R studio packages on mojave have 'non-zero exit status' - r

Question

I haven't used R for a while. Now I need to work with it again and in the meantime I updated to mac os mojave. Also, bioconductor apparently switched sth in their installations and we now have to use biocmanager instead of bioclite. Anyways, I run into several installation errors and have no idea what to do. I just downloaded xcode hoping that this was the problem but I still get the following errors:
> library(DESeq2)
Fehler: package or namespace load failed for ‘DESeq2’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
es gibt kein Paket namens ‘Hmisc’
> install.packages("Hmisc")
also installing the dependencies ‘acepack’, ‘data.table’
Warning in install.packages :
unable to access index for repository https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6:
kann URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/PACKAGES' nicht öffnen
Packages which are only available in source form, and may need compilation
of C/C++/Fortran: ‘acepack’ ‘data.table’ ‘Hmisc’
Do you want to attempt to install these from sources? (Yes/no/cancel) yes
installing the source packages ‘acepack’, ‘data.table’, ‘Hmisc’
versuche URL 'https://cran.rstudio.com/src/contrib/acepack_1.4.1.tar.gz'
Content type 'application/x-gzip' length 34848 bytes (34 KB)
==================================================
downloaded 34 KB
versuche URL 'https://cran.rstudio.com/src/contrib/data.table_1.12.8.tar.gz'
Content type 'application/x-gzip' length 4948391 bytes (4.7 MB)
==================================================
downloaded 4.7 MB
versuche URL 'https://cran.rstudio.com/src/contrib/Hmisc_4.4-0.tar.gz'
Content type 'application/x-gzip' length 744545 bytes (727 KB)
==================================================
downloaded 727 KB
* installing *source* package ‘acepack’ ...
** Paket ‘acepack’ erfolgreich entpackt und MD5 Summen überprüft
** using staged installation
** libs
gfortran -fPIC -Wall -g -O2 -c ace.f -o ace.o
make: gfortran: No such file or directory
make: *** [ace.o] Error 1
ERROR: compilation failed for package ‘acepack’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/acepack’
Warning in install.packages :
installation of package ‘acepack’ had non-zero exit status
* installing *source* package ‘data.table’ ...
** Paket ‘data.table’ erfolgreich entpackt und MD5 Summen überprüft
** using staged installation
zlib 1.2.8 is available ok
** 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’
Warning in install.packages :
installation of package ‘data.table’ had non-zero exit status
ERROR: dependencies ‘acepack’, ‘data.table’ are not available for package ‘Hmisc’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Hmisc’
Warning in install.packages :
installation of package ‘Hmisc’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/7y/tklmw3f51rz8292j144_70680000gn/T/RtmpacLY8N/downloaded_packages’
Can anyone help? Thank you in advance!

Answer 1

I am running Mojave on my laptops, and I was able to use this guide to get things working.
Try following the steps on that guide.
However, I had to use a slightly different Makevars file because I'm not on the most up-to-date OS.
Here is the contents of my ~/.R/Makevars file.
CFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CCFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CXXFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CPPFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
CXX14 = /usr/local/clang7/bin/clang++ -stdlib=libc++ -nostdinc++ -I/usr/local/clang7/include/c++/v1
SHLIB_CXX14LD = /usr/local/clang7/bin/clang++ -L/usr/local/clang7/lib
FLIBS=""
F77="/usr/local/gfortran/bin/gfortran"
FC="/usr/local/gfortran/bin/gfortran"

Answer 2

Try going to R preferences > Packages and unchecking "Use secure download method for HTTP", it looks like this is a default parameter that unables opening the URL.

Answer 3

Fixed!
I could fix the problem by typing the following into my terminal:
brew update && brew reinstall r