Conflicts during PyGMO installation on Mac OS X 11.2.2 with Anaconda - installation

I am attempting to install PyGMO on Mac OS X 11.2.2 (with Anaconda which I reinstalled so the Anaconda Navigator is now upgraded to 2.0.1.)
After the installation starts, it collects package metadata and reports it found package conflicts. How can I solve the conflict so that I can run PyGMO?
Here is the start:
$ conda install -c conda-forge pygmo
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: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: \
Found conflicts! Looking for incompatible packages.
After few hours, the Terminal returns a long report of conflicts and stops there. Here is a representative piece of output:
Package selectors2 conflicts for:
wurlitzer -> selectors2
spyder-kernels -> wurlitzer[version='>=1.0.3'] -> selectors2
Package mpmath conflicts for:
anaconda==2020.07=py38_0 -> sympy==1.6.1=py38_0 -> mpmath[version='>=0.19']
sympy -> mpmath[version='>=0.19']
anaconda==2020.07=py38_0 -> mpmath==1.1.0=py38_0
Package anyio conflicts for:
jupyterlab -> jupyter_server[version='>=1.4,<2'] -> anyio[version='>=2.0.2|>=2.0.2,<3']
jupyterlab_server -> jupyter_server[version='>=1.4,<2'] -> anyio[version='>=2.0.2|>=2.0.2,<3']
Package py-lief conflicts for:
conda-build -> py-lief
anaconda==2020.07=py38_0 -> py-lief==0.10.1=py38haf313ee_0
Note that strict channel priority may have removed packages required for satisfiability.
I followed the official installation guidelines and set the additional channel and its priority. I also checked this command but that is essentially the same thing. I also tried the installation commands from PyPI. And I tried this hint as well

There are two possible states:
Conda solver is correct. The previous package constraints you have in the environment are incompatible with installing pygmo. In that case, you either need to track down the conflicting constraints and try to manually loosen them (not recommended for Anaconda base), or you need to make a new environment:
conda create -n pygmo_env -c conda-forge pygmo
Include whatever other packages you need in there. E.g., ipykernel if you plan on using it as a Jupyter kernel.
Conda solver is bugging out. The solver is reporting trouble solving when it really shouldn't be. This happens, and especially happens when mixing channels (defaults and conda-forge). Many find Mamba, the drop-in replacement for Conda, to be more reliable (and definitely faster!).
conda install conda-forge::mamba
mamba install -c conda-forge pygmo
Unfortunately, it's hard to tell which state it's in. Many of us have been down the rabbit hole of trying to sort through the constraint reports and sometimes there really isn't a sensible conflict to be found. For practical purposes, I'd recommend trying out mamba. If it also fails, then at least you'll have good evidence that you're in state (1).
Additional Commentary
Despite upbeat documentation about installing from any channel in Anaconda Cloud, an Anaconda distribution is highly constrained - i.e., has too many packages - and only tests for co-installation of packages from the defaults channel. Additionally, Conda Forge and Anaconda have different build stacks, so there can be runtime package incompatibilities even when the solver allows co-installation.
Generally, I'd recommend making liberal use of environment creation. Aim to have separate environments for separate tasks/projects. If you plan on frequently using more than a vanilla Anaconda distribution, consider Miniforge or one of its variants. One can always create an Anaconda environment with conda create -n foo -c defaults anaconda.

Related

Cannot install tensorflow-deps for Apple Silicon

I'm trying to set-up by Apple Silicon Mac to be able to train tf models using its GPU.
I tried following the official instructions but I am getting the following error:
>>> conda install -c apple tensorflow-deps
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
PackagesNotFoundError: The following packages are not available from current channels:
- tensorflow-deps
Current channels:
- https://conda.anaconda.org/apple/osx-64
- https://conda.anaconda.org/apple/noarch
- https://repo.anaconda.com/pkgs/main/osx-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/osx-64
- https://repo.anaconda.com/pkgs/r/noarch
- https://conda.anaconda.org/conda-forge/osx-64
- https://conda.anaconda.org/conda-forge/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
Not sure if it should matter but I didn't install Miniforge because I already have Anaconda installed comprehensively. Surely, this can't be the reason? (I didn't want to install Miniforge not to mess up my env by having multiple Conda installations).
I did add the "apple" channel in the Navigator manually and the package does seem to be there:
https://anaconda.org/apple/tensorflow-deps
What am I missing here?
I also struggled with this for a while. The only way I was able to get a successful environment set up was indeed installing conda through mini forge. Based on this link I believe this is because of the other packages Anaconda pre-installs that are not ARM compatible.
I followed this thread to remove my Anaconda installation. Once that is done the instructions you linked should be successful.

