Can't able to install Seurat in Rstudio
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KOUSTAV • 0
@8a93cf98
Last seen 3.5 years ago
Japan

I need to install seurat new version. I have tried by direction of Satija Lab guideline and by different youtube video. I have install R and R studio and R tool kit. I am very new in programming and have not much knowledge. That is what I got after commend. What should I do now. Please help.

R version 4.1.0 (2021-05-18) -- "**Camp Pontanezen**"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> install.packages("seurat")
Installing package into ‘C:/Users/tosh/Documents/R/win-library/4.1’
(as ‘lib’ is unspecified)
Warning in install.packages :
  package ‘seurat’ 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
Warning in install.packages :
  Perhaps you meant ‘Seurat’ ?
> install.packages("Seurat")
Installing package into ‘C:/Users/tosh/Documents/R/win-library/4.1’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/Seurat_4.0.2.zip'
Content type 'application/zip' length 2760190 bytes (2.6 MB)
downloaded 2.6 MB

package ‘Seurat’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\tosh\AppData\Local\Temp\RtmpsvsY5N\downloaded_packages

Please help anybody to install seurat properly. Thank you so much in advance.
Rstudio Seurat • 14k views
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Kevin Blighe ★ 4.0k
@kevin
Last seen 19 days ago
Republic of Ireland

Hi,

It is indicated that the Seurat package (capital 'S') may have been installed successfully, as per:

package ‘Seurat’ successfully unpacked and MD5 sums checked

'seurat' (small 's') does not exist as a package.

Kevin
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Hi kevin, it not looks that all programs of seurat is not available? I am not sure.When I have watched u-tube videos this comment does not appear (Seurat’ successfully unpacked and MD5 sums checked). How do I confirm that the software correctly installed. Thank you for your guidance.

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Hi, what is the output of:

library(Seurat)

?

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Hi, here the output

library("seurat") 
Error in library("seurat") : there is no package called ‘seurat

another thing I like to inform I have reinstall Rstudio and I tried to install Seurat from studio package, then I got one msg "Do u want to install from sources the packages which need compilation" I clicked yes bottom. So what type of compilation I have to do further installation? Do u have any comment?

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Hi, please note the capital 'S'. Please run this literal line of code (copy-paste):

library(Seurat)
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Unfortunately same result. This is the output after reinstall of Rstudio

> library(Seurat)
Error: package or namespace load failed for ‘Seurat’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘fansi’
> detach("package:Seurat", unload = TRUE)
Error in detach("package:Seurat", unload = TRUE) : 
  invalid 'name' argument
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So, Seurat is installed, but not its dependencies, e.g., fansi. Please install fansi via:

install.packages('fansi')
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The command should be given in RStudio or R?

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Either, as they should be utilising the same R installation. It may be preferable via the RStudio menu system if your intention is to mainly use RStudio.

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Hi, could you please guide me now? I am giving the output of command

R version 4.1.0 (2021-05-18) -- "Camp Pontanezen" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.

library(Seurat) Error: package or namespace load failed for ‘Seurat’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘fansi’ install.packages('fansi') Installing package into ‘C:/Users/tosh/Documents/R/win-library/4.1’ (as ‘lib’ is unspecified)

There is a binary version available but the source version is later: binary source needs_compilation fansi 0.4.2 0.5.0 TRUE

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/fansi_0.4.2.zip' Content type 'application/zip' length 224354 bytes (219 KB) downloaded 219 KB

package ‘fansi’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Users\tosh\AppData\Local\Temp\RtmpAHCWeD\downloaded_packages

library(Seurat) Error: package or namespace load failed for ‘Seurat’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘fitdistrplus’ install.packages('fitdistrplus') Installing package into ‘C:/Users/tosh/Documents/R/win-library/4.1’ (as ‘lib’ is unspecified)

There is a binary version available but the source version is later: binary source needs_compilation fitdistrplus 1.1-3 1.1-5 FALSE

installing the source package ‘fitdistrplus’

trying URL 'https://cran.rstudio.com/src/contrib/fitdistrplus_1.1-5.tar.gz' Content type 'application/x-gzip' length 2354740 bytes (2.2 MB) downloaded 2.2 MB

  • installing source package 'fitdistrplus' ... package 'fitdistrplus' successfully unpacked and MD5 sums checked using staged installation R data inst byte-compile and prepare package for lazy loading help * installing help indices converting help for package 'fitdistrplus' finding HTML links ... done CIcdfplot html
    bootdist html
    bootdistcens html
    danish html
    dataFAQ html
    descdist html
    detectbound html
    endosulfan html
    fitdist html
    fitdistcens html
    fitdistrplus html
    fluazinam html
    gofstat html
    graphcomp html
    graphcompcens html
    groundbeef html
    logLik-plot html
    logLik-surface html
    mgedist html
    mledist html
    mmedist html
    msedist html
    plotdist html
    plotdistcens html
    prefit html
    qmedist html
    quantile html
    salinity html
    smokedfish html
    toxocara html
    building package indices installing vignettes testing if installed package can be loaded from temporary location * arch - i386 * arch - x64 testing if installed package can be loaded from final location arch - i386 arch - x64 ** testing if installed package keeps a record of temporary installation path
  • DONE (fitdistrplus)

The downloaded source packages are in ‘C:\Users\tosh\AppData\Local\Temp\RtmpAHCWeD\downloaded_packages’

install.packages("Seurat") Installing package into ‘C:/Users/tosh/Documents/R/win-library/4.1’ (as ‘lib’ is unspecified) trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/Seurat_4.0.2.zip' Content type 'application/zip' length 2760190 bytes (2.6 MB) downloaded 2.6 MB

package ‘Seurat’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Users\tosh\AppData\Local\Temp\RtmpAHCWeD\downloaded_packages

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If I run

> library("Seurat")
Error: package or namespace load failed for ‘Seurat’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘stringi’

So now again install the ‘stringi’ ?

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I have installed 'stringi’ and run > library("Seurat").The output is like

> library("Seurat")
  Attaching SeuratObject

is it ok?

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Hi, yes, you seem to have now installed it.

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When I have attaching my cell ranger output data the output looks failed. How to attached cell ranger output in seurat? am I doing something wrong or still software problem? Could you please guide me.

 library(Seurat)
Attaching SeuratObject
> detach("package:Seurat", unload = TRUE)
> library(Seurat)

Restarting R session...

> install.packages("Seurat")
Installing package into ‘C:/Users/tosh/Documents/R/win-library/4.1’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/Seurat_4.0.2.zip'
Content type 'application/zip' length 2760190 bytes (2.6 MB)
downloaded 2.6 MB

package ‘Seurat’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\tosh\AppData\Local\Temp\RtmpqkiNwD\downloaded_packages
> library(Seurat)
Attaching SeuratObject
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> library(patchwork)
> 
> ctrl_counts <- Read10X(data.dir = "data/ctrl_raw_feature_bc_matrix")
Error in Read10X(data.dir = "data/ctrl_raw_feature_bc_matrix") : 
  Directory provided does not exist
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Hi, I am unsure why you feel that there is a need to re-install Seurat. You just need to run this command once (one time only), and then never again until you get a new version of R:

install.packages("Seurat")

Then, when you want to use the package, you just need:

library(Seurat)

The other error, relating to Read10X(), is telling you that there is no directory called data/ctrl_raw_feature_bc_matrix in your current working directory.

I should state that Seurat is not a Bioconductor package. As you are now having issues pertaining to Seurat's functionality, I suggest that you post further issues on the Seurat GitHub page (https://github.com/satijalab/seurat/issues) or Biostars (https://www.biostars.org/)

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