent --cnf \" \"\$@\"" > "$out"/bin/iprover chmod a+x "$out"/bin/iprover '') ["defEnsureDir" "minInit" "doMake"]; - + meta = { description = "An automated first-order logic theorem prover"; maintainers = with a.lib.maintainers; @@ -47,7 +47,8 @@ rec { ]; platforms = with a.lib.platforms; linux; - license = "GPLv3"; + license = with a.lib.licenses; + gpl3; }; passthru = { updateInfo = { @@ -55,4 +56,3 @@ rec { }; }; }) x - diff --git a/pkgs/applications/science/logic/leo2/default.nix b/pkgs/applications/science/logic/leo2/default.nix index 913171827af1..8f673eb0f15a 100644 --- a/pkgs/applications/science/logic/leo2/default.nix +++ b/pkgs/applications/science/logic/leo2/default.nix @@ -1,5 +1,5 @@ x@{builderDefsPackage - , ocaml, eprover + , ocaml, eprover, zlib , ...}: builderDefsPackage (a : @@ -11,16 +11,16 @@ let (builtins.attrNames (builtins.removeAttrs x helperArgNames)); sourceInfo = rec { baseName="leo2"; - version="1.2.8"; + version = "1.6.2"; name="${baseName}_v${version}"; - url="http://www.ags.uni-sb.de/~leo/${name}.tgz"; - hash="d46a94f5991623386eb9061cfb0d748e258359a8c690fded173d45303e0e9e3a"; + url="page.mi.fu-berlin.de/cbenzmueller/leo/leo2_v${version}.tgz"; + hash="d46a94f5991623386eb9061cfb0d748e258359a8c690fded173d35303e0e9e3a"; }; in rec { src = a.fetchurl { url = sourceInfo.url; - sha256 = sourceInfo.hash; + sha256 = "1wjpmizb181iygnd18lx7p77fwaci2clgzs5ix5j51cc8f3pazmv"; }; name = "${sourceInfo.baseName}-${sourceInfo.version}"; @@ -43,6 +43,10 @@ rec { echo -e "e = ${eprover}/bin/eprover\\nepclextract = ${eprover}/bin/epclextract" > "$out/etc/leoatprc" '') ["minInit" "doMake" "defEnsureDir"]; + makeFlags = [ + "SHELL=${a.stdenv.shell}" + ]; + meta = { description = "A high-performance typed higher order prover"; maintainers = with a.lib.maintainers; @@ -52,11 +56,9 @@ rec { platforms = with a.lib.platforms; linux; license = "BSD"; - }; - passthru = { - updateInfo = { - downloadPage = "http://www.ags.uni-sb.de/~leo/download.html"; - }; + inherit (sourceInfo) version; + homepage = "http://page.mi.fu-berlin.de/cbenzmueller/leo/"; + downloadPage = "http://page.mi.fu-berlin.de/cbenzmueller/leo/download.html"; }; }) x diff --git a/pkgs/applications/science/logic/leo2/default.upstream b/pkgs/applications/science/logic/leo2/default.upstream new file mode 100644 index 000000000000..52b8ed1cdaa2 --- /dev/null +++ b/pkgs/applications/science/logic/leo2/default.upstream @@ -0,0 +1,6 @@ +url http://page.mi.fu-berlin.de/cbenzmueller/leo/download.html +version_link '[.]tgz' +version '.*_v([0-9.]+)[.][a-z0-9]+$' '\1' +do_overwrite () { + do_overwrite_just_version +} diff --git a/pkgs/applications/science/logic/logisim/default.nix b/pkgs/applications/science/logic/logisim/default.nix index ab46efa9a961..c71ed73a9925 100644 --- a/pkgs/applications/science/logic/logisim/default.nix +++ b/pkgs/applications/science/logic/logisim/default.nix @@ -27,6 +27,6 @@ stdenv.mkDerivation { meta = { homepage = "http://ozark.hendrix.edu/~burch/logisim"; description = "Educational tool for designing and simulating digital logic circuits"; - license = "GPLv2+"; + license = stdenv.lib.licenses.gpl2Plus; }; } diff --git a/pkgs/applications/science/logic/ltl2ba/default.nix b/pkgs/applications/science/logic/ltl2ba/default.nix new file mode 100644 index 000000000000..cdadd18ac9f5 --- /dev/null +++ b/pkgs/applications/science/logic/ltl2ba/default.nix @@ -0,0 +1,24 @@ +{ fetchurl, stdenv }: + +stdenv.mkDerivation rec { + name = "ltl2ba-${version}"; + version = "1.1"; + + src = fetchurl { + url = "http://www.lsv.ens-cachan.fr/~gastin/ltl2ba/${name}.tar.gz"; + sha256 = "16z0gc7a9dkarwn0l6rvg5jdhw1q4qyn4501zlchy0zxqddz0sx6"; + }; + + installPhase = '' + mkdir -p $out/bin + mv ltl2ba $out/bin + ''; + + meta = { + description = "fast translation from LTL formulae to Buchi automata"; + homepage = "http://www.lsv.ens-cachan.fr/~gastin/ltl2ba"; + license = stdenv.lib.licenses.gpl2Plus; + platforms = stdenv.lib.platforms.linux; + maintainers = [ stdenv.lib.maintainers.thoughtpolice ]; + }; +} diff --git a/pkgs/applications/science/logic/matita/130312.nix b/pkgs/applications/science/logic/matita/130312.nix index f77e9d34a2a8..9e98c8db3947 100644 --- a/pkgs/applications/science/logic/matita/130312.nix +++ b/pkgs/applications/science/logic/matita/130312.nix @@ -60,7 +60,7 @@ stdenv.mkDerivation { meta = { homepage = http://matita.cs.unibo.it/; description = "Matita is an experimental, interactive theorem prover"; - license = "GPLv2+"; + license = stdenv.lib.licenses.gpl2Plus; maintainers = [ stdenv.lib.maintainers.roconnor ]; }; } diff --git a/pkgs/applications/science/logic/matita/default.nix b/pkgs/applications/science/logic/matita/default.nix index 0713ff09e929..f601f97de62e 100644 --- a/pkgs/applications/science/logic/matita/default.nix +++ b/pkgs/applications/science/logic/matita/default.nix @@ -48,7 +48,7 @@ stdenv.mkDerivation { meta = { homepage = http://matita.cs.unibo.it/; description = "Matita is an experimental, interactive theorem prover"; - license = "GPLv2+"; + license = stdenv.lib.licenses.gpl2Plus; maintainers = [ stdenv.lib.maintainers.roconnor ]; }; } diff --git a/pkgs/applications/science/logic/minisat/default.nix b/pkgs/applications/science/logic/minisat/default.nix index 1f29b3aa1a11..e91ff67fc9cc 100644 --- a/pkgs/applications/science/logic/minisat/default.nix +++ b/pkgs/applications/science/logic/minisat/default.nix @@ -2,9 +2,9 @@ x@{builderDefsPackage , zlib , ...}: builderDefsPackage -(a : -let - helperArgNames = ["stdenv" "fetchurl" "builderDefsPackage"] ++ +(a : +let + helperArgNames = ["stdenv" "fetchurl" "builderDefsPackage"] ++ []; buildInputs = map (n: builtins.getAttr n x) @@ -36,7 +36,7 @@ rec { setVars = a.fullDepEntry ('' export MROOT=$PWD/../ '') ["doUnpack"]; - + meta = { description = "A compact and readable SAT-solver"; maintainers = with a.lib.maintainers; @@ -45,7 +45,7 @@ rec { ]; platforms = with a.lib.platforms; linux; - license = "MIT"; + license = a.stdenv.lib.licenses.mit; homepage = "http://minisat.se/"; }; passthru = { @@ -54,4 +54,3 @@ rec { }; }; }) x - diff --git a/pkgs/applications/science/logic/opensmt/default.nix b/pkgs/applications/science/logic/opensmt/default.nix index 430537fd57ff..62e11651175f 100644 --- a/pkgs/applications/science/logic/opensmt/default.nix +++ b/pkgs/applications/science/logic/opensmt/default.nix @@ -3,9 +3,9 @@ x@{builderDefsPackage , gmpxx, flex, bison , ...