Entering edit mode
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.
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.
Hi, what is the output of:
?
Hi, here the output
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?
Hi, please note the capital 'S'. Please run this literal line of code (copy-paste):
Unfortunately same result. This is the output after reinstall of Rstudio
So, Seurat is installed, but not its dependencies, e.g., fansi. Please install fansi via:
The command should be given in RStudio or R?
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.
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.
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
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
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
The downloaded source packages are in ‘C:\Users\tosh\AppData\Local\Temp\RtmpAHCWeD\downloaded_packages’
package ‘Seurat’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in C:\Users\tosh\AppData\Local\Temp\RtmpAHCWeD\downloaded_packages
If I run
So now again install the ‘stringi’ ?
I have installed 'stringi’ and run > library("Seurat").The output is like
is it ok?
Hi, yes, you seem to have now installed it.
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.
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:
Then, when you want to use the package, you just need:
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/)