SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
Manually installing lda beforehand fixed the issue:
conda create --name scenicplus python=3.11 -y
conda activate scenicplus
pip install lda #install lda manually because conda forge version is outdated
If the provided install instructions could ensure the appropriate repository is used, that'd be amazing. In the mean time, the above work-around is available.
Error output
error log
```
...
Collecting lazy-loader==0.3 (from scenicplus==1.0a1)
Using cached lazy_loader-0.3-py3-none-any.whl.metadata (4.3 kB)
INFO: pip is looking at multiple versions of scenicplus to determine which version is compatible with other requirements. This could take a while.
ERROR: Ignored the following versions that require a different python version: 0.5.12 Requires-Python >=3.7,<3.12; 0.5.13 Requires-Python >=3.7,<3.12; 3.0.0 Requires-Python >=3.9,<=3.12
ERROR: Could not find a version that satisfies the requirement lda==3.0.0 (from scenicplus) (from versions: 0.1.0.dev2.g0925a91, 0.1.0, 0.2.0, 0.2.1rc0, 0.3.0, 0.3.1, 0.3.2, 1.0.0, 1.0.2, 1.0.3, 1.0.4, 1.0.5, 1.1.0, 2.0.0)
ERROR: No matching distribution found for lda==3.0.0
```
Describe the bug A minor issue installing the LDA library on Rocky Linux 8.9 using the provided install instructions.
It appears that the LDA version on conda-forge is outdated, with the latest version being 2.0.0 and scenic+ requiring 3.0.0
https://anaconda.org/conda-forge/lda/labels
Manually installing lda beforehand fixed the issue:
If the provided install instructions could ensure the appropriate repository is used, that'd be amazing. In the mean time, the above work-around is available.
Error output
error log
``` ... Collecting lazy-loader==0.3 (from scenicplus==1.0a1) Using cached lazy_loader-0.3-py3-none-any.whl.metadata (4.3 kB) INFO: pip is looking at multiple versions of scenicplus to determine which version is compatible with other requirements. This could take a while. ERROR: Ignored the following versions that require a different python version: 0.5.12 Requires-Python >=3.7,<3.12; 0.5.13 Requires-Python >=3.7,<3.12; 3.0.0 Requires-Python >=3.9,<=3.12 ERROR: Could not find a version that satisfies the requirement lda==3.0.0 (from scenicplus) (from versions: 0.1.0.dev2.g0925a91, 0.1.0, 0.2.0, 0.2.1rc0, 0.3.0, 0.3.1, 0.3.2, 1.0.0, 1.0.2, 1.0.3, 1.0.4, 1.0.5, 1.1.0, 2.0.0) ERROR: No matching distribution found for lda==3.0.0 ```To Reproduce
Commands:
Expected behavior A complete and error-less installation by fetching correct library versions from appropriate repositories.
Version (please complete the following information): > scenicplus.version '1.0a1' > python Python 3.12.2 | packaged by conda-forge | (main, Feb 16 2024, 20:50:58) [GCC 12.3.0] on linux > conda --version conda 24.4.0 > cat /etc/os-release NAME="Rocky Linux" VERSION="8.9 (Green Obsidian)" ID="rocky" ID_LIKE="rhel centos fedora" VERSION_ID="8.9" PLATFORM_ID="platform:el8" PRETTY_NAME="Rocky Linux 8.9 (Green Obsidian)" ANSI_COLOR="0;32" LOGO="fedora-logo-icon" CPE_NAME="cpe:/o:rocky:rocky:8:GA" HOME_URL="https://rockylinux.org/" BUG_REPORT_URL="https://bugs.rockylinux.org/" SUPPORT_END="2029-05-31" ROCKY_SUPPORT_PRODUCT="Rocky-Linux-8" ROCKY_SUPPORT_PRODUCT_VERSION="8.9" REDHAT_SUPPORT_PRODUCT="Rocky Linux" REDHAT_SUPPORT_PRODUCT_VERSION="8.9"