How to install ROOT (cern) using Anaconda on Windows 10? [duplicate]

I am attempting to install CERNS ROOT in anaconda, for use of pyRoot. (I am using conda 4.10.3)
I have set up a new environment with python 2.7, because I believe I read somewhere that ROOT does not work well with python 3. After installing python to the new environment and activating it, I have added conda-forge to the current channels and attempted to install the following:
https://anaconda.org/conda-forge/root-dependencies
Using:
conda install -c conda-forge root-dependencies
This however returned the following:
(pyRoot) C:\Users\George>conda install -c conda-forge root-dependencies
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
PackagesNotFoundError: The following packages are not available from current channels:
- root-dependencies
Current channels:
- https://conda.anaconda.org/conda-forge/win-64
- https://conda.anaconda.org/conda-forge/noarch
- https://repo.anaconda.com/pkgs/main/win-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/free/win-64
- https://repo.anaconda.com/pkgs/free/noarch
- https://repo.anaconda.com/pkgs/r/win-64
- https://repo.anaconda.com/pkgs/r/noarch
- https://repo.anaconda.com/pkgs/msys2/win-64
- https://repo.anaconda.com/pkgs/msys2/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
I am not sure why this is not working, as I am fairly sure the root-dependencies are available on the conda-forge channel as per the link.
I have tried the following:
SET CONDA_RESTORE_FREE_CHANNEL=1
Just in case it was part of the free channel that may have been dropped, but I still get the same error.
Any ideas are appreciated :)
The package is not built for win-64 platform, which is what OP channel configuration indicates is being used. Consider WSL2 or Docker (ROOT Project provides pre-built images).
If you would like Conda Forge to build a Windows version, submit an Issue on the feedstock. Just be aware that ROOT Project itself only has beta support for Windows natively, so it's likely not a trivial task.

Install MKL using conda on IBM Power 9 machine

I cannot install mkl using conda on a IBM Power 9 machine. It seems that conda cannot find any suitable version for this machine since conda install mkl installs mkl on a RedHat machine without any error; though, on the IBM Power 9 with either conda install -c anaconda mkl or conda install mkl I get:
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
PackagesNotFoundError: The following packages are not available from current channels:
- mkl
Current channels:
- https://conda.anaconda.org/anaconda/linux-ppc64le
- https://conda.anaconda.org/anaconda/noarch
- https://repo.anaconda.com/pkgs/main/linux-ppc64le
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/linux-ppc64le
- https://repo.anaconda.com/pkgs/r/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
I also tried to download mkl from https://anaconda.org/anaconda/mkl/files and install it conda install on the machine, which was successfully installed. But, after that whenever I wanted to install a new package, I got an inconsistency error by conda:
Collecting package metadata (current_repodata.json): done
Solving environment: |
The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:
- <unknown>/osx-64::mkl==2019.4=intel_233 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: \
The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:
- <unknown>/osx-64::mkl==2019.4=intel_233 failed with initial frozen solve. Retrying with flexible solve.
Solving environment: /
Found conflicts! Looking for incompatible packages. failed
UnsatisfiableError: The following specifications were found to be incompatible with each other:
Package curl conflicts for:
cmake -> curl
anaconda==2019.07=py37_0 -> curl==7.65.2=hbc83047_0
pycurl -> curl=7.55
curl
Package libcurl conflicts for:
curl -> libcurl[version='7.59.0|7.60.0|7.61.0|7.61.1|7.62.0|7.63.0|7.63.0|7.64.0|7.64.1|7.65.2',build='h20c2e04_0|h20c2e04_0|h20c2e04_1000|h20c2e04_0|h20c2e04_0|h20c2e04_0|h1ad7b7a_0|h20c2e04_2']
cmake -> curl -> libcurl[version='7.59.0|7.60.0|7.61.0|7.61.1|7.62.0|7.63.0|7.63.0|7.64.0|7.64.1|7.65.2',build='h20c2e04_0|h20c2e04_0|h20c2e04_1000|h20c2e04_0|h20c2e04_0|h20c2e04_0|h1ad7b7a_0|h20c2e04_2']
anaconda==2019.07=py37_0 -> pycurl==7.43.0.3=py37h1ba5d50_0 -> libcurl[version='>=7.64.1,<8.0a0']
I appreciate any help or comment.

