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gfortran for phyloseq in R

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!

ade4 rcpparmadillo gfortran phyloseq
• 1,369 views • link
updated by colindaven colindaven • written by mewgia • mewgia

Please upgrade your system, it is really old and insecure. Ubuntu LTS editions like 1804, 2004 etc have standard support for 5 years.

• 0 views • link
written by colindaven colindaven

1 answer

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.

• 0 views • link
written by Arup Ghosh Arup Ghosh

Another solution will be to create a conda env for phyloseq.

Great idea, it works perfect. Thank you!

• 0 views • link
written by mewgia • mewgia

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