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wwood / CoverM

Read coverage calculator for metagenomics
GNU General Public License v3.0
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issue with installing conda #141

Closed kayanac closed 1 year ago

kayanac commented 1 year ago

Hi,

I am having the following error while installing conda. Could you please help me with fixing this issue?

conda install coverm=0.6.1 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 your system:

Your installed version is: 2.17

kayanac commented 1 year ago

I dont have any problem with installing version 0.4.0.

wwood commented 1 year ago

Hi,

I would anticipate that the error you are seeing is caused by conflicts coverm has with other installed packages in your environment.

So would expect

conda create -n coverm coverm

Should work.

If there are other things in your env that are needed, then creating an environment with both might help pin down the issue.

Hth, ben

-------------- Ben Woodcroft Group leader, Centre for Microbiome Research, QUT

From: kayanac @.> Sent: Monday, 7 November 2022, 5:53 am To: wwood/CoverM @.> Cc: Subscribed @.***> Subject: Re: [wwood/CoverM] issue with installing conda (Issue #141)

I dont have any problem with installing version 0.4.0.

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kayanac commented 1 year ago

Hi Ben,

Thank you for your quick reply. I tried your suggestion but I am still having the same problem. As I said before I dont have any problem with installing older versions. The latest version is problematic.

Thanks,

Kadir

wwood commented 1 year ago

Hi,

I tried this without issue - can you paste the command and output you are getting please?

$ mamba create -p /tmp/coverm coverm
...
To activate this environment, use

     $ mamba activate /tmp/coverm

To deactivate an active environment, use

     $ mamba deactivate

(miniconda3)b2:20221110:~$ conda activate /tmp/coverm
(coverm)b2:20221110:~$ coverm --version
coverm 0.6.1
kayanac commented 1 year ago

Hi Ben, When I used your command, it installed version 0.4.0 of coverm without any issue. Then I changed the command to "mamba create -p /tmp/coverm coverm=0.6.1" to install version 0.6.1 and I faced the error below: "Looking for: ['coverm=0.6.1']

bioconda/linux-64 Using cache bioconda/noarch Using cache pkgs/main/noarch 817.7kB @ 450.9kB/s 1.8s pkgs/r/noarch 1.3MB @ 711.5kB/s 1.8s pkgs/r/linux-64 1.4MB @ 773.4kB/s 1.9s pkgs/main/linux-64 4.9MB @ 2.0MB/s 2.6s Encountered problems while solving:

But libzlib version 1.2.13 is already installed.

Thanks,

Kadir

wwood commented 1 year ago

Hmm, what channels are you using?

I also don't understand what you mean by "But libzlib version 1.2.13 is already installed." When you create a new environment nothing is already installed right?

-------------- Ben Woodcroft Group leader, Centre for Microbiome Research, QUT

From: kayanac @.> Sent: Thursday, November 10, 2022 10:46:13 PM To: wwood/CoverM @.> Cc: Ben J Woodcroft @.>; Comment @.> Subject: Re: [wwood/CoverM] issue with installing conda (Issue #141)

Hi Ben, When I used your command, it installed version 0.4.0 of coverm without any issue. Then I changed the command to "mamba create -p /tmp/coverm coverm=0.6.1" to install version 0.6.1 and I faced the error below: "Looking for: ['coverm=0.6.1']

bioconda/linux-64 Using cache bioconda/noarch Using cache pkgs/main/noarch 817.7kB @ 450.9kB/s 1.8s pkgs/r/noarch 1.3MB @ 711.5kB/s 1.8s pkgs/r/linux-64 1.4MB @ 773.4kB/s 1.9s pkgs/main/linux-64 4.9MB @ 2.0MB/s 2.6s Encountered problems while solving:

But libzlib version 1.2.13 is already installed.

Thanks,

Kadir

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kayanac commented 1 year ago

Hi Ben,

Problem solved. I changed the channel from bioconda to conda-forge and I did not have any issue with installing coverm 0.6.1. I used this command: " conda install -c conda-forge coverm=0.6.1" after creating the environment with "conda create -n coverm". Thanks, Kadir

wwood commented 1 year ago

Thanks for closing this out. I think you added condaforge not replaced bioconda, by doing that. Might pay to add condaforge to your condarc so don't have this problem with other software installs.

-------------- Ben Woodcroft Group leader, Centre for Microbiome Research, QUT

From: kayanac @.> Sent: Saturday, November 12, 2022 11:30:40 PM To: wwood/CoverM @.> Cc: Ben J Woodcroft @.>; Comment @.> Subject: Re: [wwood/CoverM] issue with installing conda (Issue #141)

Hi Ben,

Problem solved. I changed the channel from bioconda to conda-forge and I did not have any issue with installing coverm 0.6.1. I used this command: " conda install -c conda-forge coverm=0.6.1" after creating the environment with "conda create -n coverm". Thanks, Kadir

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