Sorry, I asked this question in bioinformatics too and googled a lot but still my problem exists
after updating R, whatever package I am trying to install gives me the same error
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0' ld: library not found for -lgfortran clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [RcppEigen.so] Error 1 ERROR: compilation failed for package ‘RcppEigen’ * removing ‘/Library/Frameworks/R.framework/Versions/3.5.1-MRO/Resources/library/RcppEigen’ Warning in install.packages : installation of package ‘RcppEigen’ had non-zero exit status The downloaded source packages are in ‘/private/var/folders/4v/31py55vj2rlbpy4qcv2gqt2m0000gq/T/RtmpIyjaEZ/downloaded_packages’
How I can install R packages like already please?
Are you using Rstudio?
Yes I am using RStudio
Try to purge R completely by running these commands in terminal (not in R).
Also delete the RStudio.app from your
I'm separating out some comment threads to try and stop everything nesting too deeply.
Sorry what is the solution please?
The answer already provided by Genomax and Steve should be fine - they work for most people. As you do not favour the Python solution, you should follow the advice of Genomax.
From your current position, do the following:
Unfortunately, we are all remote from you, so, we cannot see the specific actions that you are taking.
If you download R separately, it is crucial that it installs to a 'normal' place, so that RStudio can find the R binary. Else you will need to direct RStudio to whereever R is.
This is why I suggest you allow RStudio to do it for you to avoid confusion.
Sorry I removed everything and I installed latest version of R 3.5.1 that for me did not work so I installed R 3.3.3 but again the same problem
I can not install any package yet :( :( :(
You need to install C libraries. Take a look here: https://embeddedartistry.com/blog/2017/2/20/installing-clangllvm-on-osx
Za : You may be gone for the day but did you install the two tools mentioned in: https://cran.r-project.org/bin/macosx/tools/
Thank you, yes, just yesterday as you suggested I installed clang and gfortran my iMAC is Yosemite 10.5.5 and I tried to install the compatible versions but again I am facing
You are using a ~ 8+ year old operating system that has not been maintained for a long time. It is quite possible that that could be the root cause of all the issues you have been experiencing.
Are you sure
clangwas installed without any errors?
Sorry, I just double clicked on clang-6.0.0.pkg and installed that. I checked for gcc
The graphics card of my own mac failed so I transferred my data from failed mac to this mac by a cable;
This is a Yosemite 10.10.5 version mac
Whatever R package I am trying to install if any need to be compiled I will get error
Looks like you need to install latest version of
This also may be relevant: https://community.rstudio.com/t/unable-to-install-any-packages/13053/3