Errors with latest v4.0.0 from conda - scipy issues

I have just installed v4.0.0 from conda on an Apple m1 device.

I get the following error on importing pymc.

File /opt/homebrew/Caskroom/miniforge/base/lib/python3.10/site-packages/aesara/tensor/nnet/, in
15 import warnings
17 import numpy as np
—> 18 from scipy.signal.signaltools import _bvalfromboundary, _valfrommode, convolve
19 from scipy.signal.sigtools import _convolve2d
21 import aesara

ImportError: cannot import name ‘_bvalfromboundary’ from ‘scipy.signal.signaltools’ (/opt/homebrew/Caskroom/miniforge/base/lib/python3.10/site-packages/scipy/signal/

I was using v4.0.0b6 previously, installed with pip. This was working fine.

I have version 1.8.1 of scipy installed.

Any pointers would be greatly appreciated.

I suspect you have an older version of aesara installed. I would suggest following the new installation instructions and probably installing into a fresh environment.

It seems that conda forge wants to install 4.0.0b1 (even when I specify pymc=4.0.0).

pymc conda-forge/osx-arm64::pymc-4.0.0b1-py310h8e41473_1

Odd, can you try with a fresh environment? Otherwise please post the output.

1 Like

I have just ripped out homebrew and installed the latest anaconda for m1 (2022 May edition).

Then when, as the very first thing, I try to install pymc conda now offers me 4.0.0b6 (not the latest 4.0.0). But it also downgrades python, and it does not give me the latest version of aesara.

(base) xxxxx@Bryans-Mac-Studio ~ % conda install -c conda-forge pymc=4.0.0
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: done

Package Plan

environment location: /Users/xxxxx/anaconda3

added / updated specs:
- pymc=4.0.0

The following packages will be downloaded:

package                    |            build
_anaconda_depends-2022.05  |           py39_0           7 KB
aeppl-0.0.27               |     pyhd8ed1ab_0          36 KB  conda-forge
aesara-2.5.1               |   py39hc65832e_0         2.2 MB  conda-forge
anaconda-custom            |           py39_1           3 KB
arviz-0.12.1               |     pyhd8ed1ab_0         1.4 MB  conda-forge
c-compiler-1.4.1           |       hccd94f0_0           5 KB  conda-forge
ca-certificates-2022.5.18.1|       h4653dfc_0         145 KB  conda-forge
cctools-949.0.1            |      ha9384d2_22          16 KB  conda-forge
cctools_osx-arm64-949.0.1  |      h92b3a8a_22         1.8 MB  conda-forge
certifi-2022.5.18.1        |   py39h2804cbe_0         151 KB  conda-forge
cftime-1.6.0               |   py39h43ea957_1         200 KB  conda-forge
clang-12.0.0               |       hce30654_2         125 KB  conda-forge
clang-12-12.0.0            |default_h0fdd720_2         693 KB  conda-forge
clang_osx-arm64-12.0.0     |       hcb56dc5_3          18 KB
clangxx-12.0.0             |default_h8b1a7b7_2         125 KB  conda-forge
clangxx_osx-arm64-12.0.0   |       h39b79ac_3          17 KB
compiler-rt-12.0.0         |       h94c6b0c_0          80 KB  conda-forge
compiler-rt_osx-arm64-12.0.0|       h44bac85_0         5.8 MB  conda-forge
conda-4.13.0               |   py39h2804cbe_1         992 KB  conda-forge
cons-0.4.5                 |     pyhd8ed1ab_0          13 KB  conda-forge
cxx-compiler-1.4.1         |       h3e96240_0           5 KB  conda-forge
etuples-0.3.5              |     pyhd8ed1ab_0          16 KB  conda-forge
fastprogress-1.0.2         |     pyhd8ed1ab_0          16 KB  conda-forge
hdf4-4.2.13                |    h0ef36ac_1005         875 KB  conda-forge
ld64-530                   |      h08716b2_22          14 KB  conda-forge
ld64_osx-arm64-530         |      ha291f0b_22         1.2 MB  conda-forge
ldid-2.1.2                 |       h34ab4f1_3          55 KB  conda-forge
libblas-3.9.0              |13_osxarm64_openblas          12 KB  conda-forge
libclang-cpp12-12.0.0      |default_h0fdd720_2        11.9 MB  conda-forge
liblapack-3.9.0            |13_osxarm64_openblas          12 KB  conda-forge
libllvm12-12.0.0           |       h93073aa_1        22.4 MB  conda-forge
libnetcdf-4.8.1            |       h96a5d95_1         943 KB
libzip-1.8.0               |       h3887732_1         115 KB  conda-forge
llvm-tools-12.0.0          |       h93073aa_1        10.8 MB  conda-forge
logical-unification-0.4.5  |     pyhd8ed1ab_0          16 KB  conda-forge
minikanren-1.0.3           |     pyhd8ed1ab_0          23 KB  conda-forge
netcdf4-1.5.8              |nompi_py39h37a926c_101         424 KB  conda-forge
openssl-1.1.1o             |       ha287fd2_0         1.8 MB  conda-forge
pymc-4.0.0b6               |   py39hb788106_0         916 KB  conda-forge
python-3.9.7               |h54d631c_3_cpython        11.9 MB  conda-forge
python_abi-3.9             |           2_cp39           4 KB  conda-forge
semver-2.13.0              |     pyh9f0ad1d_0          15 KB  conda-forge
tapi-1100.0.11             |       he4954df_0         187 KB  conda-forge
typing-extensions- |       hd8ed1ab_0           8 KB  conda-forge
typing_extensions- |     pyha770c72_0          28 KB  conda-forge
xarray-einstats-0.2.2      |     pyhd8ed1ab_0          32 KB  conda-forge
                                       Total:        77.5 MB

