Updating R to 4.0.3 and brms to 2.14.4 killed brms

Interfaces brms
1

I committed the fatal error of trying to update R and brms. In my defense, I had a good reason, i.e