}: builderDefsPackage -(a : -let - helperArgNames = ["stdenv" "fetchurl" "builderDefsPackage"] ++ +(a : +let + helperArgNames = ["stdenv" "fetchurl" "builderDefsPackage"] ++ []; buildInputs = map (n: builtins.getAttr n x) @@ -30,17 +30,14 @@ rec { /* doConfigure should be removed if not needed */ phaseNames = ["doAutotools" "doConfigure" "doMakeInstall"]; - + meta = { description = "A satisfiability modulo theory (SMT) solver"; - maintainers = with a.lib.maintainers; - [ - raskin - ]; - platforms = with a.lib.platforms; - linux; - license = "GPLv3"; + maintainers = [ a.lib.maintainers.raskin ]; + platforms = a.lib.platforms.linux; + license = a.stdenv.lib.licenses.gpl3; homepage = "http://code.google.com/p/opensmt/"; + broken = true; }; passthru = { updateInfo = { @@ -48,4 +45,3 @@ rec { }; }; }) x - diff --git a/pkgs/applications/science/logic/picosat/default.nix b/pkgs/applications/science/logic/picosat/default.nix index 970daf739fca..6c2cce0ea4b1 100644 --- a/pkgs/applications/science/logic/picosat/default.nix +++ b/pkgs/applications/science/logic/picosat/default.nix @@ -35,7 +35,7 @@ stdenv.mkDerivation rec { meta = { homepage = http://fmv.jku.at/picosat/; description = "SAT solver with proof and core support"; - license = "MIT"; + license = stdenv.lib.licenses.mit; maintainers = [ stdenv.lib.maintainers.roconnor ]; }; } diff --git a/pkgs/applications/science/logic/prooftree/default.nix b/pkgs/applications/science/logic/prooftree/default.nix new file mode 100644 index 000000000000..caaf4a94a1ed --- /dev/null +++ b/pkgs/applications/science/logic/prooftree/default.nix @@ -0,0 +1,40 @@ +{stdenv, fetchurl, pkgconfig, ocaml, findlib, camlp5, ncurses, lablgtk ? null}: + +stdenv.mkDerivation (rec { + name = "prooftree-${version}"; + version = "0.12"; + + src = fetchurl { + url = "http://askra.de/software/prooftree/releases/prooftree-${version}.tar.gz"; + sha256 = "08yp66j05pdkdpv9xkfqymqy82mir5xbwfh9mkzhh219xkps4b4m"; + }; + + buildInputs = [ pkgconfig ocaml findlib camlp5 ncurses lablgtk ]; + + dontAddPrefix = true; + configureFlags = [ "--prefix" "$(out)" ]; + + meta = { + description = "Prooftree is a program for proof-tree visualization"; + longDescription = '' + Prooftree is a program for proof-tree visualization during interactive + proof development in a theorem prover. It is currently being developed + for Coq and Proof General. Prooftree helps against getting lost between + different subgoals in interactive proof development. It clearly shows + where the current subgoal comes from and thus helps in developing the + right plan for solving it. + + Prooftree uses different colors for the already proven subgoals, the + current branch in the proof and the still open subgoals. Sequent texts + are not displayed in the proof tree itself, but they are shown as a + tool-tip when the mouse rests over a sequent symbol. Long proof commands + are abbreviated in the tree display, but show up in full length as + tool-tip. Both, sequents and proof commands, can be shown in the display + below the tree (on single click) or in a separate window (on double or + shift-click). + ''; + homepage = http://askra.de/software/prooftree; + platforms = stdenv.lib.platforms.unix; + maintainers = [ stdenv.lib.maintainers.jwiegley ]; + }; +}) diff --git a/pkgs/applications/science/logic/ssreflect/default.nix b/pkgs/applications/science/logic/ssreflect/default.nix index 6377db9c8955..a784e5fe1b6e 100644 --- a/pkgs/applications/science/logic/ssreflect/default.nix +++ b/pkgs/applications/science/logic/ssreflect/default.nix @@ -6,7 +6,7 @@ let pname = "ssreflect"; - version = "1.4"; + version = "1.5"; name = "${pname}-${version}"; webpage = http://www.msr-inria.inria.fr/Projects/math-components; in @@ -15,8 +15,8 @@ stdenv.mkDerivation { inherit name; src = fetchurl { - url = "http://ssr.msr-inria.inria.fr/FTP/${name}-coq8.4.tar.gz"; - sha256 = "1ysx29xw09i86lq0d92z9cnyx133jfgq4qddy3501000fn7xwi7h"; + url = "http://ssr.msr-inria.inria.fr/FTP/${name}.tar.gz"; + sha256 = "0hm1ha7sxqfqhc7iwhx6zdz3nki4rj5nfd3ab24hmz8v7mlpinds"; }; buildInputs = [ ocaml camlp5 coq makeWrapper ]; diff --git a/pkgs/applications/science/logic/stp/default.nix b/pkgs/applications/science/logic/stp/default.nix new file mode 100644 index 000000000000..cfe96bc6983a --- /dev/null +++ b/pkgs/applications/science/logic/stp/default.nix @@ -0,0 +1,23 @@ +{stdenv, cmake, boost, bison, flex, fetchgit, perl, zlib}: +stdenv.mkDerivation rec { + version = "2014.01.07"; + name = "stp-${version}"; + src = fetchgit { + url = "git://github.com/stp/stp"; + rev = "3aa11620a823d617fc033d26aedae91853d18635"; + sha256 = "832520787f57f63cf47364d080f30ad10d6d6e00f166790c19b125be3d6dd45c"; + }; + buildInputs = [ cmake boost bison flex perl zlib ]; + cmakeFlags = [ "-DBUILD_SHARED_LIBS=ON" ]; + patchPhase = '' + sed -e 's,^export(PACKAGE.*,,' -i CMakeLists.txt + patch -p1 < ${./fixbuild.diff} + patch -p1 < ${./fixrefs.diff} + ''; + meta = { + description = ''Simple Theorem Prover''; + maintainers = with stdenv.lib.maintainers; [mornfall]; + platforms = with stdenv.lib.platforms; linux; + license = with stdenv.lib.licenses; mit; + }; +} diff --git a/pkgs/applications/science/logic/stp/fixbuild.diff b/pkgs/applications/science/logic/stp/fixbuild.diff new file mode 100644 index 000000000000..01782cb4f40b --- /dev/null +++ b/pkgs/applications/science/logic/stp/fixbuild.diff @@ -0,0 +1,45 @@ +diff --git a/src/libstp/CMakeLists.txt b/src/libstp/CMakeLists.txt +index 83bd03a..9c0304b 100644 +--- a/src/libstp/CMakeLists.txt ++++ b/src/libstp/CMakeLists.txt +@@ -23,6 +23,15 @@ set(stp_lib_targets + printer + ) + ++include_directories(${CMAKE_SOURCE_DIR}/src/AST/) ++include_directories(${CMAKE_BINARY_DIR}/src/AST/) ++ ++add_library(globalstp OBJECT ++ ../main/Globals.cpp ++ ${CMAKE_CURRENT_BINARY_DIR}/../main/GitSHA1.cpp ++) ++add_dependencies(globalstp ASTKind_header) ++ + # Create list of objects and gather list of + # associated public headers. + set(stp_lib_objects "") +@@ -31,6 +40,7 @@ foreach(target ${stp_lib_targets}) + list(APPEND stp_lib_objects $<TARGET_OBJECTS:${target}>) + + get_target_property(TARGETS_PUBLIC_HEADERS ${target} PUBLIC_HEADER) ++ set_target_properties(${target} PROPERTIES POSITION_INDEPENDENT_CODE ON) + if (EXISTS "${TARGETS_PUBLIC_HEADERS}") + list(APPEND stp_public_headers "${TARGETS_PUBLIC_HEADERS}") + message("Adding public header(s) ${TARGETS_PUBLIC_HEADERS} to target libstp") +diff --git a/src/main/CMakeLists.txt b/src/main/CMakeLists.txt +index 0735137..73039f5 100644 +--- a/src/main/CMakeLists.txt ++++ b/src/main/CMakeLists.txt +@@ -3,12 +3,6 @@ include_directories(${CMAKE_BINARY_DIR}/src/AST/) + + configure_file("${CMAKE_CURRENT_SOURCE_DIR}/GitSHA1.cpp.in" "${CMAKE_CURRENT_BINARY_DIR}/GitSHA1.cpp" @ONLY) + +-add_library(globalstp OBJECT +- Globals.cpp +- ${CMAKE_CURRENT_BINARY_DIR}/GitSHA1.cpp +-) +-add_dependencies(globalstp ASTKind_header) +- + # ----------------------------------------------------------------------------- + # Create binary + # ----------------------------------------------------------------------------- diff --git a/pkgs/applications/science/logic/stp/fixrefs.diff b/pkgs/applications/science/logic/stp/fixrefs.diff new file mode 100644 index 000000000000..60ad4949f076 --- /dev/null +++ b/pkgs/applications/science/logic/stp/fixrefs.diff @@ -0,0 +1,192 @@ +commit 53b6043e25b2eba264faab845077fbf6736cf22f +Author: Petr Rockai <me@mornfall.net> +Date: Tue Jan 7 13:30:07 2014 +0100 + + aig: Comment out unused functions with undefined references in them. + +diff --git a/src/extlib-abc/aig/aig/aigPart.c b/src/extlib-abc/aig/aig/aigPart.c +index a4cc116..5bd5f08 