I managed to solve the issue at least partially. The problem appears to be some lines in my .R/Makevars
.
After my initial installation of rstan
and rstanarm
(2.19.3.), I had updated my .R/Makevars
based on this and this (if I remember correctly), and it looked like this:
# clang: start
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/l$
SHLIB_CXXLDFLAGS+=-Wl,-rpath,${R_HOME}/lib ${R_HOME}/lib/libc++abi.1.dylib
SHLIB_CXX14LDFLAGS+=-Wl,-rpath,${R_HOME}/lib ${R_HOME}/lib/libc++abi.1.dylib
SHLIB_CXX11LDFLAGS+=-Wl,-rpath,${R_HOME}/lib ${R_HOME}/lib/libc++abi.1.dylib
# clang: end
CXX14FLAGS=-O3 -march=native -mtune=native
CXX14FLAGS += -arch x86_64 -ftemplate-depth-256
After commenting out all lines in .R/Makevars
, I managed to successfully install the survival branch with
devtools::install_github("stan-dev/rstanarm@feature/survival", build_vignettes = FALSE)
and it seems to work properly.
However, trying to install the downloaded repo manually from RStudio produces the same error as above.