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pythonPackages.Rtree: init at 0.8.3

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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==
...
This commit is contained in:
Ben Gamari 2018-03-10 11:35:18 -05:00 committed by Robert Schütz
parent c490b05507
commit b9484875bc
2 changed files with 31 additions and 0 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

29
pkgs/development/python-modules/Rtree/default.nix Normal file
View file

@ -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 ];
};
}

2
pkgs/top-level/python-packages.nix
View file

@ -14467,6 +14467,8 @@ in {
};
};
Rtree = callPackage ../development/python-modules/Rtree { inherit (pkgs) libspatialindex; };
squaremap = buildPythonPackage rec {
name = "squaremap-1.0.4";
disabled = isPy3k;