diff options
Diffstat (limited to 'pkgs/development/libraries/science')
| -rw-r--r-- | pkgs/development/libraries/science/biology/elastix/default.nix | 1 | ||||
| -rw-r--r-- | pkgs/development/libraries/science/math/cudnn/generic.nix | 2 | ||||
| -rw-r--r-- | pkgs/development/libraries/science/math/lcalc/makefile.patch | 4 | ||||
| -rw-r--r-- | pkgs/development/libraries/science/math/or-tools/build.patch | 5 | ||||
| -rw-r--r-- | pkgs/development/libraries/science/math/or-tools/default.nix | 11 | ||||
| -rw-r--r-- | pkgs/development/libraries/science/math/or-tools/protobuf.patch | 10 | ||||
| -rw-r--r-- | pkgs/development/libraries/science/math/tensorflow/bin.nix | 7 | ||||
| -rw-r--r-- | pkgs/development/libraries/science/networking/ns-3/default.nix (renamed from pkgs/development/libraries/science/networking/ns3/default.nix) | 72 |
8 files changed, 76 insertions, 36 deletions
diff --git a/pkgs/development/libraries/science/biology/elastix/default.nix b/pkgs/development/libraries/science/biology/elastix/default.nix index 5f4cbbaa567..9105b1c52ac 100644 --- a/pkgs/development/libraries/science/biology/elastix/default.nix +++ b/pkgs/development/libraries/science/biology/elastix/default.nix @@ -19,5 +19,6 @@ stdenv.mkDerivation rec { maintainers = with maintainers; [ bcdarwin ]; platforms = platforms.linux; license = licenses.asl20; + broken = true; }; } diff --git a/pkgs/development/libraries/science/math/cudnn/generic.nix b/pkgs/development/libraries/science/math/cudnn/generic.nix index f0f5829ce46..5a17e807bd4 100644 --- a/pkgs/development/libraries/science/math/cudnn/generic.nix +++ b/pkgs/development/libraries/science/math/cudnn/generic.nix @@ -46,7 +46,7 @@ stdenv.mkDerivation { passthru = { inherit cudatoolkit; - majorVersion = lib.head (lib.splitString "." version); + majorVersion = lib.versions.major version; }; meta = with stdenv.lib; { diff --git a/pkgs/development/libraries/science/math/lcalc/makefile.patch b/pkgs/development/libraries/science/math/lcalc/makefile.patch index f55bbe3f24f..5c22cf0b84e 100644 --- a/pkgs/development/libraries/science/math/lcalc/makefile.patch +++ b/pkgs/development/libraries/science/math/lcalc/makefile.patch @@ -104,10 +104,10 @@ index 84e4e88..56ca676 100644 - cp -rf ../include $(INSTALL_DIR)/include/Lfunction + install -d $(INSTALL_DIR)/bin + install -d $(INSTALL_DIR)/$(LIB_DIR) -+ install -d $(INSTALL_DIR)/include/libLfunction ++ install -d $(INSTALL_DIR)/include/Lfunction + install lcalc $(INSTALL_DIR)/bin + install libLfunction.so $(INSTALL_DIR)/$(LIB_DIR) -+ install -m 644 -t $(INSTALL_DIR)/include/libLfunction ../include/*.h ++ install -m 644 -t $(INSTALL_DIR)/include/Lfunction ../include/*.h SRCS = Lcommandline.cc Lcommandline_elliptic.cc Lcommandline_globals.cc Lcommandline_misc.cc Lcommandline_numbertheory.cc Lcommandline_twist.cc Lcommandline_values_zeros.cc Lgamma.cc Lglobals.cc Lmisc.cc Lriemannsiegel.cc Lriemannsiegel_blfi.cc cmdline.c diff --git a/pkgs/development/libraries/science/math/or-tools/build.patch b/pkgs/development/libraries/science/math/or-tools/build.patch new file mode 100644 index 00000000000..a67e137ff4a --- /dev/null +++ b/pkgs/development/libraries/science/math/or-tools/build.patch @@ -0,0 +1,5 @@ +--- a/makefiles/Makefile.python.mk ++++ b/makefiles/Makefile.python.mk +@@ -1070 +1070 @@ $(PYPI_ARCHIVE_TEMP_DIR)/ortools/ortools/data: $(PYDATA_LIBS) | $(PYPI_ARCHIVE_T +-$(PYPI_ARCHIVE_TEMP_DIR)/ortools/ortools/util: $(PYUTIL_LIBS) | $(PYPI_ARCHIVE_TEMP_DIR)/ortools/ortools ++$(PYPI_ARCHIVE_TEMP_DIR)/ortools/ortools/util: $(PYSORTED_INTERVAL_LIST_LIBS) | $(PYPI_ARCHIVE_TEMP_DIR)/ortools/ortools diff --git a/pkgs/development/libraries/science/math/or-tools/default.nix b/pkgs/development/libraries/science/math/or-tools/default.nix index c6e065320a2..224f4239a22 100644 --- a/pkgs/development/libraries/science/math/or-tools/default.nix +++ b/pkgs/development/libraries/science/math/or-tools/default.nix @@ -5,15 +5,20 @@ stdenv.mkDerivation rec { pname = "or-tools"; - version = "v7.0"; + version = "7.3"; src = fetchFromGitHub { owner = "google"; repo = "or-tools"; - rev = version; - sha256 = "09rs2j3w4ljw9qhhnsjlvfii297njjszwvkbgj1i6kns3wnlr7cp"; + rev = "v${version}"; + sha256 = "0q06vxmds6nm3dpjw4y5jzr8j98qgfb9i8pbm9pfhmqigv791hwc"; }; + patches = [ + ./build.patch # https://github.com/google/or-tools/pull/1619 + ./protobuf.patch # Otherwise it tries to install protobuf from pypi. + ]; + # The original build system uses cmake which does things like pull # in dependencies through git and Makefile creation time. We # obviously don't want to do this so instead we provide the diff --git a/pkgs/development/libraries/science/math/or-tools/protobuf.patch b/pkgs/development/libraries/science/math/or-tools/protobuf.patch new file mode 100644 index 00000000000..b0cce40434c --- /dev/null +++ b/pkgs/development/libraries/science/math/or-tools/protobuf.patch @@ -0,0 +1,10 @@ +--- a/makefiles/Makefile.third_party.unix.mk ++++ b/makefiles/Makefile.third_party.unix.mk +@@ -24,1 +24,1 @@ GLOG_TAG = 0.4.0 +-PROTOBUF_TAG = 3.9.0 ++PROTOBUF_TAG = 3.7.0 +--- a/makefiles/Makefile.third_party.win.mk ++++ b/makefiles/Makefile.third_party.win.mk +@@ -40 +40 @@ GLOG_TAG = 0.4.0 +-PROTOBUF_TAG = 3.9.0 ++PROTOBUF_TAG = 3.7.0 diff --git a/pkgs/development/libraries/science/math/tensorflow/bin.nix b/pkgs/development/libraries/science/math/tensorflow/bin.nix index 3db7a6f1d1e..f9f300883a1 100644 --- a/pkgs/development/libraries/science/math/tensorflow/bin.nix +++ b/pkgs/development/libraries/science/math/tensorflow/bin.nix @@ -1,6 +1,6 @@ { stdenv , fetchurl -, patchelf +, addOpenGLRunpath , cudaSupport ? false, symlinkJoin, cudatoolkit, cudnn, nvidia_x11 }: @@ -35,6 +35,9 @@ let else '' patchelf --set-rpath "${rpath}:$out/lib" $out/lib/libtensorflow.so patchelf --set-rpath "${rpath}" $out/lib/libtensorflow_framework.so + ${optionalString cudaSupport '' + addOpenGLRunpath $out/lib/libtensorflow.so $out/lib/libtensorflow_framework.so + ''} ''; in stdenv.mkDerivation rec { @@ -43,6 +46,8 @@ in stdenv.mkDerivation rec { src = fetchurl url; + nativeBuildInputs = optional cudaSupport addOpenGLRunpath; + # Patch library to use our libc, libstdc++ and others buildCommand = '' mkdir -pv $out diff --git a/pkgs/development/libraries/science/networking/ns3/default.nix b/pkgs/development/libraries/science/networking/ns-3/default.nix index 5218de07509..73be2a8ca6c 100644 --- a/pkgs/development/libraries/science/networking/ns3/default.nix +++ b/pkgs/development/libraries/science/networking/ns-3/default.nix @@ -1,5 +1,5 @@ { stdenv -, fetchFromGitHub +, fetchFromGitLab , python , wafHook @@ -22,75 +22,89 @@ , dia, tetex ? null, ghostscript ? null, texlive ? null # generates python bindings -, generateBindings ? false, ncurses ? null +, pythonSupport ? false, ncurses ? null # All modules can be enabled by choosing 'all_modules'. # we include here the DCE mandatory ones , modules ? [ "core" "network" "internet" "point-to-point" "fd-net-device" "netanim"] -, gcc6 , lib }: let pythonEnv = python.withPackages(ps: stdenv.lib.optional withManual ps.sphinx - ++ stdenv.lib.optionals generateBindings (with ps;[ pybindgen pygccxml ]) + ++ stdenv.lib.optionals pythonSupport (with ps;[ pybindgen pygccxml ]) ); in stdenv.mkDerivation rec { - - name = "ns-3.