100644 +--- a/src/extlib-abc/aig/aig/aigPart.c ++++ b/src/extlib-abc/aig/aig/aigPart.c +@@ -869,6 +869,7 @@ Vec_Ptr_t * Aig_ManMiterPartitioned( Aig_Man_t * p1, Aig_Man_t * p2, int nPartSi + SeeAlso [] + + ***********************************************************************/ ++#if 0 + Aig_Man_t * Aig_ManChoicePartitioned( Vec_Ptr_t * vAigs, int nPartSize ) + { + extern int Cmd_CommandExecute( void * pAbc, char * sCommand ); +@@ -981,6 +982,7 @@ Aig_Man_t * Aig_ManChoicePartitioned( Vec_Ptr_t * vAigs, int nPartSize ) + Aig_ManMarkValidChoices( pAig ); + return pAig; + } ++#endif + + + //////////////////////////////////////////////////////////////////////// +diff --git a/src/extlib-abc/aig/aig/aigShow.c b/src/extlib-abc/aig/aig/aigShow.c +index ae8fa8b..f04eedc 100644 +--- a/src/extlib-abc/aig/aig/aigShow.c ++++ b/src/extlib-abc/aig/aig/aigShow.c +@@ -326,6 +326,7 @@ void Aig_WriteDotAig( Aig_Man_t * pMan, char * pFileName, int fHaig, Vec_Ptr_t * + SeeAlso [] + + ***********************************************************************/ ++#if 0 + void Aig_ManShow( Aig_Man_t * pMan, int fHaig, Vec_Ptr_t * vBold ) + { + extern void Abc_ShowFile( char * FileNameDot ); +@@ -347,7 +348,7 @@ void Aig_ManShow( Aig_Man_t * pMan, int fHaig, Vec_Ptr_t * vBold ) + // visualize the file + Abc_ShowFile( FileNameDot ); + } +- ++#endif + + //////////////////////////////////////////////////////////////////////// + /// END OF FILE /// +diff --git a/src/extlib-abc/aig/dar/darRefact.c b/src/extlib-abc/aig/dar/darRefact.c +index d744b4f..23fc3d5 100644 +--- a/src/extlib-abc/aig/dar/darRefact.c ++++ b/src/extlib-abc/aig/dar/darRefact.c +@@ -340,6 +340,7 @@ printf( "\n" ); + SeeAlso [] + + ***********************************************************************/ ++#if 0 + int Dar_ManRefactorTryCuts( Ref_Man_t * p, Aig_Obj_t * pObj, int nNodesSaved, int Required ) + { + Vec_Ptr_t * vCut; +@@ -428,6 +429,7 @@ int Dar_ManRefactorTryCuts( Ref_Man_t * p, Aig_Obj_t * pObj, int nNodesSaved, in + } + return p->GainBest; + } ++#endif + + /**Function************************************************************* + +@@ -461,6 +463,7 @@ int Dar_ObjCutLevelAchieved( Vec_Ptr_t * vCut, int nLevelMin ) + SeeAlso [] + + ***********************************************************************/ ++#if 0 + int Dar_ManRefactor( Aig_Man_t * pAig, Dar_RefPar_t * pPars ) + { + // Bar_Progress_t * pProgress; +@@ -583,6 +586,7 @@ p->timeOther = p->timeTotal - p->timeCuts - p->timeEval; + return 1; + + } ++#endif + + //////////////////////////////////////////////////////////////////////// + /// END OF FILE /// +diff --git a/src/extlib-abc/aig/dar/darScript.c b/src/extlib-abc/aig/dar/darScript.c +index e60df00..1b9c24f 100644 +--- a/src/extlib-abc/aig/dar/darScript.c ++++ b/src/extlib-abc/aig/dar/darScript.c +@@ -64,6 +64,7 @@ Aig_Man_t * Dar_ManRewriteDefault( Aig_Man_t * pAig ) + SeeAlso [] + + ***********************************************************************/ ++#if 0 + Aig_Man_t * Dar_ManRwsat( Aig_Man_t * pAig, int fBalance, int fVerbose ) + //alias rwsat "st; rw -l; b -l; rw -l; rf -l" + { +@@ -108,7 +109,7 @@ Aig_Man_t * Dar_ManRwsat( Aig_Man_t * pAig, int fBalance, int fVerbose ) + + return pAig; + } +- ++#endif + + /**Function************************************************************* + +@@ -121,6 +122,7 @@ Aig_Man_t * Dar_ManRwsat( Aig_Man_t * pAig, int fBalance, int fVerbose ) + SeeAlso [] + + ***********************************************************************/ ++#if 0 + Aig_Man_t * Dar_ManCompress( Aig_Man_t * pAig, int fBalance, int fUpdateLevel, int fVerbose ) + //alias compress2 "b -l; rw -l; rwz -l; b -l; rwz -l; b -l" + { +@@ -180,6 +182,7 @@ Aig_Man_t * Dar_ManCompress( Aig_Man_t * pAig, int fBalance, int fUpdateLevel, i + + return pAig; + } ++#endif + + /**Function************************************************************* + +@@ -192,6 +195,7 @@ Aig_Man_t * Dar_ManCompress( Aig_Man_t * pAig, int fBalance, int fUpdateLevel, i + SeeAlso [] + + ***********************************************************************/ ++#if 0 + Aig_Man_t * Dar_ManCompress2( Aig_Man_t * pAig, int fBalance, int fUpdateLevel, int fVerbose ) + //alias compress2 "b -l; rw -l; rf -l; b -l; rw -l; rwz -l; b -l; rfz -l; rwz -l; b -l" + { +@@ -285,6 +289,7 @@ Aig_Man_t * Dar_ManCompress2( Aig_Man_t * pAig, int fBalance, int fUpdateLevel, + } + return pAig; + } ++#endif + + /**Function************************************************************* + +@@ -297,6 +302,7 @@ Aig_Man_t * Dar_ManCompress2( Aig_Man_t * pAig, int fBalance, int fUpdateLevel, + SeeAlso [] + + ***********************************************************************/ ++#if 0 + Vec_Ptr_t * Dar_ManChoiceSynthesis( Aig_Man_t * pAig, int fBalance, int fUpdateLevel, int fVerbose ) + //alias resyn "b; rw; rwz; b; rwz; b" + //alias resyn2 "b; rw; rf; b; rw; rwz; b; rfz; rwz; b" +@@ -311,6 +317,7 @@ Vec_Ptr_t * Dar_ManChoiceSynthesis( Aig_Man_t * pAig, int fBalance, int fUpdateL + Vec_PtrPush( vAigs, pAig ); + return vAigs; + } ++#endif + + /**Function************************************************************* + +diff --git a/src/extlib-abc/aig/kit/kitAig.c b/src/extlib-abc/aig/kit/kitAig.c +index de301f2..7e5df0f 100644 +--- a/src/extlib-abc/aig/kit/kitAig.c ++++ b/src/extlib-abc/aig/kit/kitAig.c +@@ -95,6 +95,7 @@ Aig_Obj_t * Kit_GraphToAig( Aig_Man_t * pMan, Aig_Obj_t ** pFanins, Kit_Graph_t + SeeAlso [] + + ***********************************************************************/ ++#if 0 + Aig_Obj_t * Kit_TruthToAig( Aig_Man_t * pMan, Aig_Obj_t ** pFanins, unsigned * pTruth, int nVars, Vec_Int_t * vMemory ) + { + Aig_Obj_t * pObj; +@@ -113,6 +114,7 @@ Aig_Obj_t * Kit_TruthToAig( Aig_Man_t * pMan, Aig_Obj_t ** pFanins, unsigned * p + Kit_GraphFree( pGraph ); + return pObj; + } ++#endif + + //////////////////////////////////////////////////////////////////////// + /// END OF FILE /// +diff --git a/src/extlib-abc/aig/kit/kitGraph.c b/src/extlib-abc/aig/kit/kitGraph.c +index 39ef587..0485c66 100644 +--- a/src/extlib-abc/aig/kit/kitGraph.c ++++ b/src/extlib-abc/aig/kit/kitGraph.c +@@ -349,6 +349,7 @@ unsigned Kit_GraphToTruth( Kit_Graph_t * pGraph ) + SeeAlso [] + + ***********************************************************************/ ++#if 0 + Kit_Graph_t * Kit_TruthToGraph( unsigned * pTruth, int nVars, Vec_Int_t * vMemory ) + { + Kit_Graph_t * pGraph; +@@ -365,6 +366,7 @@ Kit_Graph_t * Kit_TruthToGraph( unsigned * pTruth, int nVars, Vec_Int_t * vMemor + pGraph = Kit_SopFactor( vMemory, RetValue, nVars, vMemory ); + return pGraph; + } ++#endif + + /**Function************************************************************* + diff --git a/pkgs/applications/science/logic/tptp/default.nix b/pkgs/applications/science/logic/tptp/default.nix index 5c8cb7203245..ef00b135c271 100644 --- a/pkgs/applications/science/logic/tptp/default.nix +++ b/pkgs/applications/science/logic/tptp/default.nix @@ -11,15 +11,19 @@ let (builtins.attrNames (builtins.removeAttrs x helperArgNames)); sourceInfo = rec { baseName="TPTP"; - version="5.4.0"; + version="6.0.0"; name="${baseName}-${version}"; - url="http://www.cs.miami.edu/~tptp/TPTP/Distribution/TPTP-v${version}.tgz"; - hash="0rvrmh3vw4bk7mj29bx1pi76g2bsqyc13gsnpa1cbjs5pzyhm780"; + urls= + [ + "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${version}.tgz" + ]; + hash="0jnjkqdz937c7mkxvh9wc3byw5h1k19jss058fbzdxxc2hkwq1af"; }; in rec { src = a.fetchurl { - url = sourceInfo.url; + urls = sourceInfo.urls; sha256 = sourceInfo.hash; }; @@ -74,8 +78,7 @@ rec { # A GiB of data. Installation is unpacking and editing a few files. # No sense in letting Hydra build it. # Also, it is unclear what is covered by "verbatim" - we will edit configs - platforms = with a.lib.platforms; - []; + hydraPlatforms = []; license = "verbatim-redistribution"; }; passthru = { diff --git a/pkgs/applications/science/logic/twelf/default.nix b/pkgs/applications/science/logic/twelf/default.nix new file mode 100644 index 000000000000..c6c7e4d9c1a7 --- /dev/null +++ b/pkgs/applications/science/logic/twelf/default.nix @@ -0,0 +1,46 @@ +{ stdenv, fetchurl, pkgconfig, smlnj, rsync }: + +stdenv.mkDerivation rec { + name = "twelf-${version}"; + version = "1.7.1"; + + src = fetchurl { + url = "http://twelf.plparty.org/releases/twelf-src-${version}.tar.gz"; + sha256 = "0fi1kbs9hrdrm1x4k13angpjasxlyd1gc3ys8ah54i75qbcd9c4i"; + }; + + buildInputs = [ pkgconfig smlnj rsync ]; + + buildPhase = '' + export SMLNJ_HOME=${smlnj} + make smlnj + ''; + + installPhase = '' + mkdir -p $out/bin + rsync -av bin/* $out/bin/ + + mkdir -p $out/share/emacs/site-lisp/twelf/ + rsync -av emacs/ $out/share/emacs/site-lisp/twelf/ + + mkdir -p $out/share/twelf/examples + rsync -av examples/ $out/share/twelf/examples/ + mkdir -p $out/share/twelf/vim + rsync -av vim/ $out/share/twelf/vim/ + ''; + + meta = { + description = "Twelf logic proof assistant"; + longDescription = '' + Twelf is a language used to specify, implement, and prove properties of + deductive systems such as programming languages and logics. Large + research projects using Twelf include the TALT typed assembly language, + a foundational proof-carrying-code system, and a type safety proof for + Standard ML. + ''; + homepage = http://twelf.org/wiki/Main_Page; + license = "MIT"; + maintainers = with stdenv.lib.maintainers; [ jwiegley ]; + platforms = stdenv.lib.platforms.unix; + }; +} diff --git a/pkgs/applications/science/logic/verifast/default.nix b/pkgs/applications/science/logic/verifast/default.nix new file mode 100644 index 000000000000..7ab08cf8799f --- /dev/null +++ b/pkgs/applications/science/logic/verifast/default.nix @@ -0,0 +1,43 @@ +{ stdenv, fetchurl, gtk, gdk_pixbuf, atk, pango, glib, cairo, freetype +, fontconfig, libxml2, gnome2 }: + +let + libPath = stdenv.lib.makeLibraryPath + [ stdenv.gcc.libc stdenv.gcc.gcc gtk gdk_pixbuf atk pango glib cairo + freetype fontconfig libxml2 gnome2.gtksourceview + ] + ":${stdenv.gcc.gcc}/lib64"; + + patchExe = x: '' + patchelf --interpreter "$(cat $NIX_GCC/nix-support/dynamic-linker)" \ + --set-rpath ${libPath} ${x} + ''; +in +stdenv.mkDerivation rec { + name = "verifast-${version}"; + version = "14.5"; + + src = fetchurl { + url = "http://people.cs.kuleuven.be/~bart.jacobs/verifast/${name}-x64.tar.gz"; + sha256 = "03y1s6s2j9vqgiad0vbxriipsypxaylxxd3q36n9rvrc3lf9xra9"; + }; + + dontStrip = true; + phases = "unpackPhase installPhase"; + installPhase = '' + mkdir -p $out/bin + cp -R bin $out/libexec + + ${patchExe "$out/libexec/verifast-core"} + ${patchExe "$out/libexec/vfide-core"} + ln -s $out/libexec/verifast-core $out/bin/verifast + ln -s $out/libexec/vfide-core $out/bin/vfide + ''; + + meta = { + description = "Verification for C and Java programs via separation logic"; + homepage = "http://people.cs.kuleuven.be/~bart.jacobs/verifast/"; + license = stdenv.lib.licenses.msrla; + platforms = [ "x86_64-linux" ]; + maintainers = [ stdenv.lib.maintainers.thoughtpolice ]; + }; +} diff --git a/pkgs/applications/science/logic/why3/default.nix b/pkgs/applications/science/logic/why3/default.nix new file mode 100644 index 000000000000..71ff1cc7fb47 --- /dev/null +++ b/pkgs/applications/science/logic/why3/default.nix @@ -0,0 +1,22 @@ +{ fetchurl, stdenv, ocaml, ocamlPackages, coq }: + +stdenv.mkDerivation rec { + name = "why3-${version}"; + version = "0.83"; + + src = fetchurl { + url = "https://gforge.inria.fr/frs/download.php/33490/${name}.tar.gz"; + sha256 = "1jcs5vj91ppbgh4q4hch89b63wgakjhg35pm3r4jwhp377lnggya"; + }; + + buildInputs = with ocamlPackages; + [ coq ocaml findlib lablgtk ocamlgraph zarith ]; + + meta = { + description = "why is a software verification platform"; + homepage = "http://why3.lri.fr/"; + license = stdenv.lib.licenses.lgpl21; + platforms = stdenv.lib.platforms.linux; + maintainers = [ stdenv.lib.maintainers.thoughtpolice ]; + }; +} diff --git a/pkgs/applications/science/logic/yices/default.nix b/pkgs/applications/science/logic/yices/default.nix new file mode 100644 index 000000000000..5a1a4ef19922 --- /dev/null +++ b/pkgs/applications/science/logic/yices/default.nix @@ -0,0 +1,40 @@ +{ stdenv, fetchurl }: + +let + libPath = stdenv.lib.makeLibraryPath [ stdenv.gcc.libc ]; +in +stdenv.mkDerivation rec { + name = "yices-${version}"; + version = "2.2.1"; + + src = + if stdenv.system == "i686-linux" + then fetchurl { + url = "http://yices.csl.sri.com/cgi-bin/yices2-newdownload.cgi?file=yices-2.2.1-i686-pc-linux-gnu-static-gmp.tar.gz&accept=I+accept"; + name = "yices-${version}-i686.tar.gz"; + sha256 = "12jzk3kqlbqa5x6rl92cpzj7dch7gm7fnbj72wifvwgdj4zyhrra"; + } + else fetchurl { + url = "http://yices.csl.sri.com/cgi-bin/yices2-newdownload.cgi?file=yices-2.2.1-x86_64-unknown-linux-gnu-static-gmp.tar.gz&accept=I+accept"; + name = "yices-${version}-x86_64.tar.gz"; + sha256 = "0fpmihf6ykcg4qbsimkamgcwp4sl1xyxmz7q28ily91rd905ijaj"; + }; + + buildPhase = false; + installPhase = '' + mkdir -p $out/bin $out/lib $out/include + cd bin && mv * $out/bin && cd .. + cd lib && mv * $out/lib && cd .. + cd include && mv * $out/include && cd .. + + patchelf --set-rpath ${libPath} $out/lib/libyices.so.