How to install deprecated/unsupported Python 3.4 on conda environment?

Since the deprecation of Python 3.4, conda has removed it from its package list. Is there a way, however, that I can install it?
I need it in order to use software written in this older version.
EDIT:
My question is different than the suggested duplicate one, because I am referring to deprecated and unsupported versions. I already know how to create a conda environment with a specific python version, but executing:
conda create --name py34env python=3.4
results in error (listed in the end), which is due to the lack of the package for Python 3.4 .
One can see the currently supported versions of Python by executing: conda search python and can confirm that Python 3.4 is not on the list.
This is the output of the error when trying to create a Python 3.4 conda enviroment:
$ conda create --name py34env python=3.4
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed
PackagesNotFoundError: The following packages are not available from current channels:
- python=3.4
Current channels:
- https://repo.anaconda.com/pkgs/main/linux-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/linux-64
- https://repo.anaconda.com/pkgs/r/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
When Anaconda dropped it's free channel (technically, Conda 4.7+ just no longer looks there), this resulted in some older package versions that had never been ported to main no longer being accessible.
Option 1: Globally enable free channel searching
However, there is an option to restore access to the free channel, namely restore_free_channel.
# Not generally recommended
conda config --set restore_free_channel True
conda create -n py34 python=3.4
This isn't generally recommended (see blog post), but if you will be working in Python v3.4 frequently and will require other older compatible packages, it might be the best option.
Option 2: Temporarily include free channel
A more temporary solution is to include the free channel using the ad hoc --channel,-c argument. For example,
# slightly better
conda create -n py34 -c defaults -c free python=3.4
Note that I include defaults prior to free so that the latter will only be used if the package cannot be sourced from the former. This assumes the channel_priority setting is set to flexible (the default).
Option 3: Use Conda Forge
Alternatively, Conda Forge has Python v3.4.5, and that won't force you to change a global configuration option.
conda create -n py34 -c conda-forge python=3.4

conda create: UnsatisfiableError

I am trying to create an environment for an installation (https://github.com/linzhi2013/MitoZ/), but I get the following error. Any suggestions what I need to install/uninstall to make it work?
:~$ conda create -n mitozEnv libgd=2.2.4 python=3.6.0 biopython=1.69 ete3=3.0.0b35 perl-list-moreutils perl-params-validate perl-clone circos=0.69 perl-bioperl blast=2.2.31 hmmer=3.1b2 bwa=0.7.12 samtools=1.3.1 infernal=1.1.1 tbl2asn openjdk
Collecting package metadata (current_repodata.json): done
Solving environment: failed
Collecting package metadata (repodata.json): done
Solving environment: failed
UnsatisfiableError: The following specifications were found to be incompatible with each other:
- biopython=1.69 -> reportlab -> pillow[version='>=2.4.0'] -> tk[version='>=8.6.9,<8.7.0a0']
- blast=2.2.31 -> boost=1.60 -> python=3.5 -> tk[version='>=8.6.8,<8.7.0a0']
- ete3=3.0.0b35 -> lxml -> python[version='>=3.6,<3.7.0a0'] -> tk[version='>=8.6.9,<8.7.0a0']
- python=3.6.0 -> tk=8.5
Take it one step at a time.
Why are you specifying a fixlevel 3.6.0 for Python? Unless you have a very good reason, relax this to python=3.6. Newer fixlevels might work with different versions of tk, which could resolve some of your problems.
blast 2.2.31 drags in a dependency on Python 3.5 via boost 1.60. Relax the version of blast, so you can pull in a version of boost that works with the Python 3.6 you want.
With those changes, try again and see what problems remain.

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