diff options
Diffstat (limited to 'pkgs/applications/science')
8 files changed, 75 insertions, 10 deletions
diff --git a/pkgs/applications/science/biology/dcm2niix/default.nix b/pkgs/applications/science/biology/dcm2niix/default.nix index 8ea3588fa8ca..59b173ac98cd 100644 --- a/pkgs/applications/science/biology/dcm2niix/default.nix +++ b/pkgs/applications/science/biology/dcm2niix/default.nix @@ -6,14 +6,14 @@ }: stdenv.mkDerivation rec { - version = "1.0.20190902"; + version = "1.0.20200331"; pname = "dcm2niix"; src = fetchFromGitHub { owner = "rordenlab"; repo = "dcm2niix"; rev = "v${version}"; - sha256 = "0h8jsadgv831lqb0jhnaxm7lldirmnp5agrhgg5bcxvn860fl15b"; + sha256 = "1cncfwhyhmg18n970lkn6yvp0i74ajznsl8dqz00asqfzmg681n1"; }; enableParallelBuilding = true; diff --git a/pkgs/applications/science/biology/picard-tools/default.nix b/pkgs/applications/science/biology/picard-tools/default.nix index 246c98768101..5073d0f0f324 100644 --- a/pkgs/applications/science/biology/picard-tools/default.nix +++ b/pkgs/applications/science/biology/picard-tools/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "picard-tools"; - version = "2.22.2"; + version = "2.22.4"; src = fetchurl { url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar"; - sha256 = "11mzz483f89pb2s8jmwhl12d0m6k41kmi4xh0i6hq69rxrqi8l4s"; + sha256 = "0gzna5df8nk42l7mc0qbp9h73gwr1030jnw10fawjp6ql6213kdd"; }; nativeBuildInputs = [ makeWrapper ]; diff --git a/pkgs/applications/science/electronics/magic-vlsi/0001-strip-bin-prefix.patch b/pkgs/applications/science/electronics/magic-vlsi/0001-strip-bin-prefix.patch new file mode 100644 index 000000000000..1cef96ea1408 --- /dev/null +++ b/pkgs/applications/science/electronics/magic-vlsi/0001-strip-bin-prefix.patch @@ -0,0 +1,10 @@ +diff --git a/scripts/makedbh b/scripts/makedbh +index 01e4fa5..d6299c6 100755 +--- a/scripts/makedbh ++++ b/scripts/makedbh +@@ -1,4 +1,4 @@ +-#!/bin/csh -f ++#!/usr/bin/env tcsh + # + # makes the "database.h" (1st argument, $1) file from "database.h.in" + # (2nd argument, $2), setting various mask operation definitions diff --git a/pkgs/applications/science/electronics/magic-vlsi/0002-fix-format-security.patch b/pkgs/applications/science/electronics/magic-vlsi/0002-fix-format-security.patch new file mode 100644 index 000000000000..37ae35195503 --- /dev/null +++ b/pkgs/applications/science/electronics/magic-vlsi/0002-fix-format-security.patch @@ -0,0 +1,19 @@ +diff --git a/database/DBio.c b/database/DBio.c +index 93c4b0b..292ea5f 100644 +--- a/database/DBio.c ++++ b/database/DBio.c +@@ -2378,12 +2378,12 @@ DBCellWriteFile(cellDef, f) + + #define FPRINTF(f,s)\ + {\ +- if (fprintf(f,s) == EOF) goto ioerror;\ ++ if (fprintf(f,"%s",s) == EOF) goto ioerror;\ + DBFileOffset += strlen(s);\ + } + #define FPRINTR(f,s)\ + {\ +- if (fprintf(f,s) == EOF) return 1;\ ++ if (fprintf(f,"%s",s) == EOF) return 1;\ + DBFileOffset += strlen(s);\ + } + diff --git a/pkgs/applications/science/electronics/magic-vlsi/default.nix b/pkgs/applications/science/electronics/magic-vlsi/default.nix