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Bug on scanpy, sc.pp.neighbors function
Hi, I am working with a big dataset and I run into a problem when computing the neigbours. Find below an small example:
Minimal code sample
import scanpy
import numpy
>
tab = scvi.data.read_csv("C:/Users/RUTBO/AML-029-01-1E.gene.expression.matrix.tsv", delimiter='\t', first_column_names=True)
sc.tl.pca(tab, svd_solver='arpack')
sc.pp.neighbors(tab, n_neighbors=10, n_pcs=40)
traceback
> The error I get:
> ---------------------------------------------------------------------------
> File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\errors.py", line 823, in new_error_context
yield
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\lowering.py", line 293, in lower_block
self.lower_inst(inst)
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\lowering.py", line 438, in lower_inst
val = self.lower_assign(ty, inst)
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\lowering.py", line 624, in lower_assign
return self.lower_expr(ty, value)
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\lowering.py", line 1159, in lower_expr
res = self.lower_call(resty, expr)
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\lowering.py", line 889, in lower_call
res = self._lower_call_normal(fnty, expr, signature)
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\lowering.py", line 1130, in _lower_call_normal
res = impl(self.builder, argvals, self.loc)
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\base.py", line 1201, in __call__
res = self._imp(self._context, builder, self._sig, args, loc=loc)
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\base.py", line 1231, in wrapper
return fn(*args, **kwargs)
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\cpython\rangeobj.py", line 40, in range1_impl
state.stop = stop
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\cgutils.py", line 164, in __setattr__
self[self._datamodel.get_field_position(field)] = value
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\cgutils.py", line 188, in __setitem__
raise TypeError("Invalid store of {value.type} to "
TypeError: Invalid store of i64 to i32 in <numba.core.datamodel.models.RangeModel object at 0x0000015592499520> (trying to write member #1)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Users\RUTBO\PycharmProjects\pvalue\single cell analysis.py", line 44, in <module>
sc.pp.neighbors(tab, n_neighbors=10, n_pcs=40)
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\scanpy\neighbors\__init__.py", line 139, in neighbors
neighbors.compute_neighbors(
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\scanpy\neighbors\__init__.py", line 808, in compute_neighbors
self._distances, self._connectivities = _compute_connectivities_umap(
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\scanpy\neighbors\__init__.py", line 387, in _compute_connectivities_umap
from umap.umap_ import fuzzy_simplicial_set
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\umap\__init__.py", line 2, in <module>
from .umap_ import UMAP
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\umap\umap_.py", line 41, in <module>
from umap.layouts import (
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\umap\layouts.py", line 39, in <module>
def rdist(x, y):
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\decorators.py", line 219, in wrapper
disp.compile(sig)
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\dispatcher.py", line 965, in compile
cres = self._compiler.compile(args, return_type)
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\dispatcher.py", line 125, in compile
status, retval = self._compile_cached(args, return_type)
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\dispatcher.py", line 139, in _compile_cached
retval = self._compile_core(args, return_type)
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\dispatcher.py", line 152, in _compile_core
cres = compiler.compile_extra(self.targetdescr.typing_context,
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\compiler.py", line 693, in compile_extra
return pipeline.compile_extra(func)
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\compiler.py", line 429, in compile_extra
return self._compile_bytecode()
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\compiler.py", line 497, in _compile_bytecode
return self._compile_core()
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\compiler.py", line 476, in _compile_core
raise e
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\compiler.py", line 463, in _compile_core
pm.run(self.state)
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\compiler_machinery.py", line 353, in run
raise patched_exception
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\compiler_machinery.py", line 341, in run
self._runPass(idx, pass_inst, state)
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\compiler_lock.py", line 35, in _acquire_compile_lock
return func(*args, **kwargs)
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\compiler_machinery.py", line 296, in _runPass
mutated |= check(pss.run_pass, internal_state)
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\compiler_machinery.py", line 269, in check
mangled = func(compiler_state)
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\typed_passes.py", line 394, in run_pass
lower.lower()
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\lowering.py", line 196, in lower
self.lower_normal_function(self.fndesc)
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\lowering.py", line 250, in lower_normal_function
entry_block_tail = self.lower_function_body()
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\lowering.py", line 279, in lower_function_body
self.lower_block(block)
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\lowering.py", line 293, in lower_block
self.lower_inst(inst)
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\contextlib.py", line 135, in __exit__
self.gen.throw(type, value, traceback)
File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\errors.py", line 837, in new_error_context
raise newerr.with_traceback(tb)
numba.core.errors.LoweringError: Failed in nopython mode pipeline (step: native lowering)
Invalid store of i64 to i32 in <numba.core.datamodel.models.RangeModel object at 0x0000015592499520> (trying to write member #1)
File "..\..\AppData\Local\Programs\Python\Python39\lib\umap\layouts.py", line 53:
def rdist(x, y):
<source elided>
dim = x.shape[0]
for i in range(dim):
^
During: lowering "$20call_function.7 = call $16load_global.5(dim, func=$16load_global.5, args=[Var(dim, layouts.py:52)], kws=(), vararg=None, target=None)" at C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\umap\layouts.py (53)
I am running scanpy using python v3.9 with numba v0.55.
