Anaconda glibc removed - urgent

Hi everyone,
I was trying to use another package which was using upgraded version of glibc so I upgraded glibc to 2.19. But it was vital for java and python apparently, now I get this:

Segmentation fault (core dumped) conda activate anaconda3

is there any way I can get Conda to work again? Or do I have to install Conda again?
Lastly, removing conda package of glibc just hurt conda, it doesn’t harm the server itself right?
Thank you,
S

1 Like

dear selmanurkeskin.

Thank you for posting. See you again.

I think the basic reason is that I’m using a far earlier version when compiling conda.

On Anaconda3-2022.05-Linux-x86_64, glib is 2.69.1.
So you have to answer your question.
that is

is there any way I can get Conda to work again?

You have to change glib in the \ anaconda3 \ lib \ directory to the normal version.
Unfortunately, the only way to do this is to reinstall it, as conda is broken.

Or do I have to install Conda again?

That is the most correct method. Specifically, I think it’s a good idea to remove the current anaconda and reinstall it.

Lastly, removing conda package of glibc just hurt conda, it does n’t harm the server itself right?

Deleting glibc under \ anaconda3, or deleting anaconda itself has no effect on the server itself. However, in windows etc., environment variables are set automatically, so it may not work unless you change the PATH setting.

see you.

ktsh.tanaka.2020

Dear ktsh.tanaka.2020, thank you so much for replying. Uninstalling and reinstalling solved my problem much quicker than trying other ways. However, now I am trying to install BUSCO again and the problem remains.

conda install -c bioconda busco

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==2.17=0
  - feature:|@/linux-64::__glibc==2.17=0

Your installed version is: 2.17

Do you have any idea how can I solve this?
Thank you so much,
Selma

1 Like

dear selmanurkeskin.

thank you for reply.

Sounds like a lot of trouble.
This issue has been known for a long time and is also discussed on github. Here is a reference URL.

And the best solution is the following on the site that distributes BUSCO.

Conda package

Ensure sure you have conda version 4.8.4 or higher. Enter conda -V to check. If necessary, update conda by entering conda update -n base conda.

To install BUSCO in the current environment, enter

conda install -c conda-forge -c bioconda busco = 5.4.2

Alternatively you can create a new environment with BUSCO installed

conda create -n <your_env_name> -c conda-forge -c bioconda busco = 5.4.2
conda activate <your_env_name>

Here, 5.42 is targeted, but it depends on the version of Python you have installed, so please refer to the following site and select it.

https://anaconda.org/bioconda/busco/files

see you.
ktsh.tanaka.2020

1 Like

Dear ktsh.tanaka.2020,
I want to thank you and wish you have a great day, but problems keep occurring. Hopefully this is the last question.

This happens when I try to install it to current environment

PackagesNotFoundError: The following packages are not available from current channels:

  - busco=5.4.2

Current channels:

  - https://conda.anaconda.org/conda-forge/linux-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://conda.anaconda.org/bioconda/linux-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://conda.anaconda.org/r/linux-64
  - https://conda.anaconda.org/r/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.

And this happens when I try to create a new one

conda create -n <busco> -c conda-forge -c bioconda busco=5.4.2

Fatal Python error: init_sys_streams: <stdin> is a directory, cannot continue

Python runtime state: core initialized

Current thread 0x00007fc2bd9eb740 (most recent call first):

<no Python frame>

(base) -bash-4.2$

condainit was not allowed because the instructions on the server I am using told me so. I am not sure if it would make any difference anyway. I am also gonna ask people at busco but is there any other solution you can come up with? Can’t thank you enough!
Selma

1 Like

dear selmanurkeskin.

thank you for reply.
In order to install BUSCO, you need to install biopython, was it done first?

First, this procedure will install biopython.
-bash-4.2 $ conda activate
(base) -bash-4.2 $ pip install biopython == 1.77

after that
(base) -bash-4.2 $ conda create -n -c conda-forge -c bioconda busco = 5.4.2 --force-reinstall

Should be installed with. The last bonus is that it has failed once, so if you do not overwrite it, it seems that it has already been written to / anaconda3 / pkgs /, so you have to run it again to install it correctly.

Perhaps the error the system spits out is due to the biopython not being installed. The required site-packages are also slightly different …

see you.
ktsh.tanaka.2020

1 Like

I installed biopython but it still didn’t work, then I downloaded the previous version. Hopefully it will do all the job. thank you so much for all your help!
-S

1 Like

dear selmanurkeskin.

thank you for your reply.
I wish you success in your work. I also hope that your anaconda life will be fulfilling.

Regards, you.
ktsh.tanaka.2020