I am trying to install selene-sdk via conda and I get this error:
conda install -c bioconda selene-sdk
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.
This can take several minutes. Press CTRL-C to abort.
failed
UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:
Specifications:
- selene-sdk -> python[version='>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0']
Your python: python=3.8
If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.
The following specifications were found to be incompatible with your system:
- feature:/linux-64::__glibc==2.35=0
- feature:/linux-64::__unix==0=0
- feature:|#/linux-64::__glibc==2.35=0
- feature:|#/linux-64::__unix==0=0
- selene-sdk -> click -> __unix
- selene-sdk -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17|>=2.17,<3.0.a0']
- selene-sdk -> pytorch[version='>=0.4.1'] -> __cuda
Your installed version is: not available
Their website at https://selene.flatironinstitute.org/master/overview/installation.html
states Please use Selene with Python 3.6+.
Do I need to setup a new environment with conda and install version compatible tools there?
Kindly advice.
Thanks and regards.
Related
I am trying to install pyoptsparse. In order to do that, I set a Conda environment on PyCharm. Then I added conda-forge channel, where the pyoptsparse package should be, but when I am trying to install it through the command : conda install pyoptsparse , it always returns me that the package does not exist.
Has someone already faced to this same problem?
I may precise that I am using a Windows machine.
https://anaconda.org/conda-forge/pyoptsparse
https://mdolab-pyoptsparse.readthedocs-hosted.com/en/latest/install.html
The documentation states that Windows is not supported. Either run through WSL or attempt installing through pip.
However, attempting to install through pip appears to fail during compilation for the win-64 platform, at least when using the following environment:
so-pyoptsparse.yaml
name: so-pyoptsparse
channels:
- conda-forge
- defaults
dependencies:
- python=3.9
- numpy
- sqlitedict >=1.6
- scipy >=1.2
- mdolab-baseclasses >=1.3.1
- swig
- compilers
- pip
- pip:
- git+https://github.com/mdolab/pyoptsparse.git#v2.8.2
Details on how it fails can be found in the logs of the GitHub Workflow run.
I recently installed python with the version 3.8.3 and upgraded pip to 20.1.1. According to enter link description here, conda install -c conda-forge tensorflow should work. However, I get this result
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.
This can take several minutes. Press CTRL-C to abort.
failed
UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:
Specifications:
- tensorflow -> python[version='3.5.*|3.6.*|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|3.7.*']
Your python: python=3.8
If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.
since I use
(base) C:\Users\ivan>python --version
Python 3.8.3
(base) C:\Users\ivan>pip --version
pip 20.1.1 from C:\Users\ivan\anaconda3\lib\site-packages\pip (python 3.8)
I wonder if it is possible to solve this issue without downgrading. For users of anaconda 2020.07, python 3.8 is used by default. Downgrading it will break anaconda.
People have reported problems using tensorflow with python 3.8, it is best to use 3.7. You are incorrect about breaking Anaconda. Here is what to do.
In Anaconda home page click on environments. At the bottom left of the page click on create. A window will appear. Give the new environment a name (say python3.7). In the drop down menu select 3.7. Now a new environment is created using python 3.7. Now in the conda terminal type conda activate python3.7. Then use conda to install tensorflow. It will install version 2.1.1, the cuda toolkit version 10.1.243 and cudnn version 7.6.5. Note conda can only install tensorflow up to version 2.1.1. If you want tensorflow 2.2 install it with pip using pip install tensorflow ==2.2.0. after you have installed 2.1. The cuda toolkit and cudnn work with version 2.2. Now use pip or conda to install any other packages you need in your python3.7 environment and you should be good to go!
I'm trying to implement YOLO3 object detection using tensorflow 2.0 on google colab : https://github.com/theAIGuysCode/Object-Detection-API
And for this particular line:
!python3 /content/Object-Detection-API/load_weights.py
I'm facing this error:
ModuleNotFoundError: No module named 'keras_preprocessing'
I tried installing 'keras_preprocessing' using this command:
!conda install keras_preprocessing
and then I'm facing this error:
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:
- keras_preprocessing
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.
