I run this script from the Anaconda terminal:
conda create -n jupyterlab-debugger -c conda-forge jupyterlab=3 ipykernel>=6 xeus-python
and I get this
Preparing transaction: done
Verifying transaction: done
Executing transaction: | WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename C:\Users\nicomp\anaconda3\envs\jupyterlab-debugger\Lib\site-packages\te
stpath\cli-32.exe. Please remove this file manually (you may need to reboot to free file handles)
done
ERROR conda.core.link:_execute(699): An error occurred while installing package 'conda-forge::pywin32-302-py310he2412df_2'.
Rolling back transaction: done
[Errno 2] No such file or directory: 'C:\\Users\\nicomp\\anaconda3\\envs\\jupyterlab-debugger\\Library\\bin\\pythoncom310.dll'
()
So it says I need to delete
C:\Users\nicomp\anaconda3\envs\jupyterlab-debugger\Lib\site-packages\te
stpath\cli-32.exe
but that file isn't on my computer in the first place.
When I try to run the experiment defined in this notebook in notebook, I encountered an error when it is creating the conda env. The error occurs when the below cell is executed:
from azureml.core import Experiment, ScriptRunConfig, Environment
from azureml.core.conda_dependencies import CondaDependencies
from azureml.widgets import RunDetails
# Create a Python environment for the experiment
sklearn_env = Environment("sklearn-env")
# Ensure the required packages are installed (we need scikit-learn, Azure ML defaults, and Azure ML dataprep)
packages = CondaDependencies.create(conda_packages=['scikit-learn','pip'],
pip_packages=['azureml-defaults','azureml-dataprep[pandas]'])
sklearn_env.python.conda_dependencies = packages
# Get the training dataset
diabetes_ds = ws.datasets.get("diabetes dataset")
# Create a script config
script_config = ScriptRunConfig(source_directory=experiment_folder,
script='diabetes_training.py',
arguments = ['--regularization', 0.1, # Regularizaton rate parameter
'--input-data', diabetes_ds.as_named_input('training_data')], # Reference to dataset
environment=sklearn_env)
# submit the experiment
experiment_name = 'mslearn-train-diabetes'
experiment = Experiment(workspace=ws, name=experiment_name)
run = experiment.submit(config=script_config)
RunDetails(run).show()
run.wait_for_completion()
Everytime I run this, I always faced the issue of creating the conda env as below:
Creating conda environment...
Running: ['conda', 'env', 'create', '-p', '/home/azureuser/.azureml/envs/azureml_000000000000', '-f', 'azureml-environment-setup/mutated_conda_dependencies.yml']
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Installing pip dependencies: ...working...
Attempting to clean up partially built conda environment: /home/azureuser/.azureml/envs/azureml_000000000000
Remove all packages in environment /home/azureuser/.azureml/envs/azureml_000000000000:
Creating conda environment failed with exit code: -15
I could not find anything useful on the internet and this is not the only script where it fail. When I am try to run other experiments I have sometimes faced this issue. One solution which worked in the above case is I moved the pandas from pip to conda and it was able to create the coonda env. Example below:
# Ensure the required packages are installed (we need scikit-learn, Azure ML defaults, and Azure ML dataprep)
packages = CondaDependencies.create(conda_packages=['scikit-learn','pip'],
pip_packages=['azureml-defaults','azureml-dataprep[pandas]'])
# Ensure the required packages are installed (we need scikit-learn, Azure ML defaults, and Azure ML dataprep)
packages = CondaDependencies.create(conda_packages=['scikit-learn','pip','pandas'],
pip_packages=['azureml-defaults','azureml-dataprep'])
The error message (or the logs from Azure) is also not much help. Would apprecite if a proper solution is available.
Edit: I have recently started learning to use Azure for Machine learning and so if I am not sure if I am missing something? I assume the example notebooks should work as is hence raised this question.
short answer
Totally been in your shoes before. This code sample seems a smidge out of date. Using this notebook as a reference, can you try the following?
packages = CondaDependencies.create(
pip_packages=['azureml-defaults','scikit-learn']
)
longer answer
Using pip with Conda is not always smooth sailing. In this instance, conda isn't reporting up the issue that pip is having. The solution is to create and test this environment locally where we can get more information, which will at least will give you a more informative error message.
