Azimuth install fails: SeuratDisk not available

[rhart604]

Trying to install everything for Seurat5, I got an error during the installation of Azimuth:

ERROR: dependency 'SeuratDisk' is not available for package 'Azimuth'

• removing 'D:/library/Azimuth'

Session info below: R version 4.3.1 (2023-06-16 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8 [4] LC_NUMERIC=C LC_TIME=English_United States.utf8

time zone: America/New_York tzcode source: internal

attached base packages: [1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached): [1] processx_3.8.2 compiler_4.3.1 R6_2.5.1 rprojroot_2.0.3 cli_3.6.1 prettyunits_1.1.1 tools_4.3.1
[8] rstudioapi_0.15.0 curl_5.0.1 crayon_1.5.2 remotes_2.4.2.1 desc_1.4.2 callr_3.7.3 ps_1.7.5
[15] pkgbuild_1.4.2

[Gesmira]

Hi, Have you tried installing SeuratDisk before Azimuth install? remotes::install_github("mojaveazure/seurat-disk")

[rhart604]

I had previously followed the installation instructions and used this: remotes::install_githubhttps://remotes.r-lib.org/reference/install_github.html("satijalab/seurat-data", "seurat5", quiet = TRUE)

But using your install command instead works, and then after that, Azimuth installs correctly.

Thanks.

From: gesmira @.> Sent: Friday, August 4, 2023 4:07 PM To: satijalab/azimuth @.> Cc: Ron Hart @.>; Author @.> Subject: Re: [satijalab/azimuth] Azimuth install fails: SeuratDisk not available (Issue #165)

Hi, Have you tried installing SeuratDisk before Azimuth install? remotes::install_github("mojaveazure/seurat-disk")

- Reply to this email directly, view it on GitHubhttps://github.com/satijalab/azimuth/issues/165#issuecomment-1666118296, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACGUBN4H4ELNOPJBJ34WEXDXTVI6BANCNFSM6AAAAAA2TEHBRU. You are receiving this because you authored the thread.Message ID: @.**@.>>

[Gesmira]

Ok great!

[mmokrejs]

Please reopen this issue and get fixed at least the documentation at https://satijalab.org/seurat/articles/install It does not even mention one needs to install SeuratDisk. I just hit this very same issue as well.

> remotes::install_github("satijalab/azimuth", "seurat5", quiet = TRUE)
Installing 3 packages: SeuratDisk, EnsDb.Hsapiens.v86, BSgenome.Hsapiens.UCSC.hg38
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Running `R CMD build`...
Warning messages:
1: package 'SeuratDisk' is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages 
2: In i.p(...) :
  installation of package '/storage/vestec1-elixir/projects/biocev/mmokrejs/tmp/Rtmp0usxyE/file8ffc41e321e41/Azimuth_0.4.6.9004.tar.gz' had non-zero exit status
>

> remotes::install_github("satijalab/azimuth", "seurat5", quiet = FALSE)
Downloading GitHub repo satijalab/azimuth@seurat5
Skipping 1 packages not available: SeuratDisk
Running `R CMD build`...
* checking for file '/auto/vestec1-elixir/projects/biocev/mmokrejs/tmp/Rtmpb9MqpN/remotes9a4683d83441e/satijalab-azimuth-3d78d3f/DESCRIPTION' ... OK
* preparing 'Azimuth':
* checking DESCRIPTION meta-information ... OK
* 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_0.4.6.9004.tar.gz'
ERROR: dependency 'SeuratDisk' is not available for package 'Azimuth'
* removing '/auto/vestec1-elixir/projects/biocev/gentoo/usr/lib64/R/library/Azimuth'
Warning message:
In i.p(...) :
  installation of package '/storage/vestec1-elixir/projects/biocev/mmokrejs/tmp/Rtmpb9MqpN/file9a4687ac0868d/Azimuth_0.4.6.9004.tar.gz' had non-zero exit status
> 

Aside from that, I cannot find any "SeuratDisk" under https://github.com/satijalab

[mmokrejs]

remotes::install_github("mojaveazure/seurat-disk")

[Gesmira]

Hi @mmokrejs SeuratDisk is not required for Seurat v5 install so we won't be updating the documentation at the link you included. The dependency has been added back into the Azimuth (seurat5) package, so it should automatically install when you install Azimuth from now on. And, yes, that is the way to install SeuratDisk regularly which I had included in my answer above.

[Projectnix]

Hi @Gesmira

Just letting you know now that the Seurat5 branch of Azimuth fails to update/install because it now requires the Seurat5 branch of seurat-disk, which does not exist yet on github.

[Gesmira]

Hi @Projectnix, thanks for reporting that! Fixed now.