${version} + ''; + + meta = { + description = "Yices is a high-performance theorem prover and SMT solver"; + homepage = "http://yices.csl.sri.com"; + license = stdenv.lib.licenses.unfreeRedistributable; + platforms = stdenv.lib.platforms.linux; + maintainers = [ stdenv.lib.maintainers.thoughtpolice ]; + }; +} diff --git a/pkgs/applications/science/logic/z3/default.nix b/pkgs/applications/science/logic/z3/default.nix new file mode 100644 index 000000000000..7a87cb5e8be0 --- /dev/null +++ b/pkgs/applications/science/logic/z3/default.nix @@ -0,0 +1,46 @@ +{ stdenv, fetchurl, python, unzip, autoreconfHook }: + +stdenv.mkDerivation rec { + name = "z3-${version}"; + version = "4.3.1"; + src = fetchurl { + url = "http://download-codeplex.sec.s-msft.com/Download/SourceControlFileDownload.ashx\?ProjectName\=z3\&changeSetId\=89c1785b73225a1b363c0e485f854613121b70a7"; + name = "${name}.zip"; + sha256 = "3b94465c52ec174350d8707dd6a1fb0cef42f0fa23f148cc1808c14f3c2c7f76"; + }; + + buildInputs = [ python unzip autoreconfHook ]; + enableParallelBuilding = true; + + # The zip file doesn't unpack a directory, just the code itself. + unpackPhase = "mkdir ${name} && cd ${name} && unzip $src"; + postConfigure = '' + python scripts/mk_make.py + cd build + ''; + + # z3's install phase is stupid because it tries to calculate the + # python package store location itself, meaning it'll attempt to + # write files into the nix store, and fail. + soext = if stdenv.system == "x86_64-darwin" then ".dylib" else ".so"; + installPhase = '' + mkdir -p $out/bin $out/lib/${python.libPrefix}/site-packages $out/include + cp ../src/api/z3.h $out/include + cp ../src/api/z3_api.h $out/include + cp ../src/api/z3_v1.h $out/include + cp ../src/api/z3_macros.h $out/include + cp ../src/api/c++/z3++.h $out/include + cp z3 $out/bin + cp libz3${soext} $out/lib + cp libz3${soext} $out/lib/${python.libPrefix}/site-packages + cp z3*.pyc $out/lib/${python.libPrefix}/site-packages + ''; + + meta = { + description = "Z3 is a high-performance theorem prover and SMT solver"; + homepage = "http://z3.codeplex.com"; + license = stdenv.lib.licenses.msrla; + platforms = stdenv.lib.platforms.unix; + maintainers = [ stdenv.lib.maintainers.thoughtpolice ]; + }; +} diff --git a/pkgs/applications/science/math/R/default.nix b/pkgs/applications/science/math/R/default.nix index 6c8ec9e68c53..edba65146a66 100644 --- a/pkgs/applications/science/math/R/default.nix +++ b/pkgs/applications/science/math/R/default.nix @@ -2,14 +2,15 @@ , libjpeg, libpng, libtiff, ncurses, pango, pcre, perl, readline, tcl , texLive, tk, xz, zlib, less, texinfo, graphviz, icu, pkgconfig, bison , imake, which, jdk, atlas +, withRecommendedPackages ? true }: stdenv.mkDerivation rec { - name = "R-3.0.2"; + name = "R-3.1.0"; src = fetchurl { url = "http://cran.r-project.org/src/base/R-3/${name}.tar.gz"; - sha256 = "0jq2vk6bgksbvgmdjvv7vfj6llp091d0nhl5j825aya4c2nhavlm"; + sha256 = "1qjzbw341bvi1h4jwbvdkvq8j0z9l3m85mpgrlfw0n2cz2806s4a"; }; buildInputs = [ blas bzip2 gfortran liblapack libX11 libXmu libXt @@ -23,6 +24,7 @@ stdenv.mkDerivation rec { preConfigure = '' configureFlagsArray=( --disable-lto + --with${stdenv.lib.optionalString (!withRecommendedPackages) "out"}-recommended-packages --with-blas="-L${atlas}/lib -lf77blas -latlas" --with-lapack="-L${liblapack}/lib -llapack" --with-readline @@ -36,6 +38,7 @@ stdenv.mkDerivation rec { --with-system-pcre --with-system-xz --with-ICU + --enable-R-shlib AR=$(type -p ar) AWK=$(type -p gawk) CC=$(type -p gcc) @@ -81,7 +84,7 @@ stdenv.mkDerivation rec { user-defined recursive functions and input and output facilities. ''; - platforms = stdenv.lib.platforms.linux; + hydraPlatforms = stdenv.lib.platforms.linux; maintainers = [ stdenv.lib.maintainers.simons ]; }; } diff --git a/pkgs/applications/science/math/content/default.nix b/pkgs/applications/science/math/content/default.nix index 87c047c29957..177efd667a39 100644 --- a/pkgs/applications/science/math/content/default.nix +++ b/pkgs/applications/science/math/content/default.nix @@ -93,5 +93,6 @@ rec { a.lib.maintainers.raskin ]; platforms = a.lib.platforms.linux; + broken = true; }; } diff --git a/pkgs/applications/science/math/eukleides/default.nix b/pkgs/applications/science/math/eukleides/default.nix index 55ea4c6216c6..fdf5c1bd8315 100644 --- a/pkgs/applications/science/math/eukleides/default.nix +++ b/pkgs/applications/science/math/eukleides/default.nix @@ -20,7 +20,7 @@ stdenv.mkDerivation { meta = { description = "Geometry Drawing Language"; homepage = "http://www.eukleides.org/"; - license = "GPLv2"; + license = stdenv.lib.licenses.gpl2; longDescription = '' Eukleides is a computer language devoted to elementary plane diff --git a/pkgs/applications/science/math/fricas/default.nix b/pkgs/applications/science/math/fricas/default.nix new file mode 100644 index 000000000000..1817c43ed7be --- /dev/null +++ b/pkgs/applications/science/math/fricas/default.nix @@ -0,0 +1,23 @@ +{ stdenv, fetchurl, sbcl, libX11, libXpm, libICE, libSM, libXt, libXau, libXdmcp }: + +stdenv.mkDerivation rec { + name = "fricas-1.2.2"; + + src = fetchurl { + url = "http://sourceforge.net/projects/fricas/files/fricas/1.2.2/${name}-full.tar.bz2"; + sha256 = "87db64a1fd4211f3b776793acea931b4271d2e7a28396414c7d7397d833defe1"; + }; + + buildInputs = [ sbcl libX11 libXpm libICE libSM libXt libXau libXdmcp ]; + + dontStrip = true; + + meta = { + homepage = http://fricas.sourceforge.net/; + description = "Fricas CAS"; + license = stdenv.lib.licenses.bsd3; + + hydraPlatforms = stdenv.lib.platforms.linux; + maintainers = stdenv.lib.maintainers.sprock; + }; +} diff --git a/pkgs/applications/science/math/gap/default.nix b/pkgs/applications/science/math/gap/default.nix index f76640567f60..0700251c3a82 100644 --- a/pkgs/applications/science/math/gap/default.nix +++ b/pkgs/applications/science/math/gap/default.nix @@ -1,10 +1,10 @@ x@{builderDefsPackage - , pari ? null + , pari ? null , ...}: builderDefsPackage -(a : -let - helperArgNames = ["stdenv" "fetchurl" "builderDefsPackage"] ++ +(a : +let + helperArgNames = ["stdenv" "fetchurl" "builderDefsPackage"] ++ []; buildInputs = map (n: builtins.getAttr n x) @@ -38,20 +38,20 @@ rec { phaseNames = ["doConfigure" "doMake" "doDeploy"]; doDeploy = a.fullDepEntry '' - ensureDir "$out/bin" "$out/share/gap/" + mkdir -p "$out/bin" "$out/share/gap/" cp -r . "$out/share/gap/build-dir" tar xf "${pkgSrc}" -C "$out/share/gap/build-dir/pkg" - ${if a.pari != null then - ''sed -e '2iexport PATH=$PATH:${pari}/bin' -i "$out/share/gap/build-dir/bin/gap.sh" '' + ${if a.pari != null then + ''sed -e '2iexport PATH=$PATH:${pari}/bin' -i "$out/share/gap/build-dir/bin/gap.sh" '' else ""} - sed -e "/GAP_DIR=/aGAP_DIR='$out/share/gap/build-dir/'" -i "$out/share/gap/build-dir/bin/gap.sh" + sed -e "/GAP_DIR=/aGAP_DIR='$out/share/gap/build-dir/'" -i "$out/share/gap/build-dir/bin/gap.sh" ln -s "$out/share/gap/build-dir/bin/gap.sh" "$out/bin" '' ["doMake" "minInit" "defEnsureDir"]; - + meta = { description = "Computational discrete algebra system"; maintainers = with a.lib.maintainers; @@ -60,8 +60,8 @@ rec { ]; platforms = with a.lib.platforms; linux; - license = "GPLv2"; + license = with a.lib.licenses; + gpl2; homepage = "http://gap-system.org/"; }; }) x - diff --git a/pkgs/applications/science/math/glsurf/default.nix b/pkgs/applications/science/math/glsurf/default.nix index a056a32c64c2..c4352c46f92e 100644 --- a/pkgs/applications/science/math/glsurf/default.nix +++ b/pkgs/applications/science/math/glsurf/default.nix @@ -9,7 +9,7 @@ stdenv.mkDerivation { src = fetchdarcs { url = "http://lama.univ-savoie.fr/~raffalli/GlSurf"; - tag = "3.3"; + rev = "3.3"; sha256 = ""; md5=""; }; diff --git a/pkgs/applications/science/math/jags/default.nix b/pkgs/applications/science/math/jags/default.nix index 3043df15da74..a93386149bd4 100644 --- a/pkgs/applications/science/math/jags/default.nix +++ b/pkgs/applications/science/math/jags/default.nix @@ -1,10 +1,10 @@ {stdenv, fetchurl, gfortran, liblapack, blas}: stdenv.mkDerivation rec { - name = "JAGS-2.2.0"; + name = "JAGS-3.4.0"; src = fetchurl { url = "mirror://sourceforge/mcmc-jags/${name}.tar.gz"; - sha256 = "016xml4k99lmdwwjiabxin95k9p3q2zh4pcci8wwcqwlq5y205b6"; + sha256 = "0ayqsz9kkmbss7mxlwr34ch2z1vsb65lryjzqpprab1ccyiaksib"; }; buildInputs = [gfortran liblapack blas]; diff --git a/pkgs/applications/science/math/mathematica/default.nix b/pkgs/applications/science/math/mathematica/default.nix index cedb491cc8b9..d4d352c95bbb 100644 --- a/pkgs/applications/science/math/mathematica/default.nix +++ b/pkgs/applications/science/math/mathematica/default.nix @@ -18,10 +18,8 @@ let platform = - if stdenv.system == "i686-linux" then + if stdenv.system == "i686-linux" || stdenv.system == "x86_64-linux" then "Linux" - else if stdenv.system == "x86_64-linux" then - "Linux-x86-64" else throw "Mathematica requires i686-linux or x86_64 linux"; in @@ -121,6 +119,6 @@ stdenv.mkDerivation rec { meta = { description = "Wolfram Mathematica computational software system"; homepage = "http://www.wolfram.com/mathematica/"; - license = "unfree"; + license = stdenv.lib.licenses.unfree; }; } diff --git a/pkgs/applications/science/math/maxima/default.nix b/pkgs/applications/science/math/maxima/default.nix index b8f7f2e65b66..096796a859d0 100644 --- a/pkgs/applications/science/math/maxima/default.nix +++ b/pkgs/applications/science/math/maxima/default.nix @@ -2,7 +2,7 @@ let name = "maxima"; - version = "5.31.2"; + version = "5.33.0"; searchPath = stdenv.lib.makeSearchPath "bin" @@ -13,7 +13,7 @@ stdenv.mkDerivation { src = fetchurl { url = "mirror://sourceforge/${name}/${name}-${version}.tar.gz"; - sha256 = "12j5irwfckl5583h7lwh0wrp0c65q7mqzcsri2v086j50xvvv398"; + sha256 = "13axm11xw0f3frx5b0qdidi7igkn1524fzz77s9rbpl2yy2nrbz2"; }; buildInputs = [sbcl texinfo perl makeWrapper]; @@ -40,7 +40,7 @@ stdenv.mkDerivation { meta = { description = "Maxima computer algebra system"; homepage = "http://maxima.sourceforge.net"; - license = "GPLv2"; + license = stdenv.lib.licenses.gpl2; longDescription = '' Maxima is a fairly complete computer algebra system written in diff --git a/pkgs/applications/science/math/pari/default.nix b/pkgs/applications/science/math/pari/default.nix index 5fda04fed4f3..576a28b054f4 100644 --- a/pkgs/applications/science/math/pari/default.nix +++ b/pkgs/applications/science/math/pari/default.nix @@ -1,11 +1,11 @@ { stdenv, fetchurl, gmp, readline }: stdenv.mkDerivation rec { - name = "pari-2.5.4"; + name = "pari-2.5.5"; src = fetchurl { url = "http://pari.math.u-bordeaux.fr/pub/pari/unix/${name}.tar.gz"; - sha256 = "0gpsj5n8d1gyl7nq2y915sscs3d334ryrv8qgjdwqf3cr95f2dwz"; + sha256 = "058nw1fhggy7idii4f124ami521lv3izvngs9idfz964aks8cvvn"; }; buildInputs = [gmp readline]; diff --git a/pkgs/applications/science/math/pssp/default.nix b/pkgs/applications/science/math/pssp/default.nix index 587f41fe998b..0a9e0e4735d0 100644 --- a/pkgs/applications/science/math/pssp/default.nix +++ b/pkgs/applications/science/math/pssp/default.nix @@ -3,11 +3,11 @@ }: stdenv.mkDerivation rec { - name = "pspp-0.8.1"; + name = "pspp-0.8.2"; src = fetchurl { url = "mirror://gnu/pspp/${name}.tar.gz"; - sha256 = "0qhxsdbwxd3cn1shc13wxvx2lg32lp4z6sz24kv3jz7p5xfi8j7x"; + sha256 = "1w7h3dglgx0jlq1wb605b8pgfsk2vr1q2q2rj7bsajh9ihbcsixr"; }; buildInputs = [ libxml2 readline zlib perl cairo gtk gsl pkgconfig diff --git a/pkgs/applications/science/math/sage/default.nix b/pkgs/applications/science/math/sage/default.nix new file mode 100644 index 000000000000..ced8b6f95bb6 --- /dev/null +++ b/pkgs/applications/science/math/sage/default.nix @@ -0,0 +1,31 @@ +{ stdenv, fetchurl, m4, perl, gfortran, texLive, ffmpeg, tk +, imagemagick, liblapack +}: + +stdenv.mkDerivation rec { + name = "sage-6.1.1"; + + src = fetchurl { + url = "http://mirrors.xmission.com/sage/src/sage-6.1.1.tar.gz"; + sha256 = "0kbzs0l9q7y34jv3f8rd1c2mrjsjkdgaw6mfdwjlpg9g4gghmq5y"; + }; + + buildInputs = [ m4 perl gfortran texLive ffmpeg tk imagemagick liblapack ]; + + enableParallelBuilding = true; + + preConfigure = '' + export SAGE_NUM_THREADS=$NIX_BUILD_CORES + sed -i 's/if ! [ -d "$HOME" ]/if [ -d "$HOME" ]/' src/bin/sage-env + '' + stdenv.lib.optionalString stdenv.isDarwin '' + sed -i "s/ld_version = try_run('ld -v')/ld_version = 'Apple'/" \ + build/pkgs/atlas/configuration.py + ''; + + meta = { + homepage = http://www.scilab.org/; + description = "Scientific software package for numerical computations (Matlab lookalike)"; + # see http://www.scilab.org/legal + license = "SciLab"; + }; +} diff --git a/pkgs/applications/science/math/singular/default.nix b/pkgs/applications/science/math/singular/default.nix index 5c5dfae8200f..1afb510e9948 100644 --- a/pkgs/applications/science/math/singular/default.nix +++ b/pkgs/applications/science/math/singular/default.nix @@ -3,9 +3,9 @@ x@{builderDefsPackage , coreutils , ...}: builderDefsPackage -(a : -let - helperArgNames = ["stdenv" "fetchurl" "builderDefsPackage"] ++ +(a : +let + helperArgNames = ["stdenv" "fetchurl" "builderDefsPackage"] ++ []; buildInputs = map (n: builtins.getAttr n x) @@ -38,9 +38,9 @@ rec { rm -rf "$out/LIB" cp -r Singular/LIB "$out" mkdir -p "$out/bin" - ln -s "$out"/*/Singular "$out/bin" + ln -s "$out/"*/Singular "$out/bin" '') ["minInit" "defEnsureDir"]; - + meta = { description = "A CAS for polynomial computations"; maintainers = with a.lib.maintainers; @@ -49,7 +49,7 @@ rec { ]; platforms = with a.lib.platforms; linux; - license = "GPLv3"; # Or GPLv2 at your option - but not GPLv4 + license = a.stdenv.lib.licenses.gpl3; # Or GPLv2 at your option - but not GPLv4 homepage = "http://www.singular.uni-kl.de/index.php"; }; passthru = { @@ -58,4 +58,3 @@ rec { }; }; }) x - diff --git a/pkgs/applications/science/math/sloane/default.nix b/pkgs/applications/science/math/sloane/default.nix new file mode 100644 index 000000000000..b3bde7874cab --- /dev/null +++ b/pkgs/applications/science/math/sloane/default.nix @@ -0,0 +1,28 @@ +# This file was auto-generated by cabal2nix. Please do NOT edit manually! + +{ cabal, ansiTerminal, cereal, downloadCurl, filepath, HTTP +, network, optparseApplicative, terminalSize, text, zlib +}: + +cabal.mkDerivation (self: { + pname = "sloane"; + version = "1.9.1"; + sha256 = "0scnvir7il8ldy3g846xmrdkk2rxnlsiyqak0jvcarf2qi251x5i"; + isLibrary = false; + isExecutable = true; + buildDepends = [ + ansiTerminal cereal downloadCurl filepath HTTP network + optparseApplicative terminalSize text zlib + ]; + postInstall = '' + mkdir -p $out/share/man/man1 + cp sloane.1 $out/share/man/man1/ + ''; + meta = { + homepage = "http://github.com/akc/sloane"; + description = "A command line interface to Sloane's On-Line Encyclopedia of Integer Sequences"; + license = self.stdenv.lib.licenses.bsd3; + platforms = self.ghc.meta.platforms; + maintainers = [ self.stdenv.lib.maintainers.akc ]; + }; +}) diff --git a/pkgs/applications/science/math/weka/default.nix b/pkgs/applications/science/math/weka/default.nix index 8471c46c8d75..66609fa58341 