Please help me solve the same!
Thank you!
From the Anaconda repository of the Keras Preprocessing package, you can install it with
conda install -c conda-forge keras-preprocessing
that is, with an - instead of _ and with selecting the conda-forge channel.
Try this
pip install Keras-Preprocessing
I'm currently trying to install scrapy when I encountered my first error:
ERROR conda.core.link:_execute_actions(337): An error occurred while installing package 'conda-forge::automat-0.7.0-py_1'.
CondaError: Cannot link a source that does not exist. D:\ProgramFiles\Python\Scripts\conda.exe
Running conda clean --packages may resolve your problem.
Attempting to roll back.
CondaError: Cannot link a source that does not exist. D:\ProgramFiles\Python\Scripts\conda.exe
Running conda clean --packages may resolve your problem.
I researched this error and followed the advice on this link:
My issues were largely similar to his until I reached the comment which advised me to run conda update -n base conda.
When I ran this code, I encountered my next error:
CondaEnvironmentNotFoundError: Could not find environment: base .
You can list all discoverable environments with conda info --envs.
Kindly advice if my steps taken were appropriate and how can I fix this issue.
The weird thing is I installed scrapy before, and these errors occurred after I recently re-installed Anaconda.
I'm not sure what other info you might require to better understand the situation. Do let me know and I will assist promptly.
Thank You
Try the conda install scrapy channel instead of the conda-forge channel.
To understand the difference between these two channels please read the answer of the following question Should conda, or conda-forge be used for Python environments?
During installation I received the following error:
This script will setup the CNTK prequisites and the CNTK Python
environment onto the machine. More help is given by calling 'get-help
.\install.ps1' in your powershell environment.
The script will analyse your machine and will determine which
components are required. The required components will be downloaded in
[C:\local\Scripts\windows\InstallCache] Repeated operation of this
script will reuse already downloaded components.
If required VS2012 Runtime and VS2013 Runtime will be installed
If required MSMPI will be installed
If required the standard Git tool will be installed
CNTK source will be cloned from Git into [c:\repos\CNTK]
Anaconda3 will be installed into [C:\local\Anaconda3-4.1.1-Windows-x86_64]
A CNTK-PY34 environment will be created in [C:\local\Anaconda3-4.1.1-Windows-x86_64\envs]
CNTK will be installed into the CNTK-PY34 environment
1 - I agree and want to continue Q - Quit the installation process
1 Determining Operations to perform. This will take a moment...
The following operations will be performed: * Setup/Update CNTK Wheel
* Clone CNTK from Github repository
Do you want to continue? (y/n) y Performing download operations
Download operations finished
Performing install operations Setup/Update of CNTK Wheel environment.
Please be patient.... You are using pip version 8.1.2, however version
9.0.0 is available. You should consider upgrading via the 'python -m pip install --upgrade pip' command. Cloning CNTK (branch v2.0.beta2.0)
repository....
Fatal error during script execution!
System.InvalidOperationException: This command cannot be run due to
the error: The system cannot find the file specifie d. at
System.Management.Automation.MshCommandRuntime.ThrowTerminatingError(ErrorRecord
errorRecord)
PS C:\local\Scripts\windows>
I'm not familiar with powershell, so I am not sure where to go from here.
Couple of questions. Are you using beta1 or beta2?
If you are using beta1, just a reminder that there is a beta2 now available with bug fixes and also some improvements to the install script, but I don't think this particular problem has been addressed!
It looks like the clone of the cntk git repository is failing.
Was Git installed on your machine? Is there a GIT.EXE in c:\Program Files\Git\bin\?
I think the install found an existing git.exe (in a different location), and is now trying to call it at the 'wrong' location.
The easiest workaround for you (if you have git installed), from a command prompt:
cd c:/
md \repos
cd repos
clone --branch v2.0.beta1.0 --recursive https://github.com/Microsoft/CNTK
If you have moved to beta2, replace the v2.0.beta1.0 with v2.0.beta2.0