Dealing with Catalina II

MegBallard · December 19, 2019, 1:50am

I’m way beyond my expertise except for solving this problem three times with the help of everyone who has posted here (when first installing and running glmmTMB, getting a new computer and doing it again for stan models via brms, and again when upgraded to Catalina).

Am I incorrect that R3.5 and 3.6 use different versions of clang? If so using the above installer will not include the clang6 required for 3.5

I have avoided installing most current R because of my terror of messing up the delicately balanced system that currently works (especially after Catalina upgrade created permissions problems that I solved but don’t remember how.)

I am unendingly grateful for the work by coatless and bgoodri and anyone I didn’t mention who has focused on helping solve a problem you didn’t create!

coatless · December 19, 2019, 3:42am

That is correct. Due to Catalina, we’re having to rethink a few things.

I’m tracking the feature need here: macOS toolchain per version · Issue #16 · coatless-mac/r-macos-rtools · GitHub

jroon · December 19, 2019, 10:01am

Hi guys yes upgrading to R3.6.2 fixed it. Models build happily now. I’m still getting oddles or runtime complier warnings - is there a way to suppress those I cannot recall ?

Thanks for your help. My bad. Recent years of MacOS and iOS updates with …issues… have trained me into not updating anything until absolutely necessary 🙈

Save · December 19, 2019, 11:27am

First of all, thanks everyone helping with this.

I did read all the info available, and did the following on Catalina 10.15.2:

Fresh installation R (v. 3.6.2) and R studio (1.2.5019)
Installed latest version of Xcode
Installed r-macos-rtools 3.2.1
Installed Rstan from source

I am still getting this error when running rstan or brms models:

[1] “Error in sampler$call_sampler(args_list[[i]]) : "
[2] " c++ exception (unknown reason)”
error occurred during calling the sampler; sampling not done

-> My .R Makevars files look 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/local/include

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

clang: end

Any ideas what I could do to fix this?

torkar · December 19, 2019, 12:20pm

Try this in Makevars:

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
SHLIB_CXXLDFLAGS+=-Wl,-rpath,/Library/Frameworks/R.framework/Resources/lib /Library/Frameworks/R.framework/Resources/lib/libc++abi.1.dylib
SHLIB_CXX11LDFLAGS+=-Wl,-rpath,/Library/Frameworks/R.framework/Resources/lib /Library/Frameworks/R.framework/Resources/lib/libc++abi.1.dylib
SHLIB_CXX14LDFLAGS+=-Wl,-rpath,/Library/Frameworks/R.framework/Resources/lib /Library/Frameworks/R.framework/Resources/lib/libc++abi.1.dylib

Save · December 19, 2019, 1:11pm

Thanks for the suggestion!

I tried… but I’m still getting the same error.

torkar · December 19, 2019, 1:41pm

Have you recompiled relevant packages, e.g., rstan?

Save · December 19, 2019, 5:07pm

I did install rstan after modifying the Makevars file. I’m still getting the same error.

I have 2 Makevars files in the .R folder:
Makevars.txt
Makevars.bck

I modified both of them, and tried also single combinations both nothing works.

bgoodri · December 19, 2019, 5:08pm

Neither of those files do anything. The filename needs to be simply called Makevars.

Save · December 19, 2019, 5:23pm

Yes. I’m sorry I did a mistake in writing. txt.
I do have one Makevars file and one Makevars.bck.

I’m getting this error message even when I only modify the Makevars file.

bgoodri · December 19, 2019, 6:19pm

It will probably work if you add

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/

to the end of Makevars, but we don’t know why it itsn’t working for you already.

Save · December 20, 2019, 10:54am

Thank you very much for the help.

I tried to uninstall and freshly install everything again a few times and tried to change makevars as suggested but I’m still getting the same error…

torkar · December 20, 2019, 11:03am

Just to be clear: You do have Makevars in ~/.R/ where ~ is your home directory, and .R is a directory in your home directory?

Save · December 20, 2019, 11:08am

Yes I do. The path is /Users/save/.R/Makevars

torkar · December 20, 2019, 1:21pm

Sorry @Save, but I’m a bit stumped here. Hopefully @coatless or @bgoodri have more things to try out.

Save · December 20, 2019, 3:05pm

When installing rstan from source I am now getting these errors. Perhaps this could help to identify the problem?

Thanks again.

warning when installing rstan.txt (65.6 KB) other errors.txt (25.1 KB)

bgoodri · December 20, 2019, 3:59pm

It is saying that it cannot install Rcpp and a bunch of other packages, which definitely should not be happening. You should be able to install those as binaries. But then your C++ header files seem to be not found, e.g.,

/usr/local/clang7/include/c++/v1/cmath:313:9: error: no member named ‘signbit’ in the global namespace

I would guess that is because you are using clang++ from Xcode, which would suggest that your PATH is wrong somehow and that you do not have

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/

in your ~/.R/Makevars file.

MegBallard · December 21, 2019, 8:08am

I’m assuming the problem is more complicated, but because I have made this error my dumb self so I’m putting it out there:

Did you restart your computer and/or Rstudio?

torkar · December 21, 2019, 8:25am

Aaah, the old Windows trick ;) Well, you never know… :)

Save · December 21, 2019, 10:15am

Thanks again for the feedback.

I know tried two freshly install R, Rstudio and r-macos-rtools 3.2.1 with and without having Xcode installed in my Mac.

My Makevars file looked like this (but I also tried without the two last lines):

#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/local/include

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

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/

#clang: end

-> I am not having rstan installations errors anymore back I’m back to the sampling error… (And of course I’m restarting the mac many times)

I wonder if these problems might be caused by the fact that I installed too many times everything and that some old files are still present and generate conflicts?

Thanks a lot again for this great support guys, I really appreciate and I hope to find a solution soon

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Dealing with Catalina II

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