Are you able to run something like:
from umap import UMAP
embedding = UMAP()
embedding.fit_transform(adata.obsm["X_pca"])
I think this may be largely upstream and due to windows issues. Also is there any chance you are using a 32 bit system?
Hello,I am having the same problem. When I run this:
from umap import UMAP
It occurs this error.
TypeError Traceback (most recent call last)
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\errors.py:823, in new_error_context(fmt_, *args, **kwargs)
[822](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/errors.py?line=821) try:
--> [823](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/errors.py?line=822) yield
[824](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/errors.py?line=823) except NumbaError as e:
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\lowering.py:293, in BaseLower.lower_block(self, block)
[291](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=290) with new_error_context('lowering "{inst}" at {loc}', inst=inst,
[292](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=291) loc=self.loc, errcls_=defaulterrcls):
--> [293](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=292) self.lower_inst(inst)
[294](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=293) self.post_block(block)
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\lowering.py:438, in Lower.lower_inst(self, inst)
[437](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=436) ty = self.typeof(inst.target.name)
--> [438](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=437) val = self.lower_assign(ty, inst)
[439](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=438) argidx = None
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\lowering.py:624, in Lower.lower_assign(self, ty, inst)
[623](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=622) elif isinstance(value, ir.Expr):
--> [624](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=623) return self.lower_expr(ty, value)
[626](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=625) elif isinstance(value, ir.Var):
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\lowering.py:1159, in Lower.lower_expr(self, resty, expr)
[1158](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=1157) elif expr.op == 'call':
-> [1159](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=1158) res = self.lower_call(resty, expr)
[1160](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=1159) return res
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\lowering.py:889, in Lower.lower_call(self, resty, expr)
[888](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=887) else:
--> [889](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=888) res = self._lower_call_normal(fnty, expr, signature)
[891](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=890) # If lowering the call returned None, interpret that as returning dummy
[892](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=891) # value if the return type of the function is void, otherwise there is
[893](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=892) # a problem
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\lowering.py:1130, in Lower._lower_call_normal(self, fnty, expr, signature)
[1128](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=1127) argvals = [the_self] + list(argvals)
-> [1130](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=1129) res = impl(self.builder, argvals, self.loc)
[1131](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=1130) return res
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\base.py:1201, in _wrap_impl.__call__(self, builder, args, loc)
[1200](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/base.py?line=1199) def __call__(self, builder, args, loc=None):
-> [1201](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/base.py?line=1200) res = self._imp(self._context, builder, self._sig, args, loc=loc)
[1202](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/base.py?line=1201) self._context.add_linking_libs(getattr(self, 'libs', ()))
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\base.py:1231, in _wrap_missing_loc.__call__.<locals>.wrapper(*args, **kwargs)
[1230](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/base.py?line=1229) kwargs.pop('loc') # drop unused loc
-> [1231](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/base.py?line=1230) return fn(*args, **kwargs)
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\cpython\rangeobj.py:40, in make_range_impl.<locals>.range1_impl(context, builder, sig, args)
[39](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/cpython/rangeobj.py?line=38) state.start = context.get_constant(int_type, 0)
---> [40](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/cpython/rangeobj.py?line=39) state.stop = stop
[41](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/cpython/rangeobj.py?line=40) state.step = context.get_constant(int_type, 1)
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\cgutils.py:164, in _StructProxy.__setattr__(self, field, value)