100644 --- a/pkgs/applications/science/math/weka/default.nix +++ b/pkgs/applications/science/math/weka/default.nix @@ -27,6 +27,6 @@ stdenv.mkDerivation { meta = { homepage = "http://www.cs.waikato.ac.nz/ml/weka/"; description = "Collection of machine learning algorithms for data mining tasks"; - license = "GPLv2+"; + license = stdenv.lib.licenses.gpl2Plus; }; } diff --git a/pkgs/applications/science/math/wxmaxima/default.nix b/pkgs/applications/science/math/wxmaxima/default.nix index 01be4ba7e6c6..75448b6965cd 100644 --- a/pkgs/applications/science/math/wxmaxima/default.nix +++ b/pkgs/applications/science/math/wxmaxima/default.nix @@ -27,7 +27,7 @@ stdenv.mkDerivation { meta = { description = "Cross platform GUI for the computer algebra system Maxima"; - license = "GPL2"; + license = stdenv.lib.licenses.gpl2; homepage = http://wxmaxima.sourceforge.net; platforms = stdenv.lib.platforms.linux; maintainers = [ stdenv.lib.maintainers.simons ]; diff --git a/pkgs/applications/science/math/yacas/default.nix b/pkgs/applications/science/math/yacas/default.nix index acc4740eb6b4..2c9d63be1b4d 100644 --- a/pkgs/applications/science/math/yacas/default.nix +++ b/pkgs/applications/science/math/yacas/default.nix @@ -35,7 +35,7 @@ stdenv.mkDerivation rec { meta = { description = "Easy to use, general purpose Computer Algebra System"; homepage = http://yacas.sourceforge.net/; - license = "GPLv2+"; + license = stdenv.lib.licenses.gpl2Plus; maintainers = with stdenv.lib.maintainers; [viric]; platforms = with stdenv.lib.platforms; all; }; diff --git a/pkgs/applications/science/misc/boinc/default.nix b/pkgs/applications/science/misc/boinc/default.nix index 0bc5c3cb7c7c..7020de0bca88 100644 --- a/pkgs/applications/science/misc/boinc/default.nix +++ b/pkgs/applications/science/misc/boinc/default.nix @@ -3,12 +3,12 @@ mesa, libXmu, libXi, freeglut, libjpeg, libtool, wxGTK, xcbutil, sqlite, gtk, patchelf, libXScrnSaver, libnotify, libX11, libxcb }: stdenv.mkDerivation rec { - name = "boinc-7.0.44"; + name = "boinc-7.2.42"; src = fetchgit { url = "git://boinc.berkeley.edu/boinc-v2.git"; - rev = "7c449b1fb8a681ceb27d6895751b62a2b3adf0f2"; - sha256 = "0hdramyl9nip3gadp7xiaz8ngyld15i93d8ai1nsd04bmrvdfqia"; + rev = "dd0d630882547c123ca0f8fda7a62e058d60f6a9"; + sha256 = "1zifpi3mjgaj68fba6kammp3x7z8n2x164zz6fj91xfiapnan56j"; }; buildInputs = [ libtool automake autoconf m4 pkgconfig curl mesa libXmu libXi @@ -36,7 +36,7 @@ stdenv.mkDerivation rec { homepage = http://boinc.berkeley.edu/; - license = "LGPLv2+"; + license = stdenv.lib.licenses.lgpl2Plus; platforms = stdenv.lib.platforms.linux; # arbitrary choice }; diff --git a/pkgs/applications/science/misc/fityk/default.nix b/pkgs/applications/science/misc/fityk/default.nix new file mode 100644 index 000000000000..db79839ba669 --- /dev/null +++ b/pkgs/applications/science/misc/fityk/default.nix @@ -0,0 +1,23 @@ +{ stdenv, fetchurl, wxGTK30, boost, lua, zlib, bzip2, xylib, readline, gnuplot }: + +let + name = "fityk"; + version = "1.2.9"; +in +stdenv.mkDerivation { + name = "${name}-${version}"; + + src = fetchurl { + url = "https://github.com/wojdyr/fityk/releases/download/v${version}/${name}-${version}.tar.bz2"; + sha256 = "1gl938nd2jyya8b3gzbagm1jab2mkc9zvr6zsg5d0vkfdqlk0pv1"; + }; + + buildInputs = [wxGTK30 boost lua zlib bzip2 xylib readline gnuplot ]; + + meta = { + description = "Fityk -- curve fitting and peak fitting software"; + license = "GPL2"; + homepage = http://fityk.nieto.pl/; + platforms = stdenv.lib.platforms.linux; + }; +} diff --git a/pkgs/applications/science/misc/golly/default.nix b/pkgs/applications/science/misc/golly/default.nix index a380f05b0915..9d198cd5c7f8 100644 --- a/pkgs/applications/science/misc/golly/default.nix +++ b/pkgs/applications/science/misc/golly/default.nix @@ -1,11 +1,11 @@ -x@{builderDefsPackage, +x@{builderDefsPackage, wxGTK, perl, python, zlib , ...}: builderDefsPackage -(a : -let +(a : +let s = import ./src-for-default.nix; - helperArgNames = ["builderDefsPackage"] ++ + helperArgNames = ["builderDefsPackage"] ++ []; buildInputs = map (n: builtins.getAttr n x) (builtins.attrNames (builtins.removeAttrs x helperArgNames)); @@ -26,7 +26,7 @@ rec { export NIX_LDFLAGS="$NIX_LDFLAGS -l$pythonLib" echo "Flags: $NIX_LDFLAGS" ''; - + meta = { description = "Cellular automata simulation program"; maintainers = with a.lib.maintainers; @@ -35,7 +35,7 @@ rec { ]; platforms = with a.lib.platforms; linux; - license = "GPLv2"; + license = with a.lib.licenses; + gpl2; }; }) x - diff --git a/pkgs/applications/science/misc/megam/default.nix b/pkgs/applications/science/misc/megam/default.nix new file mode 100644 index 000000000000..a0ee505dc97f --- /dev/null +++ b/pkgs/applications/science/misc/megam/default.nix @@ -0,0 +1,46 @@ +{ fetchurl, stdenv, ocaml, makeWrapper, ncurses }: + +let version = "0.92"; in +stdenv.mkDerivation rec { + name = "megam-${version}"; + + src = fetchurl { + url = "http://hal3.name/megam/megam_src.tgz"; + sha256 = "dc0e9f59ff8513449fe3bd40b260141f89c88a4edf6ddc8b8a394c758e49724e"; + }; + + patches = [ ./ocaml-includes.patch ./ocaml-3.12.patch ]; + + buildInputs = [ ocaml ncurses ]; + + nativeBuildInputs = [ makeWrapper ]; + + makeFlags = "CAML_INCLUDES=${ocaml}/lib/ocaml/caml"; + + # see https://bugzilla.redhat.com/show_bug.cgi?id=435559 + dontStrip = true; + + installPhase = '' + mkdir -pv $out/bin + cp -Rv megam $out/bin + ''; + + + meta = { + description = "MEGA Model Optimization Package"; + + longDescription = + '' The software here is an implementation of maximum likelihood + and maximum a posterior optimization of the parameters of + these models. The algorithms used are much more efficient + than the iterative scaling techniques used in almost every + other maxent package out there. ''; + + homepage = http://www.umiacs.umd.edu/~hal/megam; + + license = "non-commercial"; + + maintainers = [ ]; + platforms = stdenv.lib.platforms.gnu; # arbitrary choice + }; +} diff --git a/pkgs/applications/science/misc/megam/ocaml-3.12.patch b/pkgs/applications/science/misc/megam/ocaml-3.12.patch new file mode 100644 index 000000000000..8265acf6e4a7 --- /dev/null +++ b/pkgs/applications/science/misc/megam/ocaml-3.12.patch @@ -0,0 +1,12 @@ +diff -ru megam_0.92/Makefile megam_0.92-b/Makefile +--- megam_0.92/Makefile 2007-10-08 18:06:04.000000000 +0100 ++++ megam_0.92-b/Makefile 2013-11-25 10:14:20.000000000 +0000 +@@ -59,7 +59,7 @@ + + WITHUNIX =unix.cma -cclib -lunix + +-WITHSTR =str.cma -cclib -lstr ++WITHSTR =str.cma -cclib -lcamlstr + + WITHBIGARRAY =bigarray.cma -cclib -lbigarray + diff --git a/pkgs/applications/science/misc/megam/ocaml-includes.patch b/pkgs/applications/science/misc/megam/ocaml-includes.patch new file mode 100644 index 000000000000..b3a56643448c --- /dev/null +++ b/pkgs/applications/science/misc/megam/ocaml-includes.patch @@ -0,0 +1,21 @@ +diff -ru megam_0.92/Makefile megam_0.92-b/Makefile +--- megam_0.92/Makefile 2007-10-08 18:06:04.000000000 +0100 ++++ megam_0.92-b/Makefile 2013-11-25 10:14:20.000000000 +0000 +@@ -41,7 +41,7 @@ + # + # The Caml compilers. # + # You may fix here the path to access the Caml compiler on your machine +-CAMLC = ocamlc -g ++CAMLC = ocamlc -g $(WITHCLIBS) + CAMLOPT = ocamlopt -unsafe -ccopt -O4 -ccopt -ffast-math -inline 99999 + CAMLDEP = ocamldep + CAMLLEX = ocamllex +@@ -70,7 +70,7 @@ + WITHDBM =dbm.cma -cclib -lmldbm -cclib -lndbm + + #WITHCLIBS =-I /usr/lib/ocaml/3.09.2/caml +-WITHCLIBS =-I /usr/lib/ocaml/caml ++WITHCLIBS =-I $(CAML_INCLUDES) + + ################ End of user's variables ##################### + diff --git a/pkgs/applications/science/misc/root/cmake.patch b/pkgs/applications/science/misc/root/cmake.patch new file mode 100644 index 000000000000..b6efd7444fe9 --- /dev/null +++ b/pkgs/applications/science/misc/root/cmake.patch @@ -0,0 +1,11 @@ +--- cmake/modules/RootBuildOptions.cmake 1969-12-31 20:30:01.000000000 -0330 ++++ cmake/modules/RootBuildOptions.cmake 2014-01-10 14:09:29.424937408 -0330 +@@ -149,7 +149,7 @@ + + #---General Build options---------------------------------------------------------------------- + # use, i.e. don't skip the full RPATH for the build tree +-set(CMAKE_SKIP_BUILD_RPATH FALSE) ++set(CMAKE_SKIP_BUILD_RPATH TRUE) + # when building, don't use the install RPATH already (but later on when installing) + set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE) + # add the automatically determined parts of the RPATH diff --git a/pkgs/applications/science/misc/root/default.nix b/pkgs/applications/science/misc/root/default.nix new file mode 100644 index 000000000000..1227e76ac0c5 --- /dev/null +++ b/pkgs/applications/science/misc/root/default.nix @@ -0,0 +1,27 @@ +{ stdenv, fetchurl, cmake, mesa, libX11, gfortran, libXpm, libXft, libXext, zlib }: + +stdenv.mkDerivation rec { + name = "root-${version}"; + version = "5.34.15"; + + src = fetchurl { + url = "ftp://root.cern.ch/root/root_v${version}.source.tar.gz"; + sha256 = "1bkiggcyya39a794d3d2rzzmmkbdymf86hbqhh0l1pl4f38xvp6i"; + }; + + buildInputs = [ cmake gfortran mesa libX11 libXpm libXft libXext zlib ]; + + # CMAKE_INSTALL_RPATH_USE_LINK_PATH is set to FALSE in + # <rootsrc>/cmake/modules/RootBuildOptions.cmake. + # This patch sets it to TRUE. + patches = [ ./cmake.patch ]; + patchFlags = "-p0"; + + enableParallelBuilding = true; + + meta = { + homepage = "http://root.cern.ch/drupal/"; + description = "A data analysis framework"; + platforms = stdenv.lib.platforms.linux; + }; +} diff --git a/pkgs/applications/science/misc/simgrid/default.nix b/pkgs/applications/science/misc/simgrid/default.nix index 5fdede1abcdf..29a7caf769be 100644 --- a/pkgs/applications/science/misc/simgrid/default.nix +++ b/pkgs/applications/science/misc/simgrid/default.nix @@ -1,20 +1,19 @@ -{ fetchurl, stdenv, cmake, perl, ruby }: +{ fetchurl, stdenv, cmake, perl, ruby, boost, lua5_1, graphviz, libsigcxx +, libunwind, elfutils +}: stdenv.mkDerivation rec { - name = "simgrid-3.5"; + version = "3.11.1"; + name = "simgrid-${version}"; src = fetchurl { - url = "https://gforge.inria.fr/frs/download.php/28017/${name}.tar.gz"; - sha256 = "1vd4pvrcyii1nfwyca3kpbwshbc965lfpn083zd8rigg6ydchq8y"; + url = "https://gforge.inria.fr/frs/download.php/33686/${name}.tar.gz"; + sha256 = "0mkrzxpf42lmn96khfl1791vram67r2nqsgmppd2yil889nyz5kp"; }; - /* FIXME: Ruby currently disabled because of this: - - Linking C shared library ../src/.libs/libsimgrid.so - ld: cannot find -lruby-1.8.7-p72 - - */ - buildInputs = [ cmake perl /* ruby */ ]; + buildInputs = [ cmake perl ruby boost lua5_1 graphviz libsigcxx libunwind + elfutils + ]; preConfigure = # Make it so that libsimgrid.so will be found when running programs from @@ -22,8 +21,17 @@ stdenv.mkDerivation rec { '' export LD_LIBRARY_PATH="$PWD/src/.libs" export cmakeFlags="-Dprefix=$out" - # Enable tracing. - export cmakeFlags="$cmakeFlags -Denable_tracing=on" + export NIX_CFLAGS_COMPILE="$NIX_CFLAGS_COMPILE + -isystem $(echo "${libsigcxx}/lib/"sigc++*/include) + -isystem $(echo "${libsigcxx}/include"/sigc++* ) + " + export CMAKE_PREFIX_PATH="$CMAKE_PREFIX_PATH:$(echo "${libsigcxx}/lib/"sigc++*)" + + # Enable more functionality. + export cmakeFlags="$cmakeFlags -Denable_tracing=on -Denable_jedule=on + -Denable_latency_bound_tracking=on -Denable_lua=on + -Denable_ns3=on -Denable_gtnets=on + " ''; makeFlags = "VERBOSE=1"; @@ -45,6 +53,7 @@ stdenv.mkDerivation rec { patchPhase = '' for i in "src/smpi/"* do + test -f "$i" && sed -i "$i" -e's|/bin/bash|/bin/sh|g' done @@ -71,7 +80,7 @@ stdenv.mkDerivation rec { homepage = http://simgrid.gforge.inria.fr/; - license = "LGPLv2+"; + license = stdenv.lib.licenses.lgpl2Plus; maintainers = [ ]; platforms = stdenv.lib.platforms.gnu; # arbitrary choice diff --git a/pkgs/applications/science/misc/tulip/default.nix b/pkgs/applications/science/misc/tulip/default.nix index e58183a4f40b..da6e0cb2805d 100644 --- a/pkgs/applications/science/misc/tulip/default.nix +++ b/pkgs/applications/science/misc/tulip/default.nix @@ -30,7 +30,7 @@ stdenv.mkDerivation rec { homepage = http://tulip.labri.fr/; - license = "GPLv3+"; + license = stdenv.lib.licenses.gpl3Plus; maintainers = [ ]; platforms = stdenv.lib.platforms.gnu; # arbitrary choice diff --git a/pkgs/applications/science/misc/vite/default.nix b/pkgs/applications/science/misc/vite/default.nix index 4c1cf318b5a2..2e25ff582ee9 100644 --- a/pkgs/applications/science/misc/vite/default.nix +++ b/pkgs/applications/science/misc/vite/default.nix @@ -44,5 +44,7 @@ stdenv.mkDerivation { maintainers = [ stdenv.lib.maintainers.ludo ]; platforms = stdenv.lib.platforms.gnu; # arbitrary choice + + broken = true; }; } diff --git a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix index de4bb171497c..b9abf7b55b48 100644 --- a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix +++ b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix @@ -6,11 +6,11 @@ stdenv.mkDerivation { - name = "gromacs-4.5.5"; + name = "gromacs-4.6.5"; src = fetchurl { - url = "ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.5.tar.gz"; - md5 = "6a87e7cdfb25d81afa9fea073eb28468"; + url = "ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.5.tar.gz"; + sha256 = "02ggrplh8fppqib86y3rfk4qm08yddlrb1yjgzl138b3b4qjy957"; }; buildInputs = [cmake fftw]; diff --git a/pkgs/applications/science/spyder/default.nix b/pkgs/applications/science/spyder/default.nix index cd2bd4fecf3d..1079a153ca16 100644 --- a/pkgs/applications/science/spyder/default.nix +++ b/pkgs/applications/science/spyder/default.nix @@ -8,12 +8,12 @@ }: buildPythonPackage rec { - name = "spyder-2.1.13.1"; + name = "spyder-2.2.5"; namePrefix = ""; src = fetchurl { url = "https://spyderlib.googlecode.com/files/${name}.zip"; - sha256 = "1sg88shvw6k2v5428k13mah4pyqng43856rzr6ypz5qgwn0677ya"; + sha256 = "1bxc5qs2bqc21s6kxljsfxnmwgrgnyjfr9mkwzg9njpqsran3bp2"; }; buildInputs = [ unzip ]; @@ -52,6 +52,6 @@ buildPythonPackage rec { homepage = https://code.google.com/p/spyderlib/; license = licenses.mit; platforms = platforms.linux; - maintainers = [maintainers.bjornfor]; + maintainers = [ maintainers.bjornfor ]; }; } |