I attended a presentation on Spectre and Meltdown by a UCL professor. He suggested several ways to mitigate Spectre 2 (Branch Target Injection) by upgrading to High Sierra and installing all software from source with the switch --mretpoline (already deployed in LLVM and GCC). I want to install R and RStudio on macOS High Sierra this way. I downloaded the source for both. The installation procedure is similar for R and RStudio. The file INSTALL for R says that I should run


I inspected the “configure” file and the makefiles (Makeconf.in, Makefile.in, Makefile.in). I saw no obvious way to add the switch. I called the help for make, which also does not mention how to add a switch.

I searched for this online and the closest I could find was explanations of retpoline and Spectre 2.

How can I compile software from source with make and include the --mretpoline switch?

  • Just to avoid confusion there is also a SO question for this (by you) that was closed. Here. Also Passing additional variables from command line to make might be relevant. – Seth Feb 1 '18 at 10:23
  • Thanks @Seth for the link to avoid confusion and for the tip on passing variables. The passing of variables works, but not the particular flag -mretpoline. – mmorin Apr 27 '18 at 10:00

Short version: After much investigation, I was unable to install software on MacOS from source with either llvm and -mretpoline flag, or with gcc and -mindirect-branch=thunk -mfunction-return=thunk -mindirect-branch-register flags. This seems more general than R and specific to MacOS, so I changed the title accordingly. I suspect that this cannot be done on a Mac as of 27 April 2018. I am running macOS High Sierra version 10.13.3 (17D102).

Long version: The following applies to GnuPG, which I decided to install before R (because R requires gfortran, which requires gcc, which requires MPFR, which comes with a GPG signature that I wanted to verify). I followed the steps to install GPG from Git.

Latest LLVM (with Homebrew)

LLVM from Apple fails (see below), so I used LLVM clang 6 to fix this and I installed with homebrew (it defeats a bit the purpose of compiling from source with specific flags, but I was running out of time). I installed homebrew with:

ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

then updated it twice with

brew update

Installing clang with Homebrew required XCode, so I installed that from the App Store. Then I followed the steps at this page:

brew install --with-toolchain llvm

Then I added the -mretpoline flag to both C, I added the path to both C and C++ compilers, and I called the shell scripts from GPG:

export CFLAGS='-mretpoline'
export CC=/usr/local/opt/llvm/bin/clang
export CXX=/usr/local/opt/llvm/bin/clang++
./configure --sysconfdir=/etc --enable-maintainer-mode  && make

I got this error:

checking whether the C compiler works... no

The log file config.log gives more details:

configure:4049: /usr/local/opt/llvm/bin/clang -mretpoline   conftest.c  >&5
fatal error: error in backend: MachO doesn't support COMDATs, '__llvm_retpoline_r11' cannot be lowered.
clang-6.0: error: clang frontend command failed with exit code 70 (use -v to see invocation)

This thread with a comment from January 2018 at the bottom saying that Mac is not yet supported with -mretpoline:

samkellett: @chandlerc is MacOS support omitted intentionally (ie. not implemented yet)? chandlerc: Not at all, I just don't have a Mac system to test with...

It has no response since then. So installing with LLVM failed.

GCC (with Homebrew)

Another alternative was to compile with gcc instead of LLVM. I installed the latest version of clang (6.0) with

brew install gcc

And I added the gcc flags from this page, which are different from LLVM. This bash script adds the flags to both C and C++, gives the paths to both compilers, and call the shell scripts from GPG:

export CFLAGS='-mindirect-branch=thunk -mfunction-return=thunk -mindirect-branch-register'
export CC=/usr/local/opt/gcc/bin/gcc-7
export CXX=/usr/local/opt/gcc/bin/g++-7
./configure --sysconfdir=/etc --enable-maintainer-mode  && make

and again I get the error:

checking whether the C compiler works... no

The log file config.log gives more details:

configure:4027: checking whether the C compiler works
configure:4049: /usr/local/opt/gcc/bin/gcc-7 -mindirect-branch=thunk -mfunction-return=thunk -mindirect-branch-register   conftest.c  >&5
Undefined symbols for architecture x86_64:
  "__x86_return_thunk", referenced from:
      _main in ccZuBhFQ.o
     (maybe you meant: ___x86_return_thunk)
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
configure:4053: $? = 1
configure:4091: result: no

It's weird that the compiler knows about the similar sounding name with an extra underscore.

So gcc failed too. And now I'm at a loss.

Appendix: LLVM from Apple

The following bash script exports the flags for make and calls the shell scripts from GnuPG:

export CFLAGS='-mretpoline'
echo $CFLAGS
./configure --sysconfdir=/etc --enable-maintainer-mode  && make

It fails with the compiler that ships from Apple, but it shows that the flags are getting through to the compiler:

configure:4045: gcc -mretpoline -mindirect-branch=thunk -mfunction-return=thunk -mindirect-branch-register   conftest.c  >&5
clang: error: unknown argument: '-mretpoline'

So @seth's comment is right in how to send flags to the compiler.

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