[macOS] Build fails: `compute_groupcond_logl.cpp:33:3: error: 'omp_set_num_threads' was not declared in this scope`

[barracuda156]

This is a CRAN version.

* installing *source* package ‘lavacreg’ ...
** package ‘lavacreg’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-mp-13 (MacPorts gcc13 13.2.0_3) 13.2.0’
Warning in system2("xcrun", "--show-sdk-path", TRUE, TRUE) :
  running command ''xcrun' --show-sdk-path 2>&1' had status 64
using SDK: ‘NA’‘NA’‘NA’‘NA’‘NA’‘NA’
/opt/local/bin/g++-mp-13 -std=gnu++17 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppArmadillo/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c RcppExports.cpp -o RcppExports.o
/opt/local/bin/g++-mp-13 -std=gnu++17 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppArmadillo/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c compute_groupcond_logl.cpp -o compute_groupcond_logl.o
compute_groupcond_logl.cpp: In function 'double compute_groupcond_logl(arma::colvec, arma::mat, arma::mat, arma::colvec, arma::mat, arma::colvec, arma::mat, arma::mat, double, arma::colvec, arma::mat, arma::mat, arma::colvec, arma::mat, arma::mat, arma::vec, arma::colvec, arma::mat, arma::mat, int)':
compute_groupcond_logl.cpp:33:3: error: 'omp_set_num_threads' was not declared in this scope
   33 |   omp_set_num_threads(cores);
      |   ^~~~~~~~~~~~~~~~~~~
make: *** [compute_groupcond_logl.o] Error 1
ERROR: compilation failed for package ‘lavacreg’
* removing ‘/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-lavacreg/R-lavacreg/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/lavacreg’
Command failed:  cd "/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-lavacreg/R-lavacreg/work/lavacreg" && /opt/local/bin/R CMD INSTALL . --library=/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-lavacreg/R-lavacreg/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library 
Exit code: 1

I do not see -fopenmp being passed. If it needs OpenMP, it should a) check for its support and b) add flags. Otherwise it should not rely on OpenMP being present.

[barracuda156]

Ok, so there are dummy placeholders SHLIB_OPENMP_CXXFLAGS in Makevars, but nothing sets them, since there is no configure script to do that.

[barracuda156]

Once -fopenmp is added, build works:

* installing *source* package ‘lavacreg’ ...
file ‘src/Makevars’ has the wrong MD5 checksum
** using staged installation
** libs
using C++ compiler: ‘g++-mp-13 (MacPorts gcc13 13.2.0_3) 13.2.0’
Warning in system2("xcrun", "--show-sdk-path", TRUE, TRUE) :
  running command ''xcrun' --show-sdk-path 2>&1' had status 64
using SDK: ‘NA’‘NA’‘NA’‘NA’‘NA’‘NA’
/opt/local/bin/g++-mp-13 -std=gnu++17 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppArmadillo/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include   -std=c++11 -fopenmp -fPIC  -pipe -Os -arch ppc  -c RcppExports.cpp -o RcppExports.o
/opt/local/bin/g++-mp-13 -std=gnu++17 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppArmadillo/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include   -std=c++11 -fopenmp -fPIC  -pipe -Os -arch ppc  -c compute_groupcond_logl.cpp -o compute_groupcond_logl.o
/opt/local/bin/g++-mp-13 -std=gnu++17 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppArmadillo/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include   -std=c++11 -fopenmp -fPIC  -pipe -Os -arch ppc  -c creg_header_funs.cpp -o creg_header_funs.o
/opt/local/bin/g++-mp-13 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/opt/local/Library/Frameworks/R.framework/Resources/lib -Wl,-headerpad_max_install_names -Wl,-rpath,/opt/local/lib/libgcc -L/opt/local/lib -lMacportsLegacySupport -arch ppc -o lavacreg.so RcppExports.o compute_groupcond_logl.o creg_header_funs.o -fopenmp -L/opt/local/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/opt/local/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/local/lib/gcc12/gcc/powerpc-apple-darwin10/12.3.0 -L/opt/local/lib/gcc12 -lMacportsLegacySupport -lgfortran -lef_ppc -F/opt/local/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-lavacreg/R-lavacreg/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/00LOCK-lavacreg/00new/lavacreg/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (lavacreg)

[barracuda156]

For a note, Apple clangs do not support OpenMP at all, at least most of them. So the current indiscriminate version of lavareg will be broken on most versions of macOS on Intel, where default compiler is Apple clang.

