Dealing with Catalina II

Ptterz · November 29, 2019, 6:18am

Still denies changes after running that above.

torkar · November 29, 2019, 6:35am

Open a new thread in the forum. Type

ls -lsa

In that directory, and paste that into the new post.

Ptterz · November 29, 2019, 8:16am

Hi,
so I managed to change the rights for that file with somewhat obvious answer (sudo).
Thanks for your help and that code above, it solved the problems for me! :)

mans_magnusson · November 29, 2019, 9:37am

I just want to say that this fixed the problem for me as well. Thank you!

bh7 · December 7, 2019, 5:07pm

I’ve been trying to run brms code on my Mac (latest version of everything, R, RStudio, all packages, etc) and get the following error:

[1] “Error in sampler$call_sampler(args_list[[i]]) : "
[2] " c++ exception (unknown reason)”
error occurred during calling the sampler; sampling not done
some chains had errors; consider specifying chains = 1 to debughere are whatever error messages were returned

I respecified the chains but got the same error.

Any ideas how to fix this? You seem much more helpful than the brms developer…
Thanks.

bgoodri · December 7, 2019, 10:50pm

You need to install the new version of the installer mentioned in the first post on this thread.

bh7 · December 8, 2019, 12:32pm

I did install it, a day before I joined the thread. The results above are with the new version.

torkar · December 8, 2019, 1:36pm

Read this: Dealing with Catalina II, and then, if necessary, recompile all relevant packages.

bh7 · December 8, 2019, 2:20pm

I reinstalled and changed the .R/Makevars code (I have absolutely no idea what that is or what I did), restarted my Mac, and everything worked beautifully. I can’t thank you enough!! Your help is invaluable and enormously appreciated.

Evgenii · December 16, 2019, 8:45pm

Installed macos-rtools-3.2.0.pkg. It still gave me the Error in sampler error untill I added this line to .R/Makevars file:

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

Now everything works. My full .R/Makevars file is 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,/Library/Frameworks/R.framework/Resources/lib /Library/Frameworks/R.framework/Resources/lib/libc++abi.1.dylib
# clang: end

coatless · December 17, 2019, 3:05am

Mmm, interesting. Okay, we’ll add the SHLIB_CXX14LDFLAGS as well.

I’m wondering if somewhere these implicit variables aren’t getting read…

jroon · December 18, 2019, 12:22pm

Ok I’m having issues. @coatless I downloaded and ran the latest version of your installer today. It ran without complaint. When I tried to run a brms model got this error:

So I went into Terminal and tried running a few commands like make or git and was seeing this:

user$ make
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun

Ok. So then I reinstalled command line tools like so: sudo xcode-select --install and this fixed my command line issues. Make and git now run again.

However when I try to build an rstan example model I got issues:

>stanmodelcode <- "
data {
  int<lower=0> N;
  real y[N];
} 

parameters {
  real mu;
} 

model {
  target += normal_lpdf(mu | 0, 10);
  target += normal_lpdf(y  | mu, 1);
} 
"

y <- rnorm(20) 
dat <- list(N = 20, y = y); 
fit <- stan(model_code = stanmodelcode, model_name = "example", 
            data = dat, iter = 2012, chains = 3, verbose = TRUE,
            sample_file = file.path(tempdir(), 'norm.csv')) 
print(fit)


Error in compileCode(f, code, language = language, verbose = verbose) : 
  Compilation ERROR, function(s)/method(s) not created! In file included from file14a252700959.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core/build_vari_array.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/l

I’m at a loss as to what to do next - any advice appreciated.

bgoodri · December 18, 2019, 4:04pm

Post the output of

example(stan_model, package = "rstan", run.dontrun = TRUE)

coatless · December 18, 2019, 7:46pm

A few quick questions:

Which version of macOS was used?
What version of R was used?
What version of the installer? v3.2.1?
Was the computer online while the installer was run?
Was this a brand new computer or was it upgraded from a prior macOS version?

jroon · December 18, 2019, 10:52pm

Ok… this generated so much text the forum limit would not let me post it directly. I’ve stuck it into a text file so → stan_example_output.txt (64.8 KB)

jroon · December 18, 2019, 10:55pm

Catalina 10.15.2
R 3.5.1
r-macos-rtools 3.2.1
Yes
New 16" with restore from Time Machine backup from MacOs Mojave 10.14.6

bgoodri · December 18, 2019, 11:38pm

Well, the ultimate error was

clang-7: error: no such file or directory: ‘/Library/Frameworks/R.framework/Resources/lib/libc++abi.1.dylib’

So, maybe you have a different version of clang than clang-7 or your PATH is messed up or you have something in ~/.R/Makevars that sets CXX14 = clang-7 when it should just be CXX14 = clang?

jroon · December 18, 2019, 11:52pm

My r/Makevars looks 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

coatless · December 19, 2019, 12:50am

@jroon looks like the R version is outdated. Can you upgrade to R 3.6.2?

coatless · December 19, 2019, 12:54am

@bgoodri I’ll add some protection around the R version installed.

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

Maybe is only relevant on R 3.6.x

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Dealing with Catalina II

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