I'm new to R and it looks like I'm having issues setting up BiocManager and linked to the mgcv package and clang? See below. I'm running on macosx Mojave, I installed R, Rstudio, Xcode and Xcode command lines.
> BiocManager::install() Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.3 (2019-03-11) Update old packages: 'mgcv' Update all/some/none? [a/s/n]: a There is a binary version available but the source version is later: binary source needs_compilation mgcv 1.8-27 1.8-28 TRUE Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Yes installing the source package ‘mgcv’ trying URL 'https://cran.rstudio.com/src/contrib/mgcv_1.8-28.tar.gz' Content type 'application/x-gzip' length 915991 bytes (894 KB) ================================================== downloaded 894 KB * installing *source* package ‘mgcv’ ... ** package ‘mgcv’ successfully unpacked and MD5 sums checked ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c coxph.c -o coxph.o clang: error: unsupported option '-fopenmp' make: *** [coxph.o] Error 1 ERROR: compilation failed for package ‘mgcv’ * removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/mgcv’ * restoring previous ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/mgcv’ The downloaded source packages are in ‘/private/var/folders/k7/4zfz3tnj6sv7c5vx6khz09kr0000gn/T/RtmpP8RQpe/downloaded_packages’ Warning message: In install.packages(update[instlib == l, "Package"], l, repos = repos, : installation of package ‘mgcv’ had non-zero exit status