[barracuda156]

In fact with Clang it fails even when -fopenmp is passed:

  /opt/local/bin/clang++-mp-15 -std=gnu++17 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppArmadillo/include' -I/opt/local/include -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk   -std=c++11 -I/opt/local/include/libomp -fopenmp -fPIC  -pipe -Os -stdlib=libc++ -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -arch x86_64  -c compute_groupcond_logl.cpp -o compute_groupcond_logl.o
  compute_groupcond_logl.cpp:33:3: error: use of undeclared identifier 'omp_set_num_threads'
    omp_set_num_threads(cores);
    ^
  1 error generated.
  make: *** [compute_groupcond_logl.o] Error 1
  ERROR: compilation failed for package ‘lavacreg’

[chkiefer]

In the latest commit I added checks for the availability of OpenMP. Now, installation on MacOS seems to work.

* installing *source* package ‘lavacreg’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/templates/cran-build/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/templates/cran-build/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/templates/cran-build/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/templates/cran-build/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c compute_groupcond_logl.cpp -o compute_groupcond_logl.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/templates/cran-build/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/templates/cran-build/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c creg_header_funs.cpp -o creg_header_funs.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o lavacreg.so RcppExports.o compute_groupcond_logl.o creg_header_funs.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame
installing to /Volumes/PkgBuild/work/1698230412-3ed8f928a7b604bb/packages/big-sur-arm64/results/4.3/lavacreg.Rcheck/00LOCK-lavacreg/00new/lavacreg/libs
** generating debug symbols (dSYM)
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (lavacreg)
* ```

[barracuda156]

I will test this tomorrow, thank you for addressing the issue.

[barracuda156]

UPD. Sorry for a delay, we got an unrelated issue with running CI at the moment, so I wait until it is resolved to confirm the status of Clang builds. Locally it worked fine with GCC for me, but with GCC it worked earlier too.

[barracuda156]

UPD2. Still fails with OpenMP with Clangs, no idea why:

  /opt/local/bin/clang++-mp-15 -std=gnu++17 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppArmadillo/include' -I/opt/local/include -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk   -I/opt/local/include/libomp -fopenmp -fPIC  -pipe -Os -stdlib=libc++ -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -arch x86_64  -c compute_groupcond_logl.cpp -o compute_groupcond_logl.o
  compute_groupcond_logl.cpp:34:3: error: use of undeclared identifier 'omp_set_num_threads'
    omp_set_num_threads(cores);
    ^
  1 error generated.
  make: *** [compute_groupcond_logl.o] Error 1
  ERROR: compilation failed for package ‘lavacreg’
  * removing ‘/opt/local/var/macports/build/_Users_runner_work_macports-ports_macports-ports_ports_R_R-lavacreg/R-lavacreg/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/lavacreg’
  Command failed:  cd "/opt/local/var/macports/build/_Users_runner_work_macports-ports_macports-ports_ports_R_R-lavacreg/R-lavacreg/work/lavacreg" && /opt/local/bin/R CMD INSTALL . --library=/opt/local/var/macports/build/_Users_runner_work_macports-ports_macports-ports_ports_R_R-lavacreg/R-lavacreg/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library 
  Error: Failed to destroot R-lavacreg: command execution failed
  DEBUG: Error code: CHILDSTATUS 28124 1

I guess, I should just stop trying to make OpenMP work, and let it build without it.

[barracuda156]

Sorry, still fails, without patching Makevars to enable OpenMP either (here -fopenmp perhaps comes from R env, I do not explicitly set it):

  xinstall: mkdir /opt/local/var/macports/build/_Users_runner_work_macports-ports_macports-ports_ports_R_R-lavacreg/R-lavacreg/work/destroot/opt/local/Library/Frameworks/R.framework
  xinstall: mkdir /opt/local/var/macports/build/_Users_runner_work_macports-ports_macports-ports_ports_R_R-lavacreg/R-lavacreg/work/destroot/opt/local/Library/Frameworks/R.framework/Versions
