Frequently Asked Questions (FAQ)

Yichao Hua

2024-07-11

Table of Contents

  1. Running scVelo Functions in RStudio on Linux
  2. Creating ‘seuratextend’ Conda Environment
  3. Merging Multiple Samples with Seurat v5.0

Running scVelo Functions in RStudio on Linux

Q: I’m getting an error when running scVelo-related functions in RStudio on Linux. What should I do?

When running scVelo-related functions in RStudio on a Linux system, you might encounter an error similar to this:

Error in py_run_string_impl(code, local, convert) : 
  ImportError: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /home/username/.local/share/r-miniconda/envs/seuratextend/lib/python3.10/site-packages/pandas/_libs/window/aggregations.cpython-310-x86_64-linux-gnu.so)

This error occurs because RStudio can’t find the correct shared library ‘libstdc++’. Even though a higher version of libstdc++.so.6.0.32 exists in the ‘seuratextend’ conda environment, RStudio can’t locate it.

Solution:

RStudio searches for shared libraries in the paths specified by the LD_LIBRARY_PATH environment variable. You can check these paths with:

Sys.getenv("LD_LIBRARY_PATH")

To resolve this issue, manually copy the following files from /home/username/.local/share/r-miniconda/envs/seuratextend/lib/ to one of the paths in LD_LIBRARY_PATH (e.g., /usr/lib/R/lib, which may require sudo permissions):

  • libR.so
  • libstdc++.so
  • libstdc++.so.6
  • libstdc++.so.6.0.32

After copying these files, restart your R session, and the issue should be resolved.

Creating ‘seuratextend’ Conda Environment

Q: The create_condaenv_seuratextend() function is failing to create the ‘seuratextend’ conda environment. What could be the problem?

If create_condaenv_seuratextend() is failing to create the ‘seuratextend’ conda environment, it might be due to the system not finding conda or git.

Solutions:

  1. If conda is not found, you can install miniconda using:

    reticulate::install_miniconda()

  2. If git is not found, download and install it from the official website: https://git-scm.com/. Choose the appropriate version for your operating system.

After installing conda or git, restart your R session and try running create_condaenv_seuratextend() again.

Merging Multiple Samples with Seurat v5.0

Q: After merging multiple samples using the merge() function in Seurat v5.0, I’m getting an error when running certain functions. How can I fix this?

When using Seurat v5.0, you might encounter the following error after merging multiple samples and trying to run certain functions:

Error in `GetAssayData()`:
! GetAssayData doesn't work for multiple layers in v5 assay.

This error occurs because in Seurat v5.0, the merge() function creates separate count layers for each sample by default. This prevents GetAssayData() from extracting the matrix.

Solution:

To resolve this issue, you need to join the layers before using GetAssayData(). Use the following code:

seu <- JoinLayers(seu)

After joining the layers, you should be able to use GetAssayData() without errors.

Note that this issue does not occur in Seurat v4 and earlier versions.