My laptop is a mac pro. The OS version is 10.15 Catalina. The r studio version is 1.2.5001. The R version is 3.6.1.
I tried to install "WGCNA", but it failed because of the following error:
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘data.table’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
ERROR: lazy loading failed for package ‘WGCNA’
* removing ‘/Users/zhaoboao/Library/R/3.6/library/WGCNA’
Therefore, I installed 'data.table', but it also failed because of the following error:
* installing *source* package ‘data.table’ ...
** package ‘data.table’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c assign.c -o assign.o
clang: error: unsupported option '-fopenmp'
make: *** [assign.o] Error 1
ERROR: compilation failed for package ‘data.table’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/data.table’
Can anyone help me to solve this problem? I really appreciate it!
First of all...welcome to what I think is the best online community for R
users! (though others may disagree)
To address your question, I absolutely empathize with your frustration. I also had a horrid time trying to get the package data.table
to install in R
after updating to Catalina. Being a little better than a novice with the terminal at best, I still need a moderate amount of hand holding which I think accounts for many others as well. The only set of step by step directions that worked for me was laid out at The Coatless Professor .
On a side note, I did install updated versions of clang
and gfortran
using clang-8.0.0
and gfortran-6.1
, respectively. Both of these can be found on the R for Mac OS X Development Tools and Libraries by selecting this link . However, if you use the stepwise directions, I'd advise installing them when it is brought up.
I only bring this up because it is easy to miss but the very last thing is to make sure you use the correct version of clang
when running step #3 under INSTALLING THE CLANG7 R BINARY. In my case, I had to change the version 7 of clang
to 8 by amending echo 'PATH="/usr/local/clang7/bin:${PATH}"' >> ~/.Renviron
to echo 'PATH="/usr/local/clang8/bin:${PATH}"' >> ~/.Renviron
.
I hope this helps!
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