Using a Mac with M1 chip, I'm trying to install the following Bioconda packages:
cutadapt
trim-galore
samtools
bedtools.
htseq.
bowtie2.
deeptools.
macs2
I've been able to install picard and fastqc with no issues, but all others turn out one of two error messages:
PackagesNotFoundError: The following packages are not available from current channels:
or
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed
UnsatisfiableError:
I do have the correct channels though:
conda config --show channels
channels:
- conda-forge
- bioconda
- defaults
Not sure how to fix this
I had the same problem and fixed the issue like this:
Install Rosetta2 by running softwareupdate --install-rosetta
Download the x86-64 bit version of miniconda instead of the M1 version
Related
OS: Linux 4.18.0-193.28.1.el8_2.x86_64
anaconda: anaconda3/2022.10
Trying to install RAPIDS, I get:
$ conda install -c rapidsai rapids
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 each other:
Output in format: Requested package -> Available versionsThe following specifications were found to be incompatible with your system:
- feature:/linux-64::__glibc==2.28=0
- feature:|#/linux-64::__glibc==2.28=0
- rapids -> cucim=22.12 -> __glibc[version='>=2.17|>=2.17,<3.0.a0']
Your installed version is: 2.28
$
As has been asked by others (but, as far as I can tell, not answered), why is "__glibc" version 2.28 not between 2.17 & 3.0?
i've got the same problem.
My solution was to create a new conda enviroment with python 3.8/3.9 and use the pip installation recommended by RAPIDS (just create the env and install rapids)
pip install cudf-cu11 dask-cudf-cu11 --extra-index-url=https://pypi.ngc.nvidia.com
pip install cuml-cu11 --extra-index-url=https://pypi.ngc.nvidia.com
pip install cugraph-cu11 --extra-index-url=https://pypi.ngc.nvidia.com
Please try using the full install command, as show in the getting started guide, which pins the rapids, python, and cuda tool kit versions, as well as some of the channels to retrieve any supporting packages:
conda install -c rapidsai -c conda-forge -c nvidia rapids=22.12 python=3.9 cudatoolkit=11.5
I am working with Ubuntu in WSL and tried to install the required packages for a repo with:
$ conda install --file requirements.txt
I got a PackageNotFoundError for a bunch of different packages. I search on anaconda.org for the required channels and added them. But it doesn't matter which channels I add I always get a PackageNotFoundError for the last two remaining packages:
$ conda install --file requirements.txt
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:
- openssl==1.1.1=h7b6447c_0
- intel-openmp==2019.5=281
Current channels:
- https://conda.anaconda.org/fastchan/linux-64
- https://conda.anaconda.org/fastchan/noarch
- https://conda.anaconda.org/cctbx202208/linux-64
- https://conda.anaconda.org/cctbx202208/noarch
- https://conda.anaconda.org/pytorch/linux-64
- https://conda.anaconda.org/pytorch/noarch
- https://conda.anaconda.org/conda-forge/linux-64
- https://conda.anaconda.org/conda-forge/noarch
- 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.
Anaconda.org says conda-forge, fastchan, cctbx202208 for openssl but even though I added all of them it's still not found.
The next thing I tried was to install it with pip:
$ pip install openssl==1.1.1
ERROR: Could not find a version that satisfies the requirement openssl==1.1.1 (from versions: none)
ERROR: No matching distribution found for openssl==1.1.1
But pip detects none versions of this package. Same with intel-openmp, but pip does find packages but not the one I want 2019.5:
$ pip install intel-openmp==2019.5
ERROR: Could not find a version that satisfies the requirement intel-openmp==2019.5 (from versions: 2018.0.0, 2018.0.3, 2019.0, 2020.0.133, 2021.1.1, 2021.1.2, 2021.2.0, 2021.3.0, 2021.4.0, 2022.0.1, 2022.0.2, 2022.1.0, 2022.2.0, 2022.2.1)
ERROR: No matching distribution found for intel-openmp==2019.5
So my question is, is there another way to install the two packages or do they not exists anymore? Because the repo from which I got the code has its last commit from 3 years ago...
Edit:
I tried this command:
conda install -c anaconda openssl
and it installs openssl, but the latest version and than the code still says openssl is missing.
I also tried:
conda install -c anaconda openssl=1.1.1
but I get the same error as in the beginning (PackageNotFoundError in the channels).
Edit2:
TrackNPred is the repo I cloned and want to get working.
As for the required channel, I just searched for the package name on anaconda.org and add the channels i see to my anaconda config with:
conda config --add channels new_channel
I'm not sure if I need the exact version of a package as it's listed in the requirements.txt or if the code also works with another version of the two missing packages.
Edit3:
I changed in the requirements.txt:
openssl=1.1.1*
intel-openmp=2019.5
and that worked.
If you don't require exact package build replication, then edit the file to loosen up the specifications.
I see the intel channel has intel-openmp=2019.5=intel_218 and any openssl=1.1.1 should do. So, find the respective entries in the requirements.txt file and edit them to have:
openssl=1.1.1*
intel-openmp=2019.5
then recreate the environment, with intel channel added.
conda config --set channel_priority flexible
conda create -n foo -c defaults -c intel --file requirements.txt
(base) C:\Users\Lenovo>conda install -c menpo dlib
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:
- dlib -> python[version='2.7.*|3.4.*|3.5.*']
Your python: python=3.7
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.
