Dealing with Catalina II

DanOvando · January 25, 2020, 12:51am

I believe these are the three that keep repeating throughout the messages, thanks!

/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/eigen_plugins.h:22:30: error: no template named 'conditional_t' in namespace 'std'; did you mean 'conditional'?
using double_return_t = std::conditional_t<std::is_const<std::remove_reference_t<T>>::value,
                        ~~~~~^~~~~~~~~~~~~
                             conditional
/usr/local/clang7/include/c++/v1/type_traits:424:33: note: 'conditional' declared here
    struct _LIBCPP_TEMPLATE_VIS conditional {typedef _If type;};


/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/eigen_plugins.h:22:63: error: no template named 'remove_reference_t' in namespace 'std'; did you mean 'remove_reference'?
using double_return_t = std::conditional_t<std::is_const<std::remove_reference_t<T>>::value,
                                                         ~~~~~^~~~~~~~~~~~~~~~~~
                                                              remove_reference
/usr/local/clang7/include/c++/v1/type_traits:1110:50: note: 'remove_reference' declared here
template <class _Tp> struct _LIBCPP_TEMPLATE_VIS remove_reference        {typedef _Tp type;};

/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/eigen_plugins.h:60:10: error: no template named 'enable_if_t' in namespace 'std'; did you mean 'enable_if'?
    std::enable_if_t<std::is_pointer<T>::value, reverse_return_t<T>>
    ~~~~~^~~~~~~~~~~
         enable_if
/usr/local/clang7/include/c++/v1/type_traits:435:63: note: 'enable_if' declared here
template <bool, class _Tp = void> struct _LIBCPP_TEMPLATE_VIS enable_if {};

bgoodri · January 25, 2020, 12:53am

Yes, that is it. What is packageVersion("StanHeaders")?

DanOvando · January 25, 2020, 12:53am

StanHeaders version ‘2.21.0.1’

bgoodri · January 25, 2020, 12:56am

Does it work if you call in R

Sys.unsetenv("PKG_CXXFLAGS")

after calling library(rstan) but before calling sourceCpp?

DanOvando · January 25, 2020, 12:58am

Yes, that fixes it!

bgoodri · January 25, 2020, 12:59am

OK. I guess just go that way for now. We had to set that environmental variable to move StanHeaders forward on CRAN but can remove it in the future.

DanOvando · January 25, 2020, 1:01am

Good to know, many thanks

wds15 · January 29, 2020, 8:39am

Hi Everyone!

I used the latest installer linked above, but that left me with a non-working setup for running stan models. The reasons seems to be that the tools leave you with a ~/.R/Makevars with this content:

# 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
# clang: end

but for Stan we have to also modify the C++14 flags 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

CXX14FLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CPPF14LAGS=-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

With the above changes for C++14 everything works now for me.

Tagging @mcol

… and for everyone who is blocked by Catalina not being allowed to install the .pkg file… a simple CTRL+right click on the file, then clicking “Open” will get the installer going (for me).

mcol · January 29, 2020, 9:52am

Did you want to tag somebody else? I’m not on Mac.

wds15 · January 29, 2020, 10:20am

ups… sorry… I meant @coatless …

dbarneche · February 17, 2020, 2:23am

Thanks @torkar , this worked for me!

ihrke · March 30, 2020, 8:30pm

works! Thanks so much!

riko · May 21, 2020, 10:59am

I had the same problem on macOS 10.15.4, and the solution worked perfectly. Many thanks!

torkar · May 21, 2020, 1:01pm

@riko, note however that with R v4.0.0 nothing much is needed in the ~/.R/Makevars anymore (well, compiler settings perhaps, but that’s it). In mine I only have this now:

FC = /usr/local/gfortran/bin/gfortran
FLIBS = -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
CXX14FLAGS=-O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function

ankushs · May 24, 2020, 8:34pm

I´m using R v4.0.0 on macOS Catalina 10.15.2. and I´m still facing the same problem.

clang-7: error: no such file or directory: ‘/Library/Frameworks/R.framework/Resources/lib/libc++abi.1.dylib’
make: *** [rstan.so] Error 1
ERROR: compilation failed for package ‘rstan’

removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rstan’

restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rstan’
Warning in install.packages :
installation of package ‘rstan’ had non-zero exit status

The .R/Makevars file contains

`#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`

. I also tried

torkar:

FC = /usr/local/gfortran/bin/gfortran
FLIBS = -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
CXX14FLAGS=-O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function

but to no avail and showed error -
/usr/local/clang7/include/c++/v1/stdlib.h:94:15: fatal error: 'stdlib.h' file not found #include_next <stdlib.h>

Any pointers to rectify this problem ?

torkar · May 25, 2020, 6:37am

I think you’re not using the Xcode compiler? I don’t have a clang-7 on my OS X.

Typing this, g++ --version in the terminal gives this,


Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
Apple clang version 11.0.3 (clang-1103.0.32.62)
Target: x86_64-apple-darwin19.4.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

ankushs · May 25, 2020, 10:48am

Yes,
Command g++ --version in terminal shows a similar output.
How can i fix this issue?

torkar · May 25, 2020, 10:53am

Please paste your output here. Saying “similar output” means that they are not the same and that gets me curious…

ankushs · May 25, 2020, 10:58am

Apologies, its the exact same output

Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
Apple clang version 11.0.3 (clang-1103.0.32.62)
Target: x86_64-apple-darwin19.4.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

torkar · May 25, 2020, 11:06am

The above seems to be the problem. Have you removed all traces of the previous installation (clang7)? I don’t have that file on my laptop anymore…