conda install issues

[decarlin]

Hi, having trouble with the conda install. Specifically:

>>conda create --name hicexplorer hicexplorer=3.6 python=3.8 -c bioconda -c conda-forge
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 each other:

Output in format: Requested package -> Available versions

Package python conflicts for:
hicexplorer=3.6 -> python[version='>=3.6']
hicexplorer=3.6 -> biopython[version='<1.77'] -> python[version='2.7.*|3.5.*|3.6.*|3.4.*|>=3.6,<3.7.0a0|>=2.7,<2.8.0a0|>=3.8,<3.9.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0|<3.7|>=3.10,<3.11.0a0|>=3.9,<3.10.0a0|>=3|>=3.5|>=3.7.1,<3.8.0a0|>=3.7|<3.0.0|>=2.7|2.7|>=3.5']
python=3.8The following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.31=0
  - feature:|@/linux-64::__glibc==2.31=0

Your installed version is: 2.31

Note that strict channel priority may have removed packages required for satisfiability.

This is a clean install of conda, and that glibc requirement seems to be met. Any insight? Thanks

[kalavattam]

Hi, you ought to try the installation with mamba, which is a reimplementation of conda that better handles dependency solving (among other things; more info on mamba). For example, use conda to install mamba in your environment of choice:

conda install -c conda-forge mamba

Then, use mamba to install hicexplorer:

mamba install hicexplorer -c bioconda -c conda-forge

Want to make a new environment for the latest version of hicexplorer? Try something like this:

mamba create --name hicexplorer hicexplorer=3.7.2 -c bioconda -c conda-forge

[adklocko]

Hi, I am trying to install HicExplorer on a new Mac with an Apple M2 Ultra Chip running Sonoma 14.2.1 (plenty of space on the hard drive), and have been having difficulties. I was able to install Anaconda (conda version 23.11.0) and tried using the mamba install as above (mamba installed just fine; version 1.5.6). However, I have been getting this error with the installation command (I had previously created an environment called "hicexp"):

(hicexp) lab-computer_4@cent274-2 ~ % mamba install hicexplorer -c bioconda -c conda-forge

Looking for: ['hicexplorer']

bioconda/osx-arm64 (check zst)                      Checked  0.1s
bioconda/noarch (check zst)                        Checked  0.1s
pkgs/main/osx-arm64 (check zst)                    Checked  0.0s
pkgs/main/noarch (check zst)                       Checked  0.0s
pkgs/r/osx-arm64 (check zst)                       Checked  0.0s
pkgs/r/noarch (check zst)                          Checked  0.0s
r/osx-arm64 (check zst)                            Checked  0.1s
r/noarch (check zst)                                Checked  0.1s
bioconda/osx-arm64                                 124.0 B @   2.0kB/s  0.1s
pkgs/main/osx-arm64                                  2.1MB @  22.2MB/s  0.1s
r/osx-arm64                                        124.0 B @ 921.0 B/s  0.0s
pkgs/r/noarch                                        2.0MB @   7.6MB/s  0.1s
pkgs/r/osx-arm64                                   108.0 B @ 369.0 B/s  0.0s
conda-forge/osx-arm64                                8.1MB @  26.5MB/s  0.3s
pkgs/main/noarch                                   699.2kB @   2.1MB/s  0.0s
conda-forge/noarch                                  13.2MB @  35.4MB/s  0.4s
r/noarch                                           864.1kB @   2.1MB/s  0.3s
bioconda/noarch                                      5.1MB @   3.3MB/s  1.5s

Pinned packages:
  - python 3.12.*

Could not solve for environment specs
The following packages are incompatible
└─ hicexplorer is not installable because there are no viable options
   ├─ hicexplorer [2.2|2.2.1|2.2.2|2.2.3] would require
   │  └─ pybigwig, which does not exist (perhaps a missing channel);
   ├─ hicexplorer 3.0.1 would require
   │  └─ krbalancing >=0.0.4 , which does not exist (perhaps a missing channel);
   ├─ hicexplorer 3.0.2 would require
   │  └─ krbalancing 0.0.4 , which does not exist (perhaps a missing channel);
   ├─ hicexplorer [3.1|3.2|...|3.7.3] would require
   │  └─ krbalancing >=0.0.5 , which does not exist (perhaps a missing channel);
   └─ hicexplorer [3.5.2|3.5.3|...|3.7.2] would require
      └─ biopython <1.77 , which does not exist (perhaps a missing channel).

