Hi all:
I am working through a terminal on the computation center in the University. Recently, I need to install a package in R to analyze my RNA-seq data.
I am under the anaconda2 environment. So I use conda install R
to install R and call R by typing R
.
However, when I tried to install ASpli which is a package running in R(BiocManager::install("ASpli")
), I get the following error(part of the error):
Error: package or namespace load failed for 'survival' in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/home/caiqi/anaconda2/lib/R/library/Matrix/libs/Matrix.so':
libopenblas.so.0: cannot open shared object file: No such file or directory Error: package 'survival' could not be loaded Execution halted
Any advice on what should I do?
Thanks,
Cai
If you used conda to install R, why don't you use conda to install ASpli?
Thank your very much for your reply! I am trying your code to see what will happen. Can I ask another question because I don't understand very well about it: I saw I have anaconda2 folder and it contains lib which contains R : anaconda>lib>R, and I saw some packages in the R like edgeR and something like that. in my home folder I also see R>x86_64-pc-linux-gnu-library>3.5>edgeR/ASpli
I know previously I have been using R3.5 also under anaconda environment. Recently, the system got some mistake so I have to uninstall anaconda and reinstall anaconda and R. So this is how the question arise. My question is what is difference of R folder in my home and the R in the anaconda? How can use the R folder in my home folder? Appreciate a lot for your teaching.
I tried your method, and I went into R and get the following:
First of all, I would suggest you create a conda environment for the R installation (note you may need to tweak version number):
To use this R, you must activate the environment:
You can then install more packages
Install any other packages you need for this R environment. In case loading packages in this R environment still fails with "libopenblas.so.0: cannot open shared object file: No such file or directory", do:
You can try the above command before creating a new environment, but this is a sign your conda install is somewhat broken. You may need to start from scratch again.
this is what I got :
it does not work out in the end. I can not even library(ASpli) in the end. Looks that it still has the same problem.
"
> library(ASpli)
Thanks a lot for your time,
Cai