conda install may have broken (possibly with a recent update?)

Hi,

Thanks for the tools and for your time, as usual.

I have been trying to install verkko via conda, using the recommended command:

conda create -n verkko -c conda-forge -c bioconda -c defaults verkko

or its mamba variant:

mamba create -n verkko -c conda-forge -c bioconda -c defaults verkko

Both seemed to hang forever.

So I tried the simpler command (https://anaconda.org/bioconda/verkko) and its mamba variant:

conda create -n verkko bioconda::verkko

or 

mamba create -n verkko bioconda::verkko

Conda output was:

Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
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:

  - feature:/linux-64::__glibc==2.34=0
  - bioconda::verkko -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.34

Mamba had similar output:

Looking for: ['bioconda::verkko']

bioconda/linux-64        Using cache
pkgs/main/linux-64       [====================] (00m:00s) No change
pkgs/main/noarch         [====================] (00m:00s) No change
pkgs/r/linux-64          [====================] (00m:00s) No change
pkgs/r/noarch            [====================] (00m:00s) No change
bioconda/noarch          [====================] (00m:00s) No change
Encountered problems while solving:
  - nothing provides libgcc-ng >=12 needed by verkko-1.1-h64afbab_0

Some info about the OS:

uname -a
Linux login4.cm.cluster 5.14.0-362.24.1.el9_3.x86_64 #1 SMP PREEMPT_DYNAMIC Thu Feb 15 07:18:13 EST 2024 x86_64 x86_64 x86_64 GNU/Linux

I also tried on two other computers.

A mac desktop:

uname -a 
Darwin JohnUrbanSpradling.local 22.6.0 Darwin Kernel Version 22.6.0: Mon Jun 24 01:25:37 PDT 2024; root:xnu-8796.141.3.706.2~1/RELEASE_X86_64 x86_64

conda create -n verkko bioconda::verkko
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
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:

  - feature:/osx-64::__osx==10.16=0
  - bioconda::verkko -> mashmap[version='>=3.0.6'] -> __osx[version='>=10.9']

Your installed version is: 10.16

And on another remote linux machine where it is still hanging after 5-10 minutes.

Well, that is the report. Hopefully there is hope for a poor schlub like me.

Maybe it is just a simple fix of requirements to avoid conflicts...?

Thanks again.

Best,

John

marbl / meryl

conda install may have broken (possibly with a recent update?) #51