[163](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/cgutils.py?line=162) return super(_StructProxy, self).__setattr__(field, value)
--> [164](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/cgutils.py?line=163) self[self._datamodel.get_field_position(field)] = value
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\cgutils.py:188, in _StructProxy.__setitem__(self, index, value)
[187](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/cgutils.py?line=186) else:
--> [188](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/cgutils.py?line=187) raise TypeError("Invalid store of {value.type} to "
[189](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/cgutils.py?line=188) "{ptr.type.pointee} in "
[190](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/cgutils.py?line=189) "{self._datamodel} "
[191](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/cgutils.py?line=190) "(trying to write member #{index})"
[192](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/cgutils.py?line=191) .format(value=value, ptr=ptr, self=self,
[193](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/cgutils.py?line=192) index=index))
[194](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/cgutils.py?line=193) self._builder.store(value, ptr)
TypeError: Invalid store of i64 to i32 in <numba.core.datamodel.models.RangeModel object at 0x00000242239BD700> (trying to write member #1)
During handling of the above exception, another exception occurred:
LoweringError Traceback (most recent call last)
e:\Drosophila\ST\04.yao\E8-10_b_analysis\E8-10_b_analysis\8_cellbin_clustering\cellbin_scsq.ipynb Cell 10' in <cell line: 1>()
----> [1](vscode-notebook-cell:/e%3A/Drosophila/ST/04.yao/E8-10_b_analysis/E8-10_b_analysis/8_cellbin_clustering/cellbin_scsq.ipynb#ch0000016?line=0) from umap import UMAP
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\umap\__init__.py:2, in <module>
[1](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/__init__.py?line=0) from warnings import warn, catch_warnings, simplefilter
----> [2](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/__init__.py?line=1) from .umap_ import UMAP
[4](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/__init__.py?line=3) try:
[5](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/__init__.py?line=4) with catch_warnings():
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\umap\umap_.py:41, in <module>
[34](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/umap_.py?line=33) from umap.utils import (
[35](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/umap_.py?line=34) submatrix,
[36](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/umap_.py?line=35) ts,
[37](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/umap_.py?line=36) csr_unique,
[38](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/umap_.py?line=37) fast_knn_indices,
[39](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/umap_.py?line=38) )
[40](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/umap_.py?line=39) from umap.spectral import spectral_layout
---> [41](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/umap_.py?line=40) from umap.layouts import (
[42](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/umap_.py?line=41) optimize_layout_euclidean,
[43](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/umap_.py?line=42) optimize_layout_generic,
[44](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/umap_.py?line=43) optimize_layout_inverse,
[45](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/umap_.py?line=44) )
[47](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/umap_.py?line=46) from pynndescent import NNDescent
[48](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/umap_.py?line=47) from pynndescent.distances import named_distances as pynn_named_distances
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\umap\layouts.py:39, in <module>
[25](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=24) else:
[26](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=25) return val
[29](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=28) @numba.njit(
[30](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=29) "f4(f4[::1],f4[::1])",
[31](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=30) fastmath=True,
[32](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=31) cache=True,
[33](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=32) locals={
[34](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=33) "result": numba.types.float32,
[35](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=34) "diff": numba.types.float32,
[36](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=35) "dim": numba.types.int32,
[37](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=36) },
[38](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=37) )
---> [39](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=38) def rdist(x, y):
[40](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=39) """Reduced Euclidean distance.
[41](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=40)
[42](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=41) Parameters
(...)
