安裝Seurat包

安裝Seurat包

install.packages('Seurat', type = "binary")

install.packages('Seurat') 
library('Seurat') 

packageVersion("Seurat") 
相關包下載 
install.packages(c('dplyr','patchwork'))

> library("Seurat")
Error: package or namespace load failed for ‘Seurat’:
 object ‘markvario’ is not exported by 'namespace:spatstat'
In addition: Warning message:
package ‘Seurat’ was built under R version 3.6.3 

解決方法：

install.packages('devtools') 

remove.packages(grep("spatstat", installed.packages(), value = T))
.rs.restartR()
devtools::install_version("spatstat", version = "1.64-1")

> BiocManager::install("Seurat",ask = F,update = F)
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.10 (BiocManager 1.30.16), R 3.6.0 (2019-04-26)
Installing package(s) 'Seurat'
Warning message:
In .inet_warning(msg) :
  package ‘Seurat’ is not available (for R version 3.6.0)
> install.packages('Seurat')
Warning in install.packages :
  package ‘Seurat’ is not available (for R version 3.6.0)

Installation Instructions for Seurat

Source: vignettes/install.Rmd

To install Seurat, R version 4.0 or greater is required. We also recommend installing R Studio.

Install from CRAN

Seurat is available on CRAN for all platforms. To install, run:

# Enter commands in R (or R studio, if installed)
install.packages('Seurat')
library(Seurat)

If you see the warning message below, enter y:

package which is only available in source form, and may need compilation of C/C++/Fortran: 'Seurat'
Do you want to attempt to install these from sources?
y/n:

Install previous versions of Seurat

Install any version 3 release （對應R的版本為3.X）

Any of the Seurat version 3 releases can be installed with the following command:

install.packages('remotes')

remotes::install_version("Seurat", version = "3.2.3")

如果安裝失敗，可以先安裝依賴的包，一個一個安裝。

ERROR: dependencies 'leiden', 'lmtest', 'png', 'reticulate', 'ROCR', 'rsvd', 'scattermore', 'sctransform', 'spatstat', 'uwot' are not available for package 'Seurat'

install.packages('leiden')
install.packages('lmtest')
install.packages('png')
install.packages('reticulate')
install.packages('ROCR')
install.packages('rsvd')
install.packages('scattermore')
install.packages('sctransform')
install.packages('spatstat')
install.packages('uwot')

install.packages('rsvd')
Warning in install.packages :
  package ‘rsvd’ is not available (for R version 3.6.0)

https://github.com/erichson/rSVD


install.packages('rio')


> install.packages('rsvd')
Warning in install.packages :
 package ‘rsvd’ is not available (for R version 3.6.0)
> 
BiocManager::install('rio',suppressUpdates=FALSE,ask=FALSE)

BiocManager::install('rsvd',suppressUpdates=FALSE,ask=FALSE)

1: In .inet_warning(msg) :
 package ‘rsvd’ is not available (for R version 3.6.0)
2: In install.packages(update[instlib == l, "Package"], l, repos = repos, :
 installation of package ‘rio’ had non-zero exit status
 
 

Warning in system(cmd) : 'make' not found
ERROR: compilation failed for package 'Seurat'
* removing 'C:/Program Files/R/R-3.6.0/library/Seurat'
Warning messages:
1: In missing_devel_warning(pkgdir) :
  Package Seurat has compiled code, but no suitable compiler(s) were found. Installation will likely fail.
  Install Rtools (https://cran.r-project.org/bin/windows/Rtools/).Then use the pkgbuild package, or make sure that Rtools in the PATH.
2: In i.p(...) :
  installation of package ‘C:/Users/ADMINI~1/AppData/Local/Temp/Rtmpw9bH6E/remotes3878357a1a/Seurat’ had non-zero exit status

Install the last version 2 release (2.3.4)

To facilitate easy re-installation of the last version 2 release, we are hosting the binaries on our website. These can be installed with the following command:

source("https://z.umn.edu/archived-seurat")

View the script

Older versions of Seurat

Old versions of Seurat, from Seurat v2.0.1 and up, are hosted in CRAN’s archive. To install an old version of Seurat, run:

# Enter commands in R (or R studio, if installed)
# Install the remotes package 
install.packages('remotes')
# Replace '2.3.0' with your desired version
remotes::install_version(package = 'Seurat', version = package_version('2.3.0'))
library(Seurat)

For versions of Seurat older than those not hosted on CRAN (versions 1.3.0 and 1.4.0), please download the packaged source code from our releases page and install from the tarball.

Install the development version of Seurat

Install the development version of Seurat - directly from GitHub.

# Enter commands in R (or R studio, if installed)
# Install the remotes package
install.packages('remotes')
remotes::install_github(repo = 'satijalab/seurat', ref = 'develop')
library(Seurat)

Docker

We provide docker images for Seurat via dockerhub.

To pull the latest image from the command line:

docker pull satijalab/seurat:latest

To use as a base image in a new Dockerfile:

FROM satijalab/seurat:latest

https://satijalab.org/seurat/
https://satijalab.org/seurat/articles/install.html
鏈接：https://www.jianshu.com/p/d4df73ff6a2e

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