${version}"; - version = "28"; - - # the all in one https://www.nsnam.org/release/ns-allinone-3.27.tar.bz2; - # fetches everything (netanim, etc), this package focuses on ns3-core - src = fetchFromGitHub { - owner = "nsnam"; - repo = "ns-3-dev-git"; - rev = name; - sha256 = "17kzfjpgw2mvyx1c9bxccnvw67jpk09fxmcnlkqx9xisk10qnhng"; + pname = "ns-3"; + version = "30"; + + src = fetchFromGitLab { + owner = "nsnam"; + repo = "ns-3-dev"; + rev = "ns-3.${version}"; + sha256 = "0smdi3gglmafpc7a20hj2lbmwks3d5fpsicpn39lmm3svazw0bvp"; }; nativeBuildInputs = [ wafHook ]; + + outputs = [ "out" ] ++ lib.optional pythonSupport "py"; + # ncurses is a hidden dependency of waf when checking python - buildInputs = lib.optionals generateBindings [ castxml ncurses ] - ++ stdenv.lib.optional enableDoxygen [ doxygen graphviz imagemagick ] - ++ stdenv.lib.optional withManual [ dia tetex ghostscript texlive.combined.scheme-medium ]; + buildInputs = lib.optionals pythonSupport [ castxml ncurses ] + ++ lib.optional enableDoxygen [ doxygen graphviz imagemagick ] + ++ lib.optional withManual [ dia tetex ghostscript texlive.combined.scheme-medium ]; - propagatedBuildInputs = [ gcc6 pythonEnv ]; + propagatedBuildInputs = [ pythonEnv ]; postPatch = '' patchShebangs doc/ns3_html_theme/get_version.sh ''; wafConfigureFlags = with stdenv.lib; [ - "--enable-modules=${stdenv.lib.concatStringsSep "," modules}" + "--enable-modules=${concatStringsSep "," modules}" "--with-python=${pythonEnv.interpreter}" ] ++ optional (build_profile != null) "--build-profile=${build_profile}" - ++ optional generateBindings [ ] ++ optional withExamples " --enable-examples " ++ optional doCheck " --enable-tests " ; + doCheck = true; + buildTargets = "build" + lib.optionalString enableDoxygen " doxygen" + lib.optionalString withManual "sphinx"; - doCheck = true; + # to prevent fatal error: 'backward_warning.h' file not found + CXXFLAGS = "-D_GLIBCXX_PERMIT_BACKWARD_HASH"; + + postBuild = with stdenv.lib; let flags = concatStringsSep ";" ( + optional enableDoxygen "./waf doxygen" + ++ optional withManual "./waf sphinx" + ); + in "${flags}" + ; + + postInstall = '' + moveToOutput "${pythonEnv.libPrefix}" "$py" + ''; # we need to specify the proper interpreter else ns3 can check against a - # different version even though we + # different version checkPhase = '' - ${pythonEnv.interpreter} ./test.py + ${pythonEnv.interpreter} ./test.py --nowaf ''; - hardeningDisable = [ "fortify" ]; + # strictoverflow prevents clang from discovering pyembed when bindings + hardeningDisable = [ "fortify" "strictoverflow"]; - meta = { - homepage = http://www.nsnam.org; - license = stdenv.lib.licenses.gpl3; + meta = with stdenv.lib; { + homepage = "http://www.nsnam.org"; + license = licenses.gpl3; description = "A discrete time event network simulator"; - platforms = with stdenv.lib.platforms; unix; + platforms = with platforms; unix; + maintainers = with maintainers; [ teto ]; }; } |