issue about install SCENIC+ in environment

[Xinlei672]

Hello. I am opening this issue since I have issues with Installing SCENIC+ on a server using the conda environment.

I have followed the instructions in the [https://scenicplus.readthedocs.io/en/latest/install.html]:

conda create --name scenicplus python=3.11

conda activate scenicplus
git clone https://github.com/aertslab/scenicplus
cd scenicplus
git checkout development
pip install .

then I obtain this:

Error output
(base) axle@shpc-698-instance-ajKrL0oq:~$ conda create --name scenicplus python=3.11 -y
/home/axle/miniconda3/lib/python3.11/site-packages/conda/base/context.py:198: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3.

To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels:

conda config --add channels defaults

For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html

deprecated.topic(
Retrieving notices: ...working... done
/home/axle/miniconda3/lib/python3.11/site-packages/conda/base/context.py:198: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3.

To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels:

conda config --add channels defaults

For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html

deprecated.topic(
Channels:

• defaults
  Platform: linux-64
  Collecting package metadata (repodata.json): done
  Solving environment: done

Package Plan

environment location: /home/axle/miniconda3/envs/scenicplus

added / updated specs:
- python=3.11

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
bzip2-1.0.8                |       h5eee18b_6         262 KB
ld_impl_linux-64-2.40      |       h12ee557_0         710 KB
libffi-3.4.4               |       h6a678d5_1         141 KB
pip-24.2                   |  py311h06a4308_0         2.8 MB
python-3.11.10             |       he870216_0        32.9 MB
setuptools-75.1.0          |  py311h06a4308_0         2.2 MB
sqlite-3.45.3              |       h5eee18b_0         1.2 MB
tk-8.6.14                  |       h39e8969_0         3.4 MB
tzdata-2024b               |       h04d1e81_0         115 KB
wheel-0.44.0               |  py311h06a4308_0         145 KB
xz-5.4.6                   |       h5eee18b_1         643 KB
zlib-1.2.13                |       h5eee18b_1         111 KB
------------------------------------------------------------
                                       Total:        44.6 MB

The following NEW packages will be INSTALLED:

_libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main
_openmp_mutex pkgs/main/linux-64::_openmp_mutex-5.1-1_gnu
bzip2 pkgs/main/linux-64::bzip2-1.0.8-h5eee18b_6
ca-certificates pkgs/main/linux-64::ca-certificates-2024.9.24-h06a4308_0
ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.40-h12ee557_0
libffi pkgs/main/linux-64::libffi-3.4.4-h6a678d5_1
libgcc-ng pkgs/main/linux-64::libgcc-ng-11.2.0-h1234567_1
libgomp pkgs/main/linux-64::libgomp-11.2.0-h1234567_1
libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-11.2.0-h1234567_1
libuuid pkgs/main/linux-64::libuuid-1.41.5-h5eee18b_0
ncurses pkgs/main/linux-64::ncurses-6.4-h6a678d5_0
openssl pkgs/main/linux-64::openssl-3.0.15-h5eee18b_0
pip pkgs/main/linux-64::pip-24.2-py311h06a4308_0
python pkgs/main/linux-64::python-3.11.10-he870216_0
readline pkgs/main/linux-64::readline-8.2-h5eee18b_0
setuptools pkgs/main/linux-64::setuptools-75.1.0-py311h06a4308_0
sqlite pkgs/main/linux-64::sqlite-3.45.3-h5eee18b_0
tk pkgs/main/linux-64::tk-8.6.14-h39e8969_0
tzdata pkgs/main/noarch::tzdata-2024b-h04d1e81_0
wheel pkgs/main/linux-64::wheel-0.44.0-py311h06a4308_0
xz pkgs/main/linux-64::xz-5.4.6-h5eee18b_1
zlib pkgs/main/linux-64::zlib-1.2.13-h5eee18b_1

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

To activate this environment, use

$ conda activate scenicplus

To deactivate an active environment, use

$ conda deactivate

(base) axle@shpc-698-instance-ajKrL0oq:$ conda activate scenicplus
(scenicplus) axle@shpc-698-instance-ajKrL0oq:$ git clone https://github.com/aertslab/scenicplus
Cloning into 'scenicplus'...
remote: Enumerating objects: 3564, done.
remote: Counting objects: 100% (361/361), done.
remote: Compressing objects: 100% (87/87), done.
remote: Total 3564 (delta 298), reused 284 (delta 272), pack-reused 3203 (from 1)
Receiving objects: 100% (3564/3564), 42.00 MiB | 8.05 MiB/s, done.
Resolving deltas: 100% (2009/2009), done.
(scenicplus) axle@shpc-698-instance-ajKrL0oq:$ cd scenicplus
(scenicplus) axle@shpc-698-instance-ajKrL0oq:/scenicplus$ git checkout development
error: pathspec 'development' did not match any file(s) known to git
(scenicplus) axle@shpc-698-instance-ajKrL0oq:~/scenicplus$ pip install .
Processing /home/axle/scenicplus
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting loomxpy@ git+https://github.com/aertslab/LoomXpy@main (from scenicplus==1.0a1)
Cloning https://github.com/aertslab/LoomXpy (to revision main) to /tmp/pip-install-l820td80/loomxpy_6a619d8f47964bbfaa95df149613cc0e
Running command git clone --filter=blob:none --quiet https://github.com/aertslab/LoomXpy /tmp/pip-install-l820td80/loomxpy_6a619d8f47964bbfaa95df149613cc0e
Resolved https://github.com/aertslab/LoomXpy to commit 61995ff10940968eac2cee8fe48300ab477a15d0
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting pycistarget@ git+https://github.com/aertslab/pycistarget (from scenicplus==1.0a1)
Cloning https://github.com/aertslab/pycistarget to /tmp/pip-install-l820td80/pycistarget_92ad9f0333f8455e82e870165134cb51
Running command git clone --filter=blob:none --quiet https://github.com/aertslab/pycistarget /tmp/pip-install-l820td80/pycistarget_92ad9f0333f8455e82e870165134cb51
Resolved https://github.com/aertslab/pycistarget to commit 8cd78f110f4eeeb38d8f7006a1100a13d636d984
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting pycistopic@ git+https://github.com/aertslab/pycisTopic (from scenicplus==1.0a1)
Cloning https://github.com/aertslab/pycisTopic to /tmp/pip-install-l820td80/pycistopic_82b0d21954504975a6b1df74eb7fc75f
Running command git clone --filter=blob:none --quiet https://github.com/aertslab/pycisTopic /tmp/pip-install-l820td80/pycistopic_82b0d21954504975a6b1df74eb7fc75f
fatal: the remote end hung up unexpectedly
fatal: early EOF
fatal: index-pack failed
warning: Clone succeeded, but checkout failed.
You can inspect what was checked out with 'git status'
and retry with 'git restore --source=HEAD :/'

error: subprocess-exited-with-error

× git clone --filter=blob:none --quiet https://github.com/aertslab/pycisTopic /tmp/pip-install-l820td80/pycistopic_82b0d21954504975a6b1df74eb7fc75f did not run successfully.
│ exit code: 128
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× git clone --filter=blob:none --quiet https://github.com/aertslab/pycisTopic /tmp/pip-install-l820td80/pycistopic_82b0d21954504975a6b1df74eb7fc75f did not run successfully.
│ exit code: 128
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

[SeppeDeWinter]

Hi @Xinlei672

Can you try running it again? Seems like github was unresponsive for some reason.

Best,

S