I did not find a solution to this problem yet. Heeeelppp, i tried both creating a new virtualenv into which install an older version of python (ex 3.5) and run the command pip install quast, but it doesn't work.
I wanna use some libraries such as DLIB, opencv, tensorflow and tesseract for computer vision...
I want to install PythonOCC.
From the official documentation (http://www.pythonocc.org/download/), i saw that i have to use:
conda install -c conda-forge -c dlr-sc -c pythonocc -c oce pythonocc-core==0.18.1
So from the base terminal, i typed that command, but i had some conflicts that i am unable to interpet them or find a solution, since this is my first time using Anaconda.
I am on Ubuntu Linux 20.04.
This is the error message:
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:
- pythonocc-core==0.18.1 -> python[version='>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0']
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 CUDA driver:
- feature:/linux-64::__cuda==10.2=0
- feature:|#/linux-64::__cuda==10.2=0
Your installed CUDA driver is: 10.2
Any ideas on how to proceed from here?
EDIT: After following user's vc 74 suggesttions, i tried these commands:
conda create -n py36 python=3.6
conda activate py36
conda install -c conda-forge -c dlr-sc -c pythonocc -c oce pythonocc-core==0.18.1
This is the new conflict i got:
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 each other:
Output in format: Requested package -> Available versionsThe following specifications were found to be incompatible with your CUDA driver:
- feature:/linux-64::__cuda==10.2=0
Your installed CUDA driver is: 10.2
According to Conda UnsatisfiableError on GitHub, this is a problem with the meta.yaml of the package itself, and not your fault at all. I would suggest opening a support ticket with the makers of the PythonOCC module. Then they will be able to fix the issue.
I'm trying to install some packages on a remote machine (with GPUs) that is not connected to the internet.
(Some people have suggested I should be using Docker and I may well do that but here's one last chance to get this working).
FYI: I'm following the instructions here.
What I've done so far:
Downloaded Anaconda Anaconda3-2019.03-Linux-x86_64.sh file and installed it on the remote machine
$ conda --version
conda 4.6.14
Then downloaded the desired package from here and moved it to the remote machine.
$ ls pkgs-for-anaconda/linux-64/*tensorflow*
pkgs-for-anaconda/linux-64/tensorflow-gpu-1.9.0-hf154084_0.tar.bz2
Setup a new channel which is the file path on the local file system.
$ conda config --prepend channels file:///home/billtubbs/pkgs-for-anaconda
Excerpt from config to confirm this worked:
channels:
- file:///home/billtubbs/pkgs-for-anaconda
- defaults
Install the package
$ conda install pkgs-for-anaconda/linux-64/tensorflow-gpu-1.9.0-hf154084_0.tar.bz2
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Index the packages
$ conda index pkgs-for-anaconda/
Subdir: noarch: 100%|████████████████████████████████████| 2/2 [00:00<00:00, 81.80it/s]
(base) [billtubbs#localhost ~]$ ch: 0it [00:00, ?it/s]s]05 [00:00<00:00, 750741.03it/s]
Is the issue that it looked in no noarch instead of linux-64?
Try to install the package
When I use the following to create a new environment with the desired package:
$ conda create -n tf tensorflow-gpu
I get:
Collecting package metadata: done
Solving environment: failed
PackagesNotFoundError: The following packages are not available from current channels:
- tensorflow-gpu -> _tflow_190_select==0.0.1=gpu
- tensorflow-gpu -> tensorflow==1.9.0
Current channels:
- file:///home/billtubbs/pkgs-for-anaconda/linux-64
- file:///home/billtubbs/pkgs-for-anaconda/noarch
- https://repo.anaconda.com/pkgs/main/linux-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/free/linux-64
- https://repo.anaconda.com/pkgs/free/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.
What I don't understand is that it shows my channel exists. And it even seems to be looking for the right version (1.9.0). But it says it can't find it.
Just to confirm, I did the following:
$ conda search tensorflow-gpu==1.9.0
Loading channels: done
# Name Version Build Channel
tensorflow-gpu 1.9.0 hf154084_0 pkgs-for-anaconda
tensorflow-gpu 1.9.0 hf154084_0 pkgs/main
Anyone know what I am doing wrong?
UPDATE:
Here is some of the output from
$ conda list --show-channel-urls
...
sympy 1.3 py37_0 defaults
tblib 1.3.2 py37_0 defaults
tensorflow-gpu 1.9.0 hf154084_0 file:///home/billtubbs/pkgs-for-anaconda
terminado 0.8.1 py37_1 defaults
testpath 0.4.2 py37_0 defaults
I will recommend you that you uninstall the current version of anaconda that you have, when I downloaded the last version of anaconda i got some problems, I remenber that I could'nt install for example tensorflow or matplotlib..
The best version to work with tensorflow or matplotlib is having one anaconda with python 3.6. Try to install Anaconda3-4.4.0-Windows-x86_64 or Anaconda3-4.4.0-Linux-x86_64.sh which was released in 2017-05-26.
Anacoda versions
And then try to install tensorflow, matplotlib, pandas, numpy but before run
conda update conda
To update some packages of anaconda.
And you will install those the packages/libraries without problems,
Best Regards.
PD: I also tried to install docker however I got more problems than using python with pip, that's why I think anaconda is the best solution.