new file mode 100644 index 000000000000..62b830547e53 --- /dev/null +++ b/pkgs/applications/science/electronics/magic-vlsi/default.nix @@ -0,0 +1,36 @@ +{ stdenv, fetchurl, m4, tcsh, libX11, tcl, tk, cairo, ncurses, mesa_glu, python3 }: + +stdenv.mkDerivation { + pname = "magic-vlsi"; + version = "8.3.5"; + + src = fetchurl { + url = "http://opencircuitdesign.com/magic/archive/magic-8.3.5.tgz"; + sha256 = "0wv4zmxlqjfaakgp802icn0cd9f8ylkz2sppix83axq8p5cg90yq"; + }; + + buildInputs = [ m4 tcsh libX11 tcl tk cairo ncurses mesa_glu ]; + nativeBuildInputs = [ python3 ]; + + configureFlags = [ + "--with-tcl=${tcl}" + "--with-tk=${tk}" + "--disable-werror" + ]; + + postPatch = '' + patchShebangs scripts/* + ''; + + patches = [ + ./0001-strip-bin-prefix.patch + ./0002-fix-format-security.patch + ]; + + meta = with stdenv.lib; { + description = "VLSI layout tool written in Tcl"; + homepage = "http://opencircuitdesign.com/magic/"; + license = licenses.mit; + maintainers = [ maintainers.dkudriavtsev ]; + }; +} diff --git a/pkgs/applications/science/logic/cryptominisat/default.nix b/pkgs/applications/science/logic/cryptominisat/default.nix index 113c6307c40b..8c1b3bd03694 100644 --- a/pkgs/applications/science/logic/cryptominisat/default.nix +++ b/pkgs/applications/science/logic/cryptominisat/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "cryptominisat"; - version = "5.6.8"; + version = "5.7.0"; src = fetchFromGitHub { owner = "msoos"; repo = "cryptominisat"; rev = version; - sha256 = "0csimmy1nvkfcsxjra9bm4mlcyxa3ac8zarm88zfb7640ca0d0wv"; + sha256 = "0ny5ln8fc0irprs04qw01c9mppps8q27lkx01a549zazwhj4b5rm"; }; buildInputs = [ python3 boost ]; diff --git a/pkgs/applications/science/logic/lean/default.nix b/pkgs/applications/science/logic/lean/default.nix index 36df6ae0658f..c80c163562be 100644 --- a/pkgs/applications/science/logic/lean/default.nix +++ b/pkgs/applications/science/logic/lean/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "lean"; - version = "3.9.0"; + version = "3.10.0"; src = fetchFromGitHub { owner = "leanprover-community"; repo = "lean"; rev = "v${version}"; - sha256 = "0sklw211cmqp4y0c6nycfavpdxdpfwhq9a4sbwdlqd5agyf85h1j"; + sha256 = "0nmh09x3scfqg0bg1qf8b7z67s11hbfd7kr1h6k1zw94fyn2mg8q"; }; nativeBuildInputs = [ cmake ]; diff --git a/pkgs/applications/science/math/mxnet/default.nix b/pkgs/applications/science/math/mxnet/default.nix index 87d46850f140..b006a9dd18d1 100644 --- a/pkgs/applications/science/math/mxnet/default.nix +++ b/pkgs/applications/science/math/mxnet/default.nix @@ -8,11 +8,11 @@ assert cudnnSupport -> cudaSupport; stdenv.mkDerivation rec { pname = "mxnet"; - version = "1.4.1"; + version = "1.6.0"; src = fetchurl { url = "https://github.com/apache/incubator-mxnet/releases/download/${version}/apache-mxnet-src-${version}-incubating.tar.gz"; - sha256 = "1d0lhlpdaxycjzpwwrpgjd3v2q2ka89v5rr13ddxayy7ld2hxiaj"; + sha256 = "1vvdb7pfh63kb9fzs6gqp95q550a3ck4cj9mqxlk9wwhkh30dsq1"; }; nativeBuildInputs = [ cmake perl ]; |