Closed yding9 closed 4 years ago
@yding9 I get the same issue. It seems like an issue with the UMAP package and numba. see here: https://github.com/lmcinnes/umap/issues/225
I'm working on a fix now to remove umap as a dependency.
cc: @davek44
@njbernstein Thank you so much for your quick response and suggestion. Please let me know when the fix is done. And thank you again for this fantastic tool!
@yding9 this should be fixed in the latest commit into master. Please re-open if it is not fixed
Hi,
Thank you so much for creating this fantastic tool! I have previously successfully installed solo and got the pipeline running nicely. But later, I probably installed some other packages and messed up the conda environment, and I got error messages when I tried to run solo. So I decided to remove the conda environment and reinstall solo. I believe I followed everything I did before: conda create -n solo python=3.6 && conda activate solo && pip install -e . This time I got error messages I had never seen before, no matter how many times I tried. And after googling, I have no idea how to solve it. Thank you so much for any help!
Here is the screenshot of the error messages: ERROR: Command errored out with exit status 1: command: /home/yi.ding/anaconda3/envs/solo/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/home/yi.ding/solo/setup.py'"'"'; file='"'"'/home/yi.ding/solo/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info cwd: /home/yi.ding/solo/ Complete output (112 lines): Traceback (most recent call last): File "/home/yi.ding/anaconda3/envs/solo/lib/python3.6/site-packages/numba/errors.py", line 662, in new_error_context yield File "/home/yi.ding/anaconda3/envs/solo/lib/python3.6/site-packages/numba/lowering.py", line 258, in lower_block self.lower_inst(inst) File "/home/yi.ding/anaconda3/envs/solo/lib/python3.6/site-packages/numba/lowering.py", line 301, in lower_inst val = self.lower_assign(ty, inst) File "/home/yi.ding/anaconda3/envs/solo/lib/python3.6/site-packages/numba/lowering.py", line 459, in lower_assign return self.lower_expr(ty, value) File "/home/yi.ding/anaconda3/envs/solo/lib/python3.6/site-packages/numba/lowering.py", line 919, in lower_expr res = self.lower_call(resty, expr) File "/home/yi.ding/anaconda3/envs/solo/lib/python3.6/site-packages/numba/lowering.py", line 711, in lower_call res = self._lower_call_normal(fnty, expr, signature) File "/home/yi.ding/anaconda3/envs/solo/lib/python3.6/site-packages/numba/lowering.py", line 890, in _lower_call_normal res = impl(self.builder, argvals, self.loc) File "/home/yi.ding/anaconda3/envs/solo/lib/python3.6/site-packages/numba/targets/base.py", line 1132, in call res = self._imp(self._context, builder, self._sig, args, loc=loc) File "/home/yi.ding/anaconda3/envs/solo/lib/python3.6/site-packages/numba/targets/base.py", line 1157, in wrapper return fn(*args, **kwargs) File "/home/yi.ding/anaconda3/envs/solo/lib/python3.6/site-packages/numba/targets/arrayobj.py", line 3375, in numpy_zeros_nd _zero_fill_array(context, builder, ary) File "/home/yi.ding/anaconda3/envs/solo/lib/python3.6/site-packages/numba/targets/arrayobj.py", line 3305, in _zero_fill_array cgutils.memset(builder, ary.data, builder.mul(ary.itemsize, ary.nitems), 0) File "/home/yi.ding/anaconda3/envs/solo/lib/python3.6/site-packages/numba/cgutils.py", line 866, in memset builder.call(fn, [ptr, value, size, int32_t(0), bool_t(0)]) File "/home/yi.ding/anaconda3/envs/solo/lib/python3.6/site-packages/llvmlite/ir/builder.py", line 841, in call cconv=cconv, tail=tail, fastmath=fastmath) File "/home/yi.ding/anaconda3/envs/solo/lib/python3.6/site-packages/llvmlite/ir/instructions.py", line 84, in init raise TypeError(msg) TypeError: Type of #4 arg mismatch: i1 != i32
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.