Comments (3)
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.
from azimuth.
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.
from azimuth.
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
from azimuth.
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from azimuth.