I have tried independently installing krbalancing and biopython, but further installation attempts were not successful. I know my channels are properly installed:

(hicexp) lab-computer_4@cent274-2 ~ % conda config --show channels
channels:
  - bioconda
  - conda-forge
  - defaults
  - r 

Can you provide any insight into this issue? Thanks!

[kalavattam]

Hi,

Bioconda packages are not compiled for Apple architecture, so it's necessary to instruct conda/mamba to install packages compiled for osx-64, which will then run through Rosetta. You can achieve this by using the following command:

CONDA_SUBDIR=osx-64 mamba install hicexplorer -c bioconda -c conda-forge

Good luck!

On Thu, Jan 11, 2024 at 2:54 PM adklocko @.***> wrote:

Hi, I am trying to install HicExplorer on a new Mac with an Apple M2 Ultra Chip running Sonoma 14.2.1 (plenty of space on the hard drive), and have been having difficulties. I was able to install Anaconda (conda version 23.11.0) and tried using the mamba install as above (mamba installed just fine; version 1.5.6). However, I have been getting this error with the installation command (I had previously created an environment called "hicexp"):

(hicexp) @.*** ~ % mamba install hicexplorer -c bioconda -c conda-forge

Looking for: ['hicexplorer']

bioconda/osx-arm64 (check zst) Checked 0.1s bioconda/noarch (check zst) Checked 0.1s pkgs/main/osx-arm64 (check zst) Checked 0.0s pkgs/main/noarch (check zst) Checked 0.0s pkgs/r/osx-arm64 (check zst) Checked 0.0s pkgs/r/noarch (check zst) Checked 0.0s r/osx-arm64 (check zst) Checked 0.1s r/noarch (check zst) Checked 0.1s bioconda/osx-arm64 124.0 B @ 2.0kB/s 0.1s pkgs/main/osx-arm64 2.1MB @ 22.2MB/s 0.1s r/osx-arm64 124.0 B @ 921.0 B/s 0.0s pkgs/r/noarch 2.0MB @ 7.6MB/s 0.1s pkgs/r/osx-arm64 108.0 B @ 369.0 B/s 0.0s conda-forge/osx-arm64 8.1MB @ 26.5MB/s 0.3s pkgs/main/noarch 699.2kB @ 2.1MB/s 0.0s conda-forge/noarch 13.2MB @ 35.4MB/s 0.4s r/noarch 864.1kB @ 2.1MB/s 0.3s bioconda/noarch 5.1MB @ 3.3MB/s 1.5s

Pinned packages:

• python 3.12.*

Could not solve for environment specs The following packages are incompatible └─ hicexplorer is not installable because there are no viable options ├─ hicexplorer [2.2|2.2.1|2.2.2|2.2.3] would require │ └─ pybigwig, which does not exist (perhaps a missing channel); ├─ hicexplorer 3.0.1 would require │ └─ krbalancing >=0.0.4 , which does not exist (perhaps a missing channel); ├─ hicexplorer 3.0.2 would require │ └─ krbalancing 0.0.4 , which does not exist (perhaps a missing channel); ├─ hicexplorer [3.1|3.2|...|3.7.3] would require │ └─ krbalancing >=0.0.5 , which does not exist (perhaps a missing channel); └─ hicexplorer [3.5.2|3.5.3|...|3.7.2] would require └─ biopython <1.77 , which does not exist (perhaps a missing channel).

I have tried independently installing krbalancing and biopython, but further installation attempts were not successful. I know my channels are properly installed:

(hicexp) @.*** ~ % conda config --show channels channels:

• bioconda
• conda-forge
• defaults
• r

Can you provide any insight into this issue? Thanks!

— Reply to this email directly, view it on GitHub https://github.com/deeptools/HiCExplorer/issues/789#issuecomment-1887866140, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIGT6GB2SKZKVKPUGT6L37LYOA7ODAVCNFSM5RMBPG7KU5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCOBYG44DMNRRGQYA . You are receiving this because you commented.Message ID: @.***>

[adklocko]

This worked perfectly. Thank you so much!