  xinstall: mkdir /opt/local/var/macports/build/_Users_runner_work_macports-ports_macports-ports_ports_R_R-lavacreg/R-lavacreg/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3
  xinstall: mkdir /opt/local/var/macports/build/_Users_runner_work_macports-ports_macports-ports_ports_R_R-lavacreg/R-lavacreg/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources
  xinstall: mkdir /opt/local/var/macports/build/_Users_runner_work_macports-ports_macports-ports_ports_R_R-lavacreg/R-lavacreg/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library
  DEBUG: Environment: 
  CC_PRINT_OPTIONS='YES'
  CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_Users_runner_work_macports-ports_macports-ports_ports_R_R-lavacreg/R-lavacreg/work/.CC_PRINT_OPTIONS'
  CPATH='/opt/local/include'
  DEVELOPER_DIR='/Library/Developer/CommandLineTools'
  LIBRARY_PATH='/opt/local/lib'
  MACOSX_DEPLOYMENT_TARGET='11.0'
  SDKROOT='/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk'
  Executing:  cd "/opt/local/var/macports/build/_Users_runner_work_macports-ports_macports-ports_ports_R_R-lavacreg/R-lavacreg/work/lavacreg" && /opt/local/bin/R CMD INSTALL . --library=/opt/local/var/macports/build/_Users_runner_work_macports-ports_macports-ports_ports_R_R-lavacreg/R-lavacreg/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library 
  DEBUG: system:  cd "/opt/local/var/macports/build/_Users_runner_work_macports-ports_macports-ports_ports_R_R-lavacreg/R-lavacreg/work/lavacreg" && /opt/local/bin/R CMD INSTALL . --library=/opt/local/var/macports/build/_Users_runner_work_macports-ports_macports-ports_ports_R_R-lavacreg/R-lavacreg/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library 
  * installing *source* package ‘lavacreg’ ...
  ** package ‘lavacreg’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** libs
  using C++ compiler: ‘clang version 15.0.7’
  using SDK: ‘MacOSX11.3.sdk’
  /opt/local/bin/clang++-mp-15 -std=gnu++17 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppArmadillo/include' -I/opt/local/include -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk   -fopenmp -fPIC  -pipe -Os -stdlib=libc++ -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk -arch x86_64  -c RcppExports.cpp -o RcppExports.o
  /opt/local/bin/clang++-mp-15 -std=gnu++17 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppArmadillo/include' -I/opt/local/include -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk   -fopenmp -fPIC  -pipe -Os -stdlib=libc++ -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk -arch x86_64  -c compute_groupcond_logl.cpp -o compute_groupcond_logl.o
  compute_groupcond_logl.cpp:34:3: error: use of undeclared identifier 'omp_set_num_threads'
    omp_set_num_threads(cores);
    ^
  1 error generated.
  make: *** [compute_groupcond_logl.o] Error 1
  ERROR: compilation failed for package ‘lavacreg’
  * removing ‘/opt/local/var/macports/build/_Users_runner_work_macports-ports_macports-ports_ports_R_R-lavacreg/R-lavacreg/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/lavacreg’
  Command failed:  cd "/opt/local/var/macports/build/_Users_runner_work_macports-ports_macports-ports_ports_R_R-lavacreg/R-lavacreg/work/lavacreg" && /opt/local/bin/R CMD INSTALL . --library=/opt/local/var/macports/build/_Users_runner_work_macports-ports_macports-ports_ports_R_R-lavacreg/R-lavacreg/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library 
  Exit code: 1

[barracuda156]

@chkiefer Maybe you could try reproducing this in Macports?

All what is needed is edit version and checksums in R-lavacreg port, and then try installing it.

On any macOS between 10.6 and Ventura (13) there are pre-built ports, so you don’t need to compile anything. (Sonoma does not yet have.)

sudo port -v -N install R-lavacreg

This should get everything done.

[barracuda156]

Perhaps it is broken because compute_groupcond_logl.cpp does not include omp.h, which clang needs?

UPD. I can confirm that is the case. Once the leader is added, like it is done in another source file, build works fine with clang.
I.e., this should be added: https://github.com/barracuda156/macports-ports/blob/ca0a204c162517c6cdcbfcfd94f3ae4e4b70d612/R/R-lavacreg/files/patch-unbreak-clang-build.diff