Compiling error

Modeling
,
1

Hi,

I got the following error when I ran my R code on an EC2 instance. Any suggestions are aprreciated.

Thank you,
Luke

make cmd is
  make -f '/usr/lib/R/etc/Makeconf' -f '/usr/share/R/share/make/shlib.mk' CXX='$(CXX14) 
$(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB='file129b422afc26.so' OBJECTS='file129b422afc26.o'

make would use
if test  "zfile129b422afc26.o" != "z"; then \
  echo g++ -std=gnu++14 -shared -L"/usr/lib/R/lib" -Wl,-Bsymbolic-functions -Wl,-z,relro -o file129b422afc26.so file129b422afc26.o  '/home/luke/R/x86_64-pc-linux-gnu-library/4.0/rstan/lib//libStanServices.a' -L'/home/luke/R/x86_64-pc-linux-gnu-library/4.0/StanHeaders/lib/' -lStanHeaders -L'/home/luke/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/lib/' -ltbb  -L"/usr/lib/R/lib" -lR; \
  g++ -std=gnu++14 -shared -L"/usr/lib/R/lib" -Wl,-Bsymbolic-functions -Wl,-z,relro -o file129b422afc26.so file129b422afc26.o  '/home/luke/R/x86_64-pc-linux-gnu-library/4.0/rstan/lib//libStanServices.a' -L'/home/luke/R/x86_64-pc-linux-gnu-library/4.0/StanHeaders/lib/' -lStanHeaders -L'/home/luke/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/lib/' -ltbb  -L"/usr/lib/R/lib" -lR; \
fi

 Error in compileCode(f, code, language = language, verbose = verbose) : 
  file129b422afc26.cpp: In member function ‘T__ model129b1b32a613_Stan_DTP_0_namespace::model129b1b32a613_Stan_DTP_0::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T__ = double]’:file129b422afc26.cpp:13290:9: note: variable tracking size limit exceeded with -fvar-tracking-assignments, retrying without/usr/bin/ld: /home/luke/R/x86_64-pc-linux-gnu-library/4.0/rstan/lib//libStanServices.a(stan_fit.o): relocation R_X86_64_PC32 against undefined hidden symbol `_ZTCN5boost10wrapexceptISt14overflow_errorEE0_NS_16exception_detail10clone_implINS3_19error_info_injectorIS1_EEEE' can not be used when making a shared object/usr/bin/ld: final link failed: Bad valuecollect2: error: ld returned 1 exit statusmake: *** [file129b422afc26.so] Error 1
2

Hi can you try reinstalling boost, then RcppEigen, then rstan/Stanheaders? It looks like this is due to a DLL/SO not having the correct signature in it

3

Thank you! It works now.

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