The following NEW packages will be INSTALLED:

_anaconda_depends pkgs/main/osx-arm64::_anaconda_depends-2022.05-py39_0
aeppl conda-forge/noarch::aeppl-0.0.27-pyhd8ed1ab_0
aesara conda-forge/osx-arm64::aesara-2.5.1-py39hc65832e_0
arviz conda-forge/noarch::arviz-0.12.1-pyhd8ed1ab_0
c-compiler conda-forge/osx-arm64::c-compiler-1.4.1-hccd94f0_0
cctools conda-forge/osx-arm64::cctools-949.0.1-ha9384d2_22
cctools_osx-arm64 conda-forge/osx-arm64::cctools_osx-arm64-949.0.1-h92b3a8a_22
cftime conda-forge/osx-arm64::cftime-1.6.0-py39h43ea957_1
clang conda-forge/osx-arm64::clang-12.0.0-hce30654_2
clang-12 conda-forge/osx-arm64::clang-12-12.0.0-default_h0fdd720_2
clang_osx-arm64 pkgs/main/osx-arm64::clang_osx-arm64-12.0.0-hcb56dc5_3
clangxx conda-forge/osx-arm64::clangxx-12.0.0-default_h8b1a7b7_2
clangxx_osx-arm64 pkgs/main/osx-arm64::clangxx_osx-arm64-12.0.0-h39b79ac_3
compiler-rt conda-forge/osx-arm64::compiler-rt-12.0.0-h94c6b0c_0
compiler-rt_osx-a~ conda-forge/noarch::compiler-rt_osx-arm64-12.0.0-h44bac85_0
cons conda-forge/noarch::cons-0.4.5-pyhd8ed1ab_0
cxx-compiler conda-forge/osx-arm64::cxx-compiler-1.4.1-h3e96240_0
etuples conda-forge/noarch::etuples-0.3.5-pyhd8ed1ab_0
fastprogress conda-forge/noarch::fastprogress-1.0.2-pyhd8ed1ab_0
hdf4 conda-forge/osx-arm64::hdf4-4.2.13-h0ef36ac_1005
ld64 conda-forge/osx-arm64::ld64-530-h08716b2_22
ld64_osx-arm64 conda-forge/osx-arm64::ld64_osx-arm64-530-ha291f0b_22
ldid conda-forge/osx-arm64::ldid-2.1.2-h34ab4f1_3
libblas conda-forge/osx-arm64::libblas-3.9.0-13_osxarm64_openblas
libclang-cpp12 conda-forge/osx-arm64::libclang-cpp12-12.0.0-default_h0fdd720_2
liblapack conda-forge/osx-arm64::liblapack-3.9.0-13_osxarm64_openblas
libllvm12 conda-forge/osx-arm64::libllvm12-12.0.0-h93073aa_1
libnetcdf pkgs/main/osx-arm64::libnetcdf-4.8.1-h96a5d95_1
libzip conda-forge/osx-arm64::libzip-1.8.0-h3887732_1
llvm-tools conda-forge/osx-arm64::llvm-tools-12.0.0-h93073aa_1
logical-unificati~ conda-forge/noarch::logical-unification-0.4.5-pyhd8ed1ab_0
minikanren conda-forge/noarch::minikanren-1.0.3-pyhd8ed1ab_0
netcdf4 conda-forge/osx-arm64::netcdf4-1.5.8-nompi_py39h37a926c_101
pymc conda-forge/osx-arm64::pymc-4.0.0b6-py39hb788106_0
python_abi conda-forge/osx-arm64::python_abi-3.9-2_cp39
semver conda-forge/noarch::semver-2.13.0-pyh9f0ad1d_0
tapi conda-forge/osx-arm64::tapi-1100.0.11-he4954df_0
xarray-einstats conda-forge/noarch::xarray-einstats-0.2.2-pyhd8ed1ab_0

The following packages will be UPDATED:

ca-certificates pkgs/main::ca-certificates-2022.3.29-~ → conda-forge::ca-certificates-2022.5.18.1-h4653dfc_0
certifi pkgs/main::certifi-2021.10.8-py39hca0~ → conda-forge::certifi-2022.5.18.1-py39h2804cbe_0
conda pkgs/main::conda-4.13.0-py39hca03da5_0 → conda-forge::conda-4.13.0-py39h2804cbe_1
openssl pkgs/main::openssl-1.1.1n-h1a28f6b_0 → conda-forge::openssl-1.1.1o-ha287fd2_0

The following packages will be SUPERSEDED by a higher-priority channel:

python pkgs/main::python-3.9.12-hbdb9e5c_0 → conda-forge::python-3.9.7-h54d631c_3_cpython
typing-extensions pkgs/main::typing-extensions-4.1.1-hd~ → conda-forge::typing-extensions-
typing_extensions pkgs/main::typing_extensions-4.1.1-py~ → conda-forge::typing_extensions-

The following packages will be DOWNGRADED:

anaconda 2022.05-py39_0 → custom-py39_1

Proceed ([y]/n)?

Yeah, I know there were some issues with homebrew with the betas.

Not sure about that install. v4b6 was pulling aesara 2.6.2, so I’m not sure why it’s giving you 2.5.1.

1 Like

Bizarre, not sure what that is about. It could be because you are not installing into a fresh environment. Also, I recommend using mamba (mamba-forge) instead of anaconda.

Installing mamba-forge instead of anaconda worked.

1 Like