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nclark-lab / RERconverge

Analysis of convergence between organismal traits and DNA/protein sequences
GNU General Public License v3.0
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Issues installing RERconverge on R 4.0 (Mac OS Catalina 10.15.5) #55

Closed kjf319 closed 3 years ago

kjf319 commented 4 years ago

Unable to install RERconverge on R 4.0.2. Using on a Mac OS Catalina 10.15.5. Attempted to bypass error through process listed in comments error report #52. I installed dependencies for devtools, installed Xcode , slang6 and gfortran, created a .bash_profile in home directory and added '''export PATH=/usr/local/clang6/bin:$PATH''' and then reinstalled from GitHub in Rstudio. I also tried using R console and reinstalling as opposed to Rstudio. I received the same error message as before-

'''ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0' ld: warning: directory not found for option '-L/usr/local/gfortran/lib' ld: library not found for -lgfortran clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [RERconverge.so] Error 1 ERROR: compilation failed for package ‘RERconverge’

wgmao commented 4 years ago

Thank you for your feedback. I have tried the following solutions on Catalina 10.15 & R 4.0.2. and both of these two solutions work for me.

Solution 1

Could you try the following steps: 1) delete the .bashrc_profile 2) Try install RERconverge from the R console

library(devtools)
install_github("nclark-lab/RERconverge")

Solution 2

If the first solution doesn't work, could you try this pre-compiled binary installation? RERconverge_0.1.0.tgz.zip 1) Unzip the file to get RERconverge_0.1.0.tgz 2) R CMD INSTALL RERconverge_0.1.0.tgz

kjf319 commented 4 years ago

Hi @wgmao,

Thank you for the potential solutions. I tried solution one, but deleted the bash profile (.bash_profile) with recommended edits in issue #52. There was no .bashrc_profile. When I tried this, installation failed with the following error message : /usr/local/clang8/bin/clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/ape/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:26: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/RcppCommon.h:29: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/r/headers.h:67: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100: In file included from /usr/local/clang8/bin/../include/c++/v1/cmath:305: /usr/local/clang8/bin/../include/c++/v1/math.h:301:15: fatal error: 'math.h' file not found

include_next 

          ^~~~~~~~

1 error generated. make: *** [RcppExports.o] Error 1 ERROR: compilation failed for package ‘RERconverge’

I also tried solution 2. The unzipped file downloaded from your link (https://github.com/nclark-lab/RERconverge/files/5106710/RERconverge_0.1.0.tgz.zip) was named RERconverge.0.1.0.tar. After downloading and unzipping, I tried to install RERconverge using the code you provided. The install appeared to work, as I got the following message: * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’

When I went to look at the library in R library(RERconverge), I got the following error message : Error: package or namespace load failed for ‘RERconverge’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RERconverge/libs/RERconverge.so': dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RERconverge/libs/RERconverge.so, 6): Library not loaded: /usr/local/gfortran/lib/libgfortran.3.dylib Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RERconverge/libs/RERconverge.so Reason: image not found

Let me know something I could check in differences in my environment and what you're using. Thanks!

kjf319 commented 4 years ago

Hi @wgmao,

I successfully installed RERconverge through instructions on https://thecoatlessprofessor.com/programming/cpp/r-compiler-tools-for-rcpp-on-macos/ and then installing through GitHub (as recommended on the installation page) on the R console (not R Studio). It might be worth updating the install page for RERconverge with these instructions, as the current instructions didn't work well with macOS Catalina 10.15.5.

Thanks!

wgmao commented 3 years ago

Thank you for directing us to this great resource. This also works for Big Sur which is awesome. Many thanks.