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author | Ben Gamari <ben@smart-cactus.org> | 2018-03-10 11:35:18 -0500 |
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committer | Robert Schütz <rschuetz17@gmail.com> | 2018-04-04 18:39:01 +0200 |
commit | b9484875bcc1918945d373e0ea46ffff938adb05 (patch) | |
tree | c0d541ad20c43cf651e4d92bdb3741347c80a670 /pkgs/development/python-modules | |
parent | c490b0550715ca0b76258c27ccf4b24b85b7fb87 (diff) | |
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pythonPackages.Rtree: init at 0.8.3
This is a commonly-used package for spatial indexing. Strangely enough, the tests are broken due to memory unsafety that I was unable to reproduce under Debian. For instance, when run with Python 3.6 valgrind reports, ==10453== Invalid read of size 4 ==10453== at 0x4EF1DFA: _PyObject_Free (in /nix/store/azw9ys2m2fpfzf730xjcxja890gpyp58-python3-3.6.4/lib/libpython3.6m.so.1.0) ==10453== by 0x4FE7D96: _PyFaulthandler_Fini (in /nix/store/azw9ys2m2fpfzf730xjcxja890gpyp58-python3-3.6.4/lib/libpython3.6m.so.1.0) ==10453== by 0x4F8438D: Py_FinalizeEx (in /nix/store/azw9ys2m2fpfzf730xjcxja890gpyp58-python3-3.6.4/lib/libpython3.6m.so.1.0) ==10453== by 0x4F9F398: Py_Main (in /nix/store/azw9ys2m2fpfzf730xjcxja890gpyp58-python3-3.6.4/lib/libpython3.6m.so.1.0) ==10453== by 0x400BDF: main (in /nix/store/azw9ys2m2fpfzf730xjcxja890gpyp58-python3-3.6.4/bin/python3.6) ==10453== Address 0x67b1020 is 352 bytes inside a block of size 640 free'd ==10453== at 0x4C2DD6B: free (in /nix/store/6z028lfnxyhh8dlngpm6zrkwqxmbglj4-valgrind-3.13.0/lib/valgrind/vgpreload_memcheck-amd64-linux.so) ==10453== by 0x4EDDC4A: free_keys_object (in /nix/store/azw9ys2m2fpfzf730xjcxja890gpyp58-python3-3.6.4/lib/libpython3.6m.so.1.0) ==10453== by 0x4EDEE63: dict_dealloc (in /nix/store/azw9ys2m2fpfzf730xjcxja890gpyp58-python3-3.6.4/lib/libpython3.6m.so.1.0) ==10453== by 0x4EECF59: module_clear (in /nix/store/azw9ys2m2fpfzf730xjcxja890gpyp58-python3-3.6.4/lib/libpython3.6m.so.1.0) ==10453== by 0x4FA062B: collect (in /nix/store/azw9ys2m2fpfzf730xjcxja890gpyp58-python3-3.6.4/lib/libpython3.6m.so.1.0) ==10453== by 0x4FA13A0: _PyGC_CollectNoFail (in /nix/store/azw9ys2m2fpfzf730xjcxja890gpyp58-python3-3.6.4/lib/libpython3.6m.so.1.0) ==10453== by 0x4F79CED: PyImport_Cleanup (in /nix/store/azw9ys2m2fpfzf730xjcxja890gpyp58-python3-3.6.4/lib/libpython3.6m.so.1.0) ==10453== by 0x4F8436F: Py_FinalizeEx (in /nix/store/azw9ys2m2fpfzf730xjcxja890gpyp58-python3-3.6.4/lib/libpython3.6m.so.1.0) ==10453== by 0x4F9F398: Py_Main (in /nix/store/azw9ys2m2fpfzf730xjcxja890gpyp58-python3-3.6.4/lib/libpython3.6m.so.1.0) ==10453== by 0x400BDF: main (in /nix/store/azw9ys2m2fpfzf730xjcxja890gpyp58-python3-3.6.4/bin/python3.6) ==10453== ==10453== Conditional jump or move depends on uninitialised value(s) ==10453== at 0x4EF1E03: _PyObject_Free (in /nix/store/azw9ys2m2fpfzf730xjcxja890gpyp58-python3-3.6.4/lib/libpython3.6m.so.1.0) ==10453== by 0x4EFEF2D: type_dealloc (in /nix/store/azw9ys2m2fpfzf730xjcxja890gpyp58-python3-3.6.4/lib/libpython3.6m.so.1.0) ==10453== by 0x4EFD009: subtype_dealloc (in /nix/store/azw9ys2m2fpfzf730xjcxja890gpyp58-python3-3.6.4/lib/libpython3.6m.so.1.0) ==10453== by 0x4FA063E: collect (in /nix/store/azw9ys2m2fpfzf730xjcxja890gpyp58-python3-3.6.4/lib/libpython3.6m.so.1.0) ==10453== by 0x4FA13A0: _PyGC_CollectNoFail (in /nix/store/azw9ys2m2fpfzf730xjcxja890gpyp58-python3-3.6.4/lib/libpython3.6m.so.1.0) ==10453== by 0x4F79DF8: PyImport_Cleanup (in /nix/store/azw9ys2m2fpfzf730xjcxja890gpyp58-python3-3.6.4/lib/libpython3.6m.so.1.0) ==10453== by 0x4F8436F: Py_FinalizeEx (in /nix/store/azw9ys2m2fpfzf730xjcxja890gpyp58-python3-3.6.4/lib/libpython3.6m.so.1.0) ==10453== by 0x4F9F398: Py_Main (in /nix/store/azw9ys2m2fpfzf730xjcxja890gpyp58-python3-3.6.4/lib/libpython3.6m.so.1.0) ==10453== by 0x400BDF: main (in /nix/store/azw9ys2m2fpfzf730xjcxja890gpyp58-python3-3.6.4/bin/python3.6) ==10453== ...
Diffstat (limited to 'pkgs/development/python-modules')
-rw-r--r-- | pkgs/development/python-modules/Rtree/default.nix | 29 |
1 files changed, 29 insertions, 0 deletions
diff --git a/pkgs/development/python-modules/Rtree/default.nix b/pkgs/development/python-modules/Rtree/default.nix new file mode 100644 index 000000000000..7953829465b9 --- /dev/null +++ b/pkgs/development/python-modules/Rtree/default.nix @@ -0,0 +1,29 @@ +{ stdenv, buildPythonPackage, fetchPypi, libspatialindex, numpy }: + +buildPythonPackage rec { + pname = "Rtree"; + version = "0.8.3"; + + src = fetchPypi { + inherit pname version; + sha256 = "0jc62jbcqqpjcwcly7l9zk25bg72mrxmjykpvfiscgln00qczfbc"; + }; + + propagatedBuildInputs = [ libspatialindex ]; + + patchPhase = '' + substituteInPlace rtree/core.py --replace \ + "find_library('spatialindex_c')" "'${libspatialindex}/lib/libspatialindex_c${stdenv.hostPlatform.extensions.sharedLibrary}'" + ''; + + # Tests appear to be broken due to mysterious memory unsafe issues. See #36760 + doCheck = false; + checkInputs = [ numpy ]; + + meta = with stdenv.lib; { + description = "R-Tree spatial index for Python GIS"; + homepage = https://toblerity.org/rtree/; + license = licenses.lgpl21; + maintainers = with maintainers; [ bgamari ]; + }; +} |