Install anaconda or miniconda (or use an Azure ML Compute Instance which has conda pre-installed)
Make a file called environment.yml that looks like this
name: aml_env
dependencies:
- python=3.8
- pip=21.0.1
- pip:
- azureml-defaults
- azureml-dataprep[pandas]
- scikit-learn==0.24.1
Create this environment with the command conda env create -f environment.yml.
respond to any discovered error message
If there' no error, use this new environment.yml with Azure ML like so
sklearn_env = Environment.from_conda_specification(name = 'sklearn-env', file_path = './environment.yml')
more context
the error I'm guessing that's happening is when you reference a pip requirements file from a conda environment file. In this scenario, conda calls pip install -r requirements.txt and if that command errors out, conda can't report the error.
requirements.txt
scikit-learn==0.24.1
azureml-dataprep[pandas]
environment.yml
name: aml_env
dependencies:
- python=3.8
- pip=21.0.1
- pip:
- -rrequirements.txt
What worked for me looking at the previous notebook 05 - Train Models.ipynb:
packages = CondaDependencies.create(conda_packages=['pip', 'scikit-learn'],
pip_packages=['azureml-defaults'])
You have to:
Remove 'azureml-dataprep[pandas]' from pip_packages
Change the order of conda_packages - pip should go first
I have installed bioconda following the instructions at https://bioconda.github.io/user/install.html#set-up-channels. Then I tried
conda install bwa
conda install bcftools
conda install plink2
They all installed fine. However, when I tried
conda install bcftools-gtc2vcf-plugin
or
conda install -c bioconda bcftools-gtc2vcf-plugin
as instructed at https://bioconda.github.io/recipes/bcftools-gtc2vcf-plugin/README.html, I got errors as follows:
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:
- bcftools-gtc2vcf-plugin
Current channels:
- https://conda.anaconda.org/bioconda/osx-64
- https://conda.anaconda.org/bioconda/noarch
- https://conda.anaconda.org/conda-forge/osx-64
- https://conda.anaconda.org/conda-forge/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
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.
Any help would be highly appreciated.
Thanks in advance!
I would advise (as of 2020-01-06) not to use the bcftools-gtc2vcf-plugin as it is an old version missing many features compared to the current version. I would advise either to compile from source (https://github.com/freeseek/gtc2vcf) or alternatively to download pre-compiled binaries (https://personal.broadinstitute.org/giulio/gtc2vcf) that should work on systems with ≥GLIBC_2.3 installed (and making sure you are running the latest version of BCFtools)
If you get the error:
No functional bcftools plugins were found in
BCFTOOLS_PLUGINS="/Users/moxu/xbin/seq/bcftools/plugins".
- Is the plugin path correct?
- Run "bcftools plugin -lv" for more detailed error output.
Could not load "gtc2vcf".
(a bcftools plugin bug that the maintainers will fix soon), can you try to run one of the following commands instead:
$ bcftools plugin gtc2vcf -vv
$ bcftools +gtc2vcf -vv
$ bcftools plugin /Users/moxu/xbin/seq/bcftools/plugins/gtc2vcf.so -vv
$ bcftools +/Users/moxu/xbin/seq/bcftools/plugins/gtc2vcf.so -vv
You should get a reason for why the plugin is not loading. A typical error message could look like this:
/Users/moxu/xbin/seq/bcftools/plugins/gtc2vcf.so:
dlopen .. /lib64/libc.so.6: version `GLIBC_2.3' not found (required by /Users/moxu/xbin/seq/bcftools/plugins/gtc2vcf.so)
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.
I am trying to install SNMP package in SUSE Linux enterprise server 11. I downloaded net-snmp-5.6.1-3.3.x86_64.rpm and installed with the below command
UKGBDCESRPL048:/opt/packages # rpm -ivh --nodeps net-snmp-5.6.1-3.3.x86_64.rpm
warning: net-snmp-5.6.1-3.3.x86_64.rpm: Header V3 RSA/SHA256 signature: NOKEY, key ID 3dbdc284
Preparing...
##################################### [100%]
1:net-snmp
##################################### [100%]
Updating /etc/sysconfig/net-snmp...
But when I try to start snmpd service, I am getting an error below:
UKGBDCESRPL048:/opt/packages # /etc/init.d/snmpd start
Starting snmpd/usr/sbin/snmpd: error while loading shared libraries: libnetsnmpagent.so.25: cannot open shared object file: No such file or directory
startproc: exit status of parent of /usr/sbin/snmpd: 127
Please help me to properly install SNMP package.
Why are you trying to install the RPM with --nodeps? This breaks your RPM dependencies! Please remove the package again and try to install it without that option. This should fail with a list of additionally required RPM's.
You'll have to install them, too. BTW, I'm sure that at least the RPM libsnmp15 is missing, because libnetsnmpagent.so.25 is in there.
You could also configure SLES to use one or more (online) repositories after registering your machine with a license key. After that, a simple
zypper in net-snmp
should solve all dependencies automatically.
One more thing: net-snmp-5.6.1-3.3.x86_64.rpm doesn't seem to be a valid SLES 11 package. Latest version (even SP4) is 5.4.2.1-8.12.24.1. Where did you get the RPM from? Just wondering...