Fatal error: gnu/stubs-64.h

Interfaces RStan
, ,
1

[edit: escaped code]

I can run simple models in brms but I am not even remotely qualified to try and debug errors so please bear with me. Our institution recently switched to a new high performance computing cluster and much has changed, including the need for me reinstall brms. On the old system everything worked fine, I was able to install rstan and brms as per the guide however upon running a model I get the following error:

Compiling Stan program…
make cmd is

  make -f '/gpfs01/software/easybuild-ada-uon/software/R/4.2.1-foss-2022a/lib64/R/etc/Makeconf' -f '/gpfs01/software/easybuild-ada-uon/software/R/4.2.1-foss-2022a/lib64/R/share/make/shlib.mk' CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB='file1e168619269137.so' OBJECTS='file1e168619269137.o'

make would use

g++ -std=gnu++17 -I"/gpfs01/software/easybuild-ada-uon/software/R/4.2.1-foss-2022a/lib64/R/include" -DNDEBUG   -I"/gpfs01/software/easybuild-ada-uon/software/R/4.2.1-foss-2022a/lib64/R/library/Rcpp/include/"  -I"/gpfs01/home/svxmt1/R/x86_64-pc-linux-gnu-library/4.2/RcppEigen/include/"  -I"/gpfs01/home/svxmt1/R/x86_64-pc-linux-gnu-library/4.2/RcppEigen/include/unsupported"  -I"/gpfs01/software/easybuild-ada-uon/software/R/4.2.1-foss-2022a/lib64/R/library/BH/include" -I"/gpfs01/home/svxmt1/R/x86_64-pc-linux-gnu-library/4.2/StanHeaders/include/src/"  -I"/gpfs01/home/svxmt1/R/x86_64-pc-linux-gnu-library/4.2/StanHeaders/include/"  -I"/gpfs01/software/easybuild-ada-uon/software/R/4.2.1-foss-2022a/lib64/R/library/RcppParallel/include/"  -I"/gpfs01/home/svxmt1/R/x86_64-pc-linux-gnu-library/4.2/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DUSE_STANC3 -DSTRICT_R_HEADERS  -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION  -D_HAS_AUTO_PTR_ETC=0  -include '/gpfs01/home/svxmt1/R/x86_64-pc-linux-gnu-library/4.2/StanHeaders/include/stan/math/prim/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1   -I/gpfs01/software/easybuild-ada-uon/software/OpenSSL/1.1/include -I/gpfs01/software/easybuild-ada-uon/software/libgit2/1.4.3-GCCcore-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/FriBidi/1.0.12-GCCcore-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/HarfBuzz/4.2.1-GCCcore-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/MPFR/4.1.0-GCCcore-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/GDAL/3.5.0-foss-2022a/include -I/gpfs01/software/easybuild-ada-uon/software/nodejs/16.15.1-GCCcore-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/GLPK/5.0-GCCcore-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/ImageMagick/7.1.0-37-GCCcore-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/GSL/2.7-GCC-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/UDUNITS/2.2.28-GCCcore-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/HDF5/1.12.2-gompi-2022a/include -I/gpfs01/software/easybuild-ada-uon/software/ICU/71.1-GCCcore-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/libsndfile/1.1.0-GCCcore-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/FFTW/3.3.10-GCC-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/NLopt/2.7.1-GCCcore-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/GMP/6.2.1-GCCcore-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/libxml2/2.9.13-GCCcore-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/cURL/7.83.0-GCCcore-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/Tk/8.6.12-GCCcore-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/Java/11.0.20/include -I/gpfs01/software/easybuild-ada-uon/software/LibTIFF/4.3.0-GCCcore-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/libpng/1.6.37-GCCcore-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/PCRE2/10.40-GCCcore-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/SQLite/3.38.3-GCCcore-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/zlib/1.2.12-GCCcore-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/XZ/5.2.5-GCCcore-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/bzip2/1.0.8-GCCcore-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/ncurses/6.3-GCCcore-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/libreadline/8.1.2-GCCcore-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/cairo/1.17.4-GCCcore-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/libGLU/9.0.2-GCCcore-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/Mesa/22.0.3-GCCcore-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/X11/20220504-GCCcore-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/Xvfb/21.1.3-GCCcore-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/pkgconf/1.8.0-GCCcore-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/FlexiBLAS/3.2.0-GCC-11.3.0/include -I/gpfs01/software/easybuild-ada-uon/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas   -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c file1e168619269137.cpp -o file1e168619269137.o
if test  "zfile1e168619269137.o" != "z"; then \
  echo g++ -std=gnu++17 -shared -L"/gpfs01/software/easybuild-ada-uon/software/R/4.2.1-foss-2022a/lib64/R/lib" -L/gpfs01/software/easybuild-ada-uon/software/OpenSSL/1.1/lib64 -L/gpfs01/software/easybuild-ada-uon/software/OpenSSL/1.1/lib -L/gpfs01/software/easybuild-ada-uon/software/libgit2/1.4.3-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/libgit2/1.4.3-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/FriBidi/1.0.12-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/FriBidi/1.0.12-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/HarfBuzz/4.2.1-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/HarfBuzz/4.2.1-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/MPFR/4.1.0-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/MPFR/4.1.0-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/GDAL/3.5.0-foss-2022a/lib64 -L/gpfs01/software/easybuild-ada-uon/software/GDAL/3.5.0-foss-2022a/lib -L/gpfs01/software/easybuild-ada-uon/software/nodejs/16.15.1-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/nodejs/16.15.1-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/GLPK/5.0-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/GLPK/5.0-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/ImageMagick/7.1.0-37-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/ImageMagick/7.1.0-37-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/GSL/2.7-GCC-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/GSL/2.7-GCC-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/UDUNITS/2.2.28-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/UDUNITS/2.2.28-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/HDF5/1.12.2-gompi-2022a/lib64 -L/gpfs01/software/easybuild-ada-uon/software/HDF5/1.12.2-gompi-2022a/lib -L/gpfs01/software/easybuild-ada-uon/software/ICU/71.1-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/ICU/71.1-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/libsndfile/1.1.0-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/libsndfile/1.1.0-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/FFTW/3.3.10-GCC-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/FFTW/3.3.10-GCC-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/NLopt/2.7.1-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/NLopt/2.7.1-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/GMP/6.2.1-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/GMP/6.2.1-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/libxml2/2.9.13-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/libxml2/2.9.13-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/cURL/7.83.0-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/cURL/7.83.0-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/Tk/8.6.12-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/Tk/8.6.12-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/Java/11.0.20/lib64 -L/gpfs01/software/easybuild-ada-uon/software/Java/11.0.20/lib -L/gpfs01/software/easybuild-ada-uon/software/LibTIFF/4.3.0-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/LibTIFF/4.3.0-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/libpng/1.6.37-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/libpng/1.6.37-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/PCRE2/10.40-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/PCRE2/10.40-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/SQLite/3.38.3-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/SQLite/3.38.3-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/zlib/1.2.12-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/zlib/1.2.12-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/XZ/5.2.5-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/XZ/5.2.5-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/bzip2/1.0.8-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/bzip2/1.0.8-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/ncurses/6.3-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/ncurses/6.3-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/libreadline/8.1.2-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/libreadline/8.1.2-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/cairo/1.17.4-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/cairo/1.17.4-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/libGLU/9.0.2-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/libGLU/9.0.2-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/Mesa/22.0.3-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/Mesa/22.0.3-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/X11/20220504-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/X11/20220504-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/Xvfb/21.1.3-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/Xvfb/21.1.3-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/pkgconf/1.8.0-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/pkgconf/1.8.0-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib64 -L/gpfs01/software/easybuild-ada-uon/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib -L/gpfs01/software/easybuild-ada-uon/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/GCCcore/11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/GCCcore/11.3.0/lib -o file1e168619269137.so file1e168619269137.o  '/gpfs01/home/svxmt1/R/x86_64-pc-linux-gnu-library/4.2/rstan/lib//libStanServices.a' -L'/gpfs01/home/svxmt1/R/x86_64-pc-linux-gnu-library/4.2/StanHeaders/lib/' -lStanHeaders -L'/gpfs01/software/easybuild-ada-uon/software/R/4.2.1-foss-2022a/lib64/R/library/RcppParallel/lib/' -ltbb   -L"/gpfs01/software/easybuild-ada-uon/software/R/4.2.1-foss-2022a/lib64/R/lib" -lR; \
  g++ -std=gnu++17 -shared -L"/gpfs01/software/easybuild-ada-uon/software/R/4.2.1-foss-2022a/lib64/R/lib" -L/gpfs01/software/easybuild-ada-uon/software/OpenSSL/1.1/lib64 -L/gpfs01/software/easybuild-ada-uon/software/OpenSSL/1.1/lib -L/gpfs01/software/easybuild-ada-uon/software/libgit2/1.4.3-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/libgit2/1.4.3-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/FriBidi/1.0.12-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/FriBidi/1.0.12-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/HarfBuzz/4.2.1-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/HarfBuzz/4.2.1-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/MPFR/4.1.0-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/MPFR/4.1.0-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/GDAL/3.5.0-foss-2022a/lib64 -L/gpfs01/software/easybuild-ada-uon/software/GDAL/3.5.0-foss-2022a/lib -L/gpfs01/software/easybuild-ada-uon/software/nodejs/16.15.1-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/nodejs/16.15.1-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/GLPK/5.0-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/GLPK/5.0-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/ImageMagick/7.1.0-37-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/ImageMagick/7.1.0-37-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/GSL/2.7-GCC-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/GSL/2.7-GCC-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/UDUNITS/2.2.28-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/UDUNITS/2.2.28-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/HDF5/1.12.2-gompi-2022a/lib64 -L/gpfs01/software/easybuild-ada-uon/software/HDF5/1.12.2-gompi-2022a/lib -L/gpfs01/software/easybuild-ada-uon/software/ICU/71.1-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/ICU/71.1-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/libsndfile/1.1.0-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/libsndfile/1.1.0-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/FFTW/3.3.10-GCC-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/FFTW/3.3.10-GCC-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/NLopt/2.7.1-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/NLopt/2.7.1-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/GMP/6.2.1-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/GMP/6.2.1-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/libxml2/2.9.13-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/libxml2/2.9.13-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/cURL/7.83.0-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/cURL/7.83.0-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/Tk/8.6.12-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/Tk/8.6.12-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/Java/11.0.20/lib64 -L/gpfs01/software/easybuild-ada-uon/software/Java/11.0.20/lib -L/gpfs01/software/easybuild-ada-uon/software/LibTIFF/4.3.0-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/LibTIFF/4.3.0-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/libpng/1.6.37-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/libpng/1.6.37-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/PCRE2/10.40-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/PCRE2/10.40-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/SQLite/3.38.3-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/SQLite/3.38.3-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/zlib/1.2.12-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/zlib/1.2.12-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/XZ/5.2.5-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/XZ/5.2.5-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/bzip2/1.0.8-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/bzip2/1.0.8-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/ncurses/6.3-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/ncurses/6.3-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/libreadline/8.1.2-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/libreadline/8.1.2-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/cairo/1.17.4-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/cairo/1.17.4-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/libGLU/9.0.2-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/libGLU/9.0.2-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/Mesa/22.0.3-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/Mesa/22.0.3-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/X11/20220504-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/X11/20220504-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/Xvfb/21.1.3-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/Xvfb/21.1.3-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/pkgconf/1.8.0-GCCcore-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/pkgconf/1.8.0-GCCcore-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib64 -L/gpfs01/software/easybuild-ada-uon/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib -L/gpfs01/software/easybuild-ada-uon/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib -L/gpfs01/software/easybuild-ada-uon/software/GCCcore/11.3.0/lib64 -L/gpfs01/software/easybuild-ada-uon/software/GCCcore/11.3.0/lib -o file1e168619269137.so file1e168619269137.o  '/gpfs01/home/svxmt1/R/x86_64-pc-linux-gnu-library/4.2/rstan/lib//libStanServices.a' -L'/gpfs01/home/svxmt1/R/x86_64-pc-linux-gnu-library/4.2/StanHeaders/lib/' -lStanHeaders -L'/gpfs01/software/easybuild-ada-uon/software/R/4.2.1-foss-2022a/lib64/R/library/RcppParallel/lib/' -ltbb   -L"/gpfs01/software/easybuild-ada-uon/software/R/4.2.1-foss-2022a/lib64/R/lib" -lR; \
fi
Error in compileCode(f, code, language = language, verbose = verbose) : 
                   from <command-line>:/usr/include/gnu/stubs.h:10:11: fatal error: gnu/stubs-64.h: No such file or directory   10 | # include <gnu/stubs-64.h>      |           ^~~~~~~~~~~~~~~~compilation terminated.make: *** [/gpfs01/software/easybuild-ada-uon/software/R/4.2.1-foss-2022a/lib64/R/etc/Makeconf:177: file1e168619269137.o] Error 1
Calls: brm ... cxxfunctionplus -> <Anonymous> -> cxxfunction -> compileCode
In addition: Warning message:
Rows containing NAs were excluded from the model. 
Error in sink(type = "output") : invalid connection
Calls: brm ... eval2 -> eval -> eval -> .fun -> cxxfunctionplus -> sink
Execution halted

Any ideas? Thanks in advance!

2

Sorry that nobody has responded. There are more brms questions than there are brms users among our devs to answer them. I know this message isn’t helping, but maybe someone who does know something about brms will see it.

If you just gave up on trying because you couldn’t get it installed, I would like to know. I fear we’re losing users on the brms side because we can’t cover answering their questions on the forums.

3

Hi Bob,

Thanks for your reply. Our IT department did eventually fix this, apparently there were some Linux packages missing from our compute nodes. They installed the glibc development package and a kernel header package that resolved the issue.

Many thanks for reply,

Matt