install seuratWrappers failed

[jinyuanchun]

remotes::install_github('satijalab/seurat-wrappers') Downloading GitHub repo satijalab/seurat-wrappers@HEAD Error in utils::download.file(url, path, method = method, quiet = quiet, : download from 'https://api.github.com/repos/satijalab/seurat-wrappers/tarball/HEAD' failed

[kenneditodd]

I had the same problem

[zhalenima]

I had the same problem！！！！！

[Jiayi-Zheng]

@jinyuanchun @kenneditodd @zhalenima I solved this problem by:

1. type https://api.github.com/repos/satijalab/seurat-wrappers/tarball/HEAD in any web server and you'll see a file named 'satijalab-seurat-wrappers-d28512f.tar.gz' downloading, it's around 50M. (do not use wget https://api.github.com/repos/satijalab/seurat-wrappers/tarball/HEAD somehow it ended up giving me an empty folder)
2. In R, type install.packages("/User/username/Downloads/satijalab-seurat-wrappers-d28512f.tar.gz",type='source',repos = NULL) #change the directory accordingly

Supposedly it should be this simple, though I encountered a few problems like telling me to update Seurat (and therefore its dependencies like SeuratObject)... which I solved (eventually) by remove.packages('xxx') then install.packages('xxx', dependencies = TRUE) or some other things I tried along the way, not sure which worked, not sure if it's my own problem on local system or so.

Hope this could work for you!

[jinyuanchun]

thank u

[Jiayi-Zheng]

Hi Andrea,

The xxx is the name of packages telling you version not compatible or need update or other (really there's a bunch of them) issues when doing the Seurat wrappers installation.

[rouninnomi]

Same problem. Unfortunately, Zheng's solution did not work for me. Any help?

Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) Warning: invalid package ‘MyDownloadDirectory/satijalab-seurat-wrappers-d28512f.tar.gz’ Error: ERROR: no packages specified

[michaeleekk]

I had the same issue and arrived to this post. In case if people got this error also, changing the timeout to a larger number will solve the issue.

options(timeout=9999999)
remotes::install_github('satijalab/seurat-wrappers')

I found this from a stack overflow thread.

[ynuozhang]

do the following in your environment: sudo apt-get install -y cmake sudo apt-get install -y libharfbuzz-dev libfribidi-dev sudo apt-get install -y libudunits2-dev and then these in R: install.packages("devtools", dependencies=TRUE) devtools::install_github('satijalab/seurat-wrappers')

[khalilnezhadasghar]

@Jiayi-Zheng Thanks!

it worked for me by :

install.packages("R.utils") library(R.utils) install.packages("./satijalab-seurat-wrappers-d28512f.tar.gz",type='source',repos = NULL)

@jinyuanchun @kenneditodd @zhalenima I solved this problem by:

1. type https://api.github.com/repos/satijalab/seurat-wrappers/tarball/HEAD in any web server and you'll see a file named 'satijalab-seurat-wrappers-d28512f.tar.gz' downloading, it's around 50M. (do not use wget https://api.github.com/repos/satijalab/seurat-wrappers/tarball/HEAD somehow it ended up giving me an empty folder)
2. In R, type install.packages("/User/username/Downloads/satijalab-seurat-wrappers-d28512f.tar.gz",type='source',repos = NULL) #change the directory accordingly

Supposedly it should be this simple, though I encountered a few problems like telling me to update Seurat (and therefore its dependencies like SeuratObject)... which I solved (eventually) by remove.packages('xxx') then install.packages('xxx', dependencies = TRUE) or some other things I tried along the way, not sure which worked, not sure if it's my own problem on local system or so.

Hope this could work for you!

[Than0904]

@jinyuanchun @kenneditodd @zhalenima I solved this problem by:

1. type https://api.github.com/repos/satijalab/seurat-wrappers/tarball/HEAD in any web server and you'll see a file named 'satijalab-seurat-wrappers-d28512f.tar.gz' downloading, it's around 50M. (do not use wget https://api.github.com/repos/satijalab/seurat-wrappers/tarball/HEAD somehow it ended up giving me an empty folder)
2. In R, type install.packages("/User/username/Downloads/satijalab-seurat-wrappers-d28512f.tar.gz",type='source',repos = NULL) #change the directory accordingly

Supposedly it should be this simple, though I encountered a few problems like telling me to update Seurat (and therefore its dependencies like SeuratObject)... which I solved (eventually) by remove.packages('xxx') then install.packages('xxx', dependencies = TRUE) or some other things I tried along the way, not sure which worked, not sure if it's my own problem on local system or so.

Hope this could work for you!

Thanks, this method works for me!