Question

Problem with DESeq2 installation (RcppArmadillo error)

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Entering edit mode

kassiopeass • 0

@kassiopeass-9391

Last seen 8.3 years ago

Hello,

I am new to R and I having some issues installing packages. I am trying to install DESeq2 and I am getting and error when installing the dependency 'RcppArmadillo':

install.packages("RcppArmadillo")

ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [RcppArmadillo.so] Error 1
ERROR: compilation failed for package 'RcppArmadillo'

removing '/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppArmadillo'

Could you please help me?

Some info: I use OSX el Capitan 10.11.
R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree"
Platform: x86_64-apple-darwin13.4.0 (64-bit)
R Studio Version 0.99.489

Thanks a lot,

Isabel

DESeq2 • 3.1k views

ADD COMMENT • link updated 8.3 years ago by Michael Love 41k • written 8.3 years ago by kassiopeass • 0

score 0 · Answer 1 · 2015-12-17

When I've seen this problem before, it was due to an incompatibility between the version of gfortran you have installed, and the version that was used to compile the R binary that you're running.

I fixed it by downloading the file gfortran-4.8.2-darwin13.tar.bz2 from http://r.research.att.com/libs/ and then installing in the root directory.

There are instructions on that site, but something like this should do it:

curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2
sudo tar fvxz gmp-4.2.4-darwin8-bin4.tar.gz -C /

score 0 · Answer 2 · 2015-12-17

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Entering edit mode

Michael Love 41k

@mikelove

Last seen 1 day ago

United States

Have you tried installing with biocLite("DESeq2")? Bioconductor has binaries for the dependencies of Bioconductor packages, and will install these automatically.

ADD COMMENT • link 8.3 years ago Michael Love 41k

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Entering edit mode

I am also having the same problem with DESeq2 (returning a non-zero exit status), even though I use biocLite. I have also tried to install RcppArmadillo independently from R (on the command line), but I get an error message that says I need to use a different compiler.

Many of the suggestions that I have seen, including the reply above this one, suggest using sudo; however, I do not have root privileges. I do have a work around. I could use my current institute's server, but the project is for my previous institute. It would just be nice to understand why I'm having such troubles.

Thank you.

ADD REPLY • link 7.6 years ago haas • 0