While installing seurat, I had to install several dependencies in linux system. Keeping a log of them.
install.packages('Seurat')
Had an issue with curl:
ERROR: configuration failed for package ‘curl’
* removing ‘/home/ramadatta/R/x86_64-pc-linux-gnu-library/4.1/curl’
Warning in install.packages :
installation of package ‘curl’ had non-zero exit status
sudo apt-get install libcurl4-openssl-dev
configure: error: geos-config not found or not executable.
ERROR: configuration failed for package ‘rgeos’
* removing ‘/home/ramadatta/R/x86_64-pc-linux-gnu-library/4.1/rgeos’
sudo apt install libgeos-dev
install.packages('Seurat')
ERROR: configuration failed for package ‘nloptr’
* removing ‘/home/ramadatta/R/x86_64-pc-linux-gnu-library/4.1/nloptr’
Warning in install.packages :
installation of package ‘nloptr’ had non-zero exit status
sudo apt-get install libnlopt-dev
ERROR: configuration failed for package ‘xml2’
* removing ‘/home/ramadatta/R/x86_64-pc-linux-gnu-library/4.1/xml2’
Warning in install.packages :
installation of package ‘xml2’ had non-zero exit status
sudo apt-get install libxml2-dev
install.packages("xml2")
ERROR: configuration failed for package ‘hdf5r’
* removing ‘/home/ramadatta/R/x86_64-pc-linux-gnu-library/4.1/hdf5r’
sudo apt-get install libhdf5-dev
---------------------------
The below are not necessary for Seurat but I needed to run for other packages
ERROR: configuration failed for package ‘systemfonts’
* removing ‘/home/ramadatta/R/x86_64-pc-linux-gnu-library/4.1/systemfonts’
sudo apt -y install libfontconfig1-dev
No comments:
Post a Comment