Compatibility between azimuth with seurat v4

[Montsecb]

Hi! I'm trying to install azimuth with seurat v4 but I'm getting an error, is there any way to do it?

This is the error:

installing to /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/00LOCK-Azimuth/00new/Azimuth/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  namespace 'Seurat' 4.3.0 is being loaded, but >= 5.0.0 is required
Calls: <Anonymous> ... namespaceImportFrom -> asNamespace -> loadNamespace
Execution halted
ERROR: lazy loading failed for package ‘Azimuth’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Azimuth’
Warning message:
In i.p(...) :
  installation of package '/var/folders/dc/z1qwsbtd6x57k8dxtds97rgr0000gn/T//RtmpJtsTsd/file6eb450f5d93/Azimuth_0.5.0.tar.gz' had non-zero exit status

I would like to know if there is an option to use with seurat v4. Thank you.

[Niubile001]

I think you should installed Azimuth-0.4.6 locally. It can be downloaded from https://github.com/satijalab/azimuth/tags. Azimuth-0.4.6 works fine with seurat-4.4.0.

[hwick]

Niubile001, can you clarify how to install it from the link you provided? Is there a way to do this from R? If not, what is to be done with the downloaded folder/files? I am having the same issue re: compatibility with Seurat v4

When using remotes::install_github('satijalab/azimuth', ref = 'v0.4.6') to install the package, I get this error:

* installing *source* package ‘SeuratData’ ...
** using staged installation
** R
** exec
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  namespace ‘SeuratObject’ 4.1.3 is already loaded, but >= 5.0.0 is required
Calls: <Anonymous> ... namespaceImportFrom -> asNamespace -> loadNamespace
Execution halted
ERROR: lazy loading failed for package ‘SeuratData’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/SeuratData’
Downloading GitHub repo satijalab/seurat-data@HEAD
Skipping SeuratData, it is already being installed
── R CMD build ──────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/private/var/folders/4w/n5cf_y4x30v8qzydc74ksygm0000gq/T/RtmpqpQUk0/remotes16a2b1e5d2713/satijalab-azimuth-f3c7904/DESCRIPTION’ ...
─  preparing ‘Azimuth’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
   Omitted ‘LazyData’ from DESCRIPTION
─  building ‘Azimuth_0.4.6.tar.gz’

ERROR: dependency ‘SeuratData’ is not available for package ‘Azimuth’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Azimuth’
Warning messages:
1: In i.p(...) :
  installation of package ‘/var/folders/4w/n5cf_y4x30v8qzydc74ksygm0000gq/T//RtmpqpQUk0/file16a2b1124b5a8/SeuratData_0.2.2.9001.tar.gz’ had non-zero exit status
2: In i.p(...) :
  installation of package ‘/var/folders/4w/n5cf_y4x30v8qzydc74ksygm0000gq/T//RtmpqpQUk0/file16a2b220b4217/Azimuth_0.4.6.tar.gz’ had non-zero exit status

It appears to still want v5, unless this method of installation is not doing what I think it's doing.

[hwick]

I was able to install it with remotes::install_github('satijalab/azimuth', ref = 'v0.4.4') neither 4.6 nor 4.5 appear to be compatible with seurat v4