Dealing with Catalina III

jeremy.koster · February 29, 2020, 9:14pm

Hi leomarameo7,

Can you explain the steps you followed to get it working?

Thanks,
Jeremy

leomarameo7 · February 29, 2020, 9:21pm

Hi Jeremy,

Well, I opened OS Terminal. And then I wrote as follow:
mkdir -p ~/.R
cat <<- EOF > ~/.R/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,${R_HOME}/lib ${R_HOME}/lib/libc++abi.1.dylib
SHLIB_CXX14LDFLAGS+=-Wl,-rpath,${R_HOME}/lib ${R_HOME}/lib/libc++abi.1.dylib

EOF

jeremy.koster · February 29, 2020, 9:31pm

Thanks, @leomarameo7.

It looks like I’ve had success by doing the same. I can now estimate a Stan model.

I’ve been trying all kinds of combinations, so I’m not sure if I can summarize exactly what should be done. But this seems to work by:

Downloading and installing the rtools package from the link in the opening message of this thread.
Then open Terminal and enter the changes to the Markvars that @yuling recommended.

That seems to work, but maybe I’m overlooking something.

The strange thing, though, is that I continue to get a prompt about the installation of rtools:

And yet the models estimate if I dismiss the prompt. Dismissing the prompt will be a minor nuisance when it’s time to estimate a model, but at least I’m back in business.

bgoodri · February 29, 2020, 10:01pm

It should not normally be asking you to keep reinstalling the build tools. What does it say when you do in a fresh R session

pkgbuild::has_build_tools(debug = TRUE)

?

jeremy.koster · February 29, 2020, 10:02pm

@bgoodri

First it throws the same prompt for reinstalling.

Then when I click “no”, it comes back with:

pkgbuild::has_build_tools(debug = TRUE)
[1] FALSE

bgoodri · March 1, 2020, 2:07am

What about

pkgbuild::has_compiler(debug = TRUE)

?

jeremy.koster · March 1, 2020, 2:53pm

Lots of syntax, concluding with:

In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:1:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#include <complex>
         ^~~~~~~~~
3 errors generated.
make: *** [foo.o] Error 1
[1] FALSE

bgoodri · March 1, 2020, 4:14pm

And

packageVersion("StanHeaders")

is 2.19.2 ?

jeremy.koster · March 1, 2020, 4:15pm

2.19.0

bgoodri · March 1, 2020, 6:03pm

OK. Try a

install.packages("StanHeaders", type = "source")

jeremy.koster · March 1, 2020, 6:07pm

That seemingly took care of it. There are no more prompts to install rtools. As far I can tell, everything seems to be functioning normally. Changing the Makevars file was evidently key. Thanks to all.

schnack · March 2, 2020, 1:26pm

Works thanks!
install.packages(“rstan”, repos = “https://cloud.r-project.org/”, dependencies = TRUE)

Stephen_Martin · April 7, 2020, 8:13am

Adding another datapoint to this. I have Catalina, freshly installed, in a VM to test rstan.

I took the following steps:

     - Requirements: R 3.6.3; Rstudio; XQuartz
       + After XQuartz: Must log out, and back in.
     - In terminal: xcode-select --install
     - Macos-Rtools
       + Download r-macos-rtools from https://github.com/rmacoslib/r-macos-rtools/releases/tag/v3.2.2
       + When downloaded, click "Downloads", go to "Open in Finder"; hold CTRL and right click on macos-rtools-3.2.2.pkg; click open. Install it.
     - RStan:
       + Open R (Not Rstudio? Was crashing in the VM)
       + Run the following: install.packages("Rcpp", repos = "https://rcppcore.github.io/drat")
	 * Say "Yes" when prompted to install from sources.
       + Run the following: install.packages("rstan", type = "source")

And changed literally nothing else. No makevars, nothing.

It worked fine. Ran the example in rstan::stan, and it seemed fine to me. Brms also worked fine.

The .R/Makevars contains the same as (Dealing with Catalina III). Note that I did not add that, nor modify it. I assume the R tools package did (?).

bgoodri · April 7, 2020, 1:13pm

That is what is supposed to happen, but Catalina fails in different ways for different people so sometimes there are more steps to get rstan working.

Stephen_Martin · April 7, 2020, 7:19pm

Is there an organized list of ‘if it fails like ____, then try ____’ anywhere? We are going to introduce Stan to students on May 4, and we want them to install it a week prior to that using a document that tells them each step, and each step to take if something goes wrong.

Have the failures been due to ‘dirty’ Makevars files (e.g., having one Makevars pre-catalina, that does not work postupgrade)?

bgoodri · April 7, 2020, 7:29pm

The plan is to hope that with CRAN switching back to an XCode based toolchain for R 4.0 in late April that there won’t have to be a Dealing with Catalina V thread.

lakemonster · April 8, 2020, 2:37pm

I hope there is…I’ve given up on gettin rstan to work on my Mac and am running on ubuntu.

bgoodri · April 8, 2020, 4:07pm

You shouldn’t give up. I think we have gotten 100% of Macs with Catalina to work eventually, but hopefully in a couple of weeks it won’t require extra effort.

daaronr · May 23, 2020, 10:55am

minor thing – need to match the quote types in the above

daaronr · May 23, 2020, 11:11am

Also, in the Coatless professor’s instructions…

curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2

apparently needs to be

curl -OL http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2

instead