I am working on the Rivanna
cluster that is of SLURM
-type. Because of that I do not have write permissions and need to install the newest R
version myself locally, and use it. For it to be successfully built from source, I needed to also build from source libcurl4-openssl-dev
, so I downloaded tar.gz
file from here:
https://packages.debian.org/ru/jessie/libcurl4-openssl-dev
and did:
mkdir build
./configure --prefix=/scratch/nv4e/curl/build
make
make install
Then, in the same way I built from source R
3.5.1
, the latest current version. It was compiled without any errors, but with some warnings. Then, I submitted the R
script that uses SCnorm
package:
https://bioconductor.org/packages/release/bioc/html/SCnorm.html
Inside of the script I am having:
source("https://bioconductor.org/biocLite.R")
biocLite("SCnorm")
biocLite("SingleCellExperiment")
library(SCnorm)
library(SingleCellExperiment)
Of course, I am submitting it through .slurm
file where I have the main command:
Rscript --vanilla scnorm.R
It fails, apparently because SCnorm
requires RCurl
, but it can not get one, even though in the log file it is trying to access it correctly:
The libcurl
library was built from source in the /scratch/nv4e/curl/build
folder. The only suspicion that I have here is that maybe its version is wrong and SCnorm
needs another libcurl
version? Any suggestions would be greatly appreciated.
Update
I tried reinstalling libcurl
library from the official website, using the latest version:
But it did not fix the issue. I have also tried using libcurl
from Anaconda
but it gave the same error. So, neither 7.61.0
(latest), nor 7.29.0
(Anaconda
), nor 7.38.0
(Debian
link) are working.