Entering edit mode
4 hours ago
mewgia
•
0
Hello! I'm trying to install phyloseq. Ubuntu 18.04. R 4.4.2. And see that:
/usr/bin/ld: cannot find -lgfortran
collect2: error: ld returned 1 exit status
/usr/share/R/share/make/shlib.mk:10: recipe for target 'igraph.so' failed
make: *** [igraph.so] Error 1
ERROR: compilation failed for package ‘igraph’
* removing ‘/home/bobii/R/x86_64-pc-linux-gnu-library/4.4/igraph’
ERROR: dependency ‘RcppArmadillo’ is not available for package ‘ade4’
* removing ‘/home/bobii/R/x86_64-pc-linux-gnu-library/4.4/ade4’
ERROR: dependencies ‘ade4’, ‘igraph’ are not available for package ‘phyloseq’
* removing ‘/home/bobii/R/x86_64-pc-linux-gnu-library/4.4/phyloseq’
But I have gfortan installed in my ubuntu:
gfortran --version
GNU Fortran (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0
Copyright (C) 2017 Free Software Foundation, Inc.
So, the question is what I do wrong? and how to fix it? Thank you!
Likely a shared library path issue. Can you check https://askubuntu.com/questions/1128112/ld-cannot-find-shared-library and see which exact file from gfortran the linker is looking for.
Some of the solutions mentioned in the following Stackoverflow thread may not work as the OS has reached EOL.
https://stackoverflow.com/questions/6302209/building-r-package-and-error-ld-cannot-find-lgfortran
Another solution will be to create a conda env for phyloseq.