[49](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=48) The squared euclidean distance between x and y
[50](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=49) """
[51](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=50) result = 0.0
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\decorators.py:219, in _jit.<locals>.wrapper(func)
[217](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/decorators.py?line=216) with typeinfer.register_dispatcher(disp):
[218](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/decorators.py?line=217) for sig in sigs:
--> [219](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/decorators.py?line=218) disp.compile(sig)
[220](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/decorators.py?line=219) disp.disable_compile()
[221](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/decorators.py?line=220) return disp
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\dispatcher.py:965, in Dispatcher.compile(self, sig)
[963](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=962) with ev.trigger_event("numba:compile", data=ev_details):
[964](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=963) try:
--> [965](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=964) cres = self._compiler.compile(args, return_type)
[966](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=965) except errors.ForceLiteralArg as e:
[967](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=966) def folded(args, kws):
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\dispatcher.py:125, in _FunctionCompiler.compile(self, args, return_type)
[124](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=123) def compile(self, args, return_type):
--> [125](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=124) status, retval = self._compile_cached(args, return_type)
[126](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=125) if status:
[127](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=126) return retval
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\dispatcher.py:139, in _FunctionCompiler._compile_cached(self, args, return_type)
[136](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=135) pass
[138](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=137) try:
--> [139](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=138) retval = self._compile_core(args, return_type)
[140](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=139) except errors.TypingError as e:
[141](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=140) self._failed_cache[key] = e
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\dispatcher.py:152, in _FunctionCompiler._compile_core(self, args, return_type)
[149](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=148) flags = self._customize_flags(flags)
[151](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=150) impl = self._get_implementation(args, {})
--> [152](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=151) cres = compiler.compile_extra(self.targetdescr.typing_context,
[153](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=152) self.targetdescr.target_context,
[154](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=153) impl,
[155](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=154) args=args, return_type=return_type,
[156](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=155) flags=flags, locals=self.locals,
[157](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=156) pipeline_class=self.pipeline_class)
[158](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=157) # Check typing error if object mode is used
[159](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=158) if cres.typing_error is not None and not flags.enable_pyobject:
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\compiler.py:693, in compile_extra(typingctx, targetctx, func, args, return_type, flags, locals, library, pipeline_class)
[669](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=668) """Compiler entry point
[670](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=669)
[671](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=670) Parameter
(...)
[689](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=688) compiler pipeline
[690](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=689) """
[691](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=690) pipeline = pipeline_class(typingctx, targetctx, library,
[692](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=691) args, return_type, flags, locals)
--> [693](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=692) return pipeline.compile_extra(func)
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\compiler.py:429, in CompilerBase.compile_extra(self, func)
[427](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=426) self.state.lifted = ()
[428](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=427) self.state.lifted_from = None
--> [429](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=428) return self._compile_bytecode()
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\compiler.py:497, in CompilerBase._compile_bytecode(self)
[493](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=492) """
[494](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=493) Populate and run pipeline for bytecode input
[495](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=494) """
[496](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=495) assert self.state.func_ir is None
--> [497](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=496) return self._compile_core()
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\compiler.py:476, in CompilerBase._compile_core(self)
[474](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=473) self.state.status.fail_reason = e
[475](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=474) if is_final_pipeline:
--> [476](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=475) raise e
[477](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=476) else:
[478](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=477) raise CompilerError("All available pipelines exhausted")
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\compiler.py:463, in CompilerBase._compile_core(self)
[461](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=460) res = None
[462](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=461) try:
--> [463](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=462) pm.run(self.state)
[464](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=463) if self.state.cr is not None:
[465](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=464) break
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\compiler_machinery.py:353, in PassManager.run(self, state)
[350](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=349) msg = "Failed in %s mode pipeline (step: %s)" % \
[351](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=350) (self.pipeline_name, pass_desc)
[352](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=351) patched_exception = self._patch_error(msg, e)
--> [353](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=352) raise patched_exception
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\compiler_machinery.py:341, in PassManager.run(self, state)
[339](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=338) pass_inst = _pass_registry.get(pss).pass_inst
[340](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=339) if isinstance(pass_inst, CompilerPass):
--> [341](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=340) self._runPass(idx, pass_inst, state)
[342](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=341) else:
[343](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=342) raise BaseException("Legacy pass in use")
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\compiler_lock.py:35, in _CompilerLock.__call__.<locals>._acquire_compile_lock(*args, **kwargs)
[32](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_lock.py?line=31) @functools.wraps(func)
[33](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_lock.py?line=32) def _acquire_compile_lock(*args, **kwargs):
[34](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_lock.py?line=33) with self:
---> [35](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_lock.py?line=34) return func(*args, **kwargs)
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\compiler_machinery.py:296, in PassManager._runPass(self, index, pss, internal_state)
[294](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=293) mutated |= check(pss.run_initialization, internal_state)
[295](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=294) with SimpleTimer() as pass_time:
--> [296](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=295) mutated |= check(pss.run_pass, internal_state)
[297](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=296) with SimpleTimer() as finalize_time:
[298](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=297) mutated |= check(pss.run_finalizer, internal_state)
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\compiler_machinery.py:269, in PassManager._runPass.<locals>.check(func, compiler_state)
[268](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=267) def check(func, compiler_state):
--> [269](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=268) mangled = func(compiler_state)
[270](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=269) if mangled not in (True, False):
[271](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=270) msg = ("CompilerPass implementations should return True/False. "
[272](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=271) "CompilerPass with name '%s' did not.")
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\typed_passes.py:394, in NativeLowering.run_pass(self, state)
[391](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/typed_passes.py?line=390) with targetctx.push_code_library(library):
[392](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/typed_passes.py?line=391) lower = lowering.Lower(targetctx, library, fndesc, interp,
[393](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/typed_passes.py?line=392) metadata=metadata)
--> [394](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/typed_passes.py?line=393) lower.lower()
[395](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/typed_passes.py?line=394) if not flags.no_cpython_wrapper:
[396](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/typed_passes.py?line=395) lower.create_cpython_wrapper(flags.release_gil)
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\lowering.py:196, in BaseLower.lower(self)
[194](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=193) if self.generator_info is None:
[195](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=194) self.genlower = None
--> [196](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=195) self.lower_normal_function(self.fndesc)
[197](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=196) else:
[198](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=197) self.genlower = self.GeneratorLower(self)
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\lowering.py:250, in BaseLower.lower_normal_function(self, fndesc)
[248](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=247) # Init argument values
[249](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=248) self.extract_function_arguments()
--> [250](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=249) entry_block_tail = self.lower_function_body()
[252](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=251) # Close tail of entry block, do not emit debug metadata else the
[253](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=252) # unconditional jump gets associated with the metadata from the function
[254](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=253) # body end.
[255](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=254) with debuginfo.suspend_emission(self.builder):
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\lowering.py:279, in BaseLower.lower_function_body(self)
[277](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=276) bb = self.blkmap[offset]
[278](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=277) self.builder.position_at_end(bb)
--> [279](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=278) self.lower_block(block)
[280](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=279) self.post_lower()
[281](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=280) return entry_block_tail
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\lowering.py:293, in BaseLower.lower_block(self, block)
[290](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=289) defaulterrcls = partial(LoweringError, loc=self.loc)
[291](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=290) with new_error_context('lowering "{inst}" at {loc}', inst=inst,
[292](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=291) loc=self.loc, errcls_=defaulterrcls):
--> [293](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=292) self.lower_inst(inst)
[294](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=293) self.post_block(block)
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\contextlib.py:131, in _GeneratorContextManager.__exit__(self, type, value, traceback)
[129](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/contextlib.py?line=128) value = type()
[130](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/contextlib.py?line=129) try:
--> [131](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/contextlib.py?line=130) self.gen.throw(type, value, traceback)
[132](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/contextlib.py?line=131) except StopIteration as exc:
[133](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/contextlib.py?line=132) # Suppress StopIteration *unless* it's the same exception that
[134](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/contextlib.py?line=133) # was passed to throw(). This prevents a StopIteration
[135](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/contextlib.py?line=134) # raised inside the "with" statement from being suppressed.
[136](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/contextlib.py?line=135) return exc is not value
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\errors.py:837, in new_error_context(fmt_, *args, **kwargs)
[835](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/errors.py?line=834) else:
[836](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/errors.py?line=835) tb = None
--> [837](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/errors.py?line=836) raise newerr.with_traceback(tb)
[838](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/errors.py?line=837) elif use_new_style_errors():
[839](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/errors.py?line=838) raise e
LoweringError: Failed in nopython mode pipeline (step: native lowering)
Invalid store of i64 to i32 in <numba.core.datamodel.models.RangeModel object at 0x00000242239BD700> (trying to write member #1)
File "D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\umap\layouts.py", line 53:
def rdist(x, y):
<source elided>
dim = x.shape[0]
for i in range(dim):
^
During: lowering "$20call_function.7 = call $16load_global.5(dim, func=$16load_global.5, args=[Var(dim, layouts.py:52)], kws=(), vararg=None, target=None)" at D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\umap\layouts.py (53)
