RunAzimuth() error: Error in curl::handle_setopt(handle, .list = req$options) :

[aaronwolf1995]

In learning tutorial of Integrative analysis in Seurat v5 (https://satijalab.org/seurat/articles/seurat5_integration.html): I have followed instructions for "seurat5" version installing of Azimuth and other packages, as it has mentioned. However, when I came to this line:

obj <- RunAzimuth(obj,reference = "pbmcref")

It went error as it follows:

Error in curl::handle_setopt(handle, .list = req$options) : A libcurl function was given a bad argument In addition: Warning message: In curl::handle_setopt(handle, .list = req$options) : NAs introduced by coercion to integer range

First I thought it might be because of the reference, so I changed to another reference (lungref, e.g.), but it did not work. Secondly I changed Azimuth to older version by : remotes::install_github('satijalab/azimuth') It was running into another error and still did not work (error is the same as reference for RunAzimuth() #154)

[Gesmira]

Hi, Do you have internet connection? I've previously seen curl issues related to trying to download the homolog table required for converting the gene names of the query.

You could download the homolog table and try the fix here if that is the problem: https://github.com/satijalab/seurat/issues/7357

[Gesmira]

Closing now due to lack of response. Please feel free to reopen if the issue persists.

[vandontduong]

I've ran into the same issue. I have internet connection, as I'm connected through my university's compute cluster (SLURM-based).

obj <- RunAzimuth(obj, reference = "pbmcref")
Using cached data manifest, last updated at 2023-09-25 16:01:26
Using cached data manifest, last updated at 2023-09-25 16:01:26
Using cached data manifest, last updated at 2023-09-25 16:01:26
Using cached data manifest, last updated at 2023-09-25 16:01:26
Warning: Overwriting miscellanous data for model
Warning: Adding a dimensional reduction (refUMAP) without the associated assay being present
Warning: Adding a dimensional reduction (refUMAP) without the associated assay being present
Error in curl::curl_fetch_memory(url, handle = handle) : 
  SSL connect error

[Gesmira]

Hi, as shown in this issue, you can download the homology table and run the app locally. If you want to run RunAzimuth(), instead of the app, we don't currently offer a way to use a downloaded homolog table, but you can change the source code of the function using commands like trace(). Or you could run the internal functions individually. The homolog table is specifically provided to the ConvertGeneNames function.