How to resolve 'libRblas.so: No such file or directory' during package installation?

Issue

When I try to install certain packages (imputeTS) that need libRblas.so which AFAIK refers to OpenBLAS I get an error that it was not found:

Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/jay/R/x86_64-pc-linux-gnu-library/4.2/fracdiff/libs/fracdiff.so':
  libRblas.so: cannot open shared object file: No such file or directory
Calls: <Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted

However, the sessionInfo() indicates, that R actually finds it.

> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so

I learned from this thread that "maybe … another version of R [was built] and it sits in … [the] $PATH before the packaged version", which is likely to be the case; my former R version 4.2.0 was a self-compiled one, and I removed it by downloading the source again and ./configuremake uninstall. This one is installed via sudo apt install r-base-core, though. Probably now there is a mess somewhere. Unfortunately the cited thread was solved differently, and I’m looking now for the respective conclusion.

Here is some more information:

whereis R gives

~$ whereis R
R: /usr/bin/R /usr/lib/R /usr/lib64/R /etc/R /usr/local/lib/R /usr/share/R /usr/share/man/man1/R.1.gz

From the respective files from the error message, using sudo find ~ -name '<file>', fracdiff.so was found, whereas libRblas.so wasn’t.

~/R/x86_64-pc-linux-gnu-library/4.2/fracdiff/libs/fracdiff.so

I already tried,

~$ sudo apt install libopenblas-dev

but obviously it is installed.

libopenblas-dev is already the newest version (0.3.20+ds-1).

Following the suggestions of this, libRlapack.so and libRblas.so obviously don’t exist on my system, and the other suggestion just gives:

~$ sudo update-alternatives --config libblas.so
update-alternatives: error: no alternatives for libblas.so

Solution

Some comments have put me on the right track and helped me to solve the problem—I will briefly summarize.

Since a dependencies issue was suspected, I installed the package from which the error message originated (fracdiff in this case) and tried again to install the target package. The error reoccurred, but came from a different package indicating cascading problems. Weirdly enough, I definitely knew the package was installed, so I felt my initial suspicion confirmed, that I might have made a mess with the libs folders when updating R as described in the OP.

Since I could assume that this would happen again and again, the conclusion was to uninstall R completely, and this time the packages as well, and then reinstall everything. Now I could install the target package among others without any problems.

Fortunately, this is quite easy on Linux. Also all packages can be reinstalled relatively unattended. The how-to’s are spread out over several threads and sites, I’ll put the strings together, adding the references.

Here is what I did in R and in Bash (you will need su/sudo):

  1. Store packages (in R) 1
tmp <- installed.packages()
installedpkgs <- as.vector(tmp[is.na(tmp[,"Priority"]), 1])
saveRDS(installedpkgs, 'installed_old.rds')
  1. Remove R completely 2
dpkg -l | grep ^ii | awk '$2 ~ /^r-/ { print $2 }' | sudo xargs apt-get remove --purge -y
  1. Remove all R packages 3

The locations might differ from yours.

R -e '.libPaths()'
rm -rf /home/jay/R/x86_64-pc-linux-gnu-library/4.2 /usr/local/lib/R/site-library /usr/lib/R/site-library /usr/lib/R/library
  1. Install R (here with apt) 4
apt install r-base-core
  1. Restore R packages 5

This runs for a while. Note that only packages that can be found in repositories are installed.

installedpkgs <- readRDS("installed_old.rds")
tmp <- installed.packages()
installedpkgs.new <- as.vector(tmp[is.na(tmp[,"Priority"]), 1])
missing <- setdiff(installedpkgs, installedpkgs.new)
install.packages(missing)
update.packages(ask=FALSE)

Answered By – jay.sf

This Answer collected from stackoverflow, is licensed under cc by-sa 2.5 , cc by-sa 3.0 and cc by-sa 4.0

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