install seurat 4.0.3

Question

[Andy]

Good afternoon,

I am trying to install Seurat 4.0.3, but I have been unsuccessful.

I attempted to use the install.packages() function, but it only installed version 4.3.0 of Seurat.

Then, I tried using remotes::install_version("Seurat", version = "4.0.3"), but it only installed version 3.2.0 of Seurat.

I am wondering how I can install Seurat 4.0.3.

Thank you very much,
Andy

Answer 1

[ATpoint]

library(remotes)
remotes::install_version("Seurat", "4.0.3")

[Andy]

I used these two line command to install the Seurat, but I got following:

make: *** [parse.o] Error 1
ERROR: compilation failed for package ‘RcppTOML’
* removing ‘/rsrch4/home/canbio/dsha/R/x86_64-pc-linux-gnu-library/4.0/RcppTOML’
* restoring previous ‘/rsrch4/home/canbio/dsha/R/x86_64-pc-linux-gnu-library/4.0/RcppTOML’

The downloaded source packages are in
        ‘/tmp/RtmpGKmgwW/downloaded_packages’
Installing package into ‘/rsrch4/home/canbio/dsha/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
ERROR: dependency ‘spatstat.core’ is not available for package ‘Seurat’
* removing ‘/rsrch4/home/canbio/dsha/R/x86_64-pc-linux-gnu-library/4.0/Seurat’
Error in file(file, if (append) "a" else "w") : 
  cannot open the connection
In addition: Warning messages:
1: package ‘spatstat.core’ is not available (for R version 4.0.0) 
2: In i.p(...) :
  installation of package ‘RcppTOML’ had non-zero exit status
3: In i.p(...) :
  installation of package ‘/tmp/RtmpGKmgwW/remotes23eca48a076d0/Seurat’ had non-zero exit status
4: In file(file, if (append) "a" else "w") :
  cannot open file '/risapps/rhel7/R/4.0.0/lib64/R/library/Seurat/DESCRIPTION': Permission denied

[ATpoint]

The usual mess with these super dependency-heavy packages (rolleyes). spatstat.core apparently has been archived from cran. Try remotes::install_github("cran/spatstat.core") Then repeat Seurat. Why not just using the latest Seurat version anyway, that seems to work as you say?

[Andy]

Thank you! The problem has been solved, but I cannot use the latest one as I need to be in line with other lab members.

Answer 2

[Ram]

Seurat 4.0.3 is available on conda.

conda create -n seurat403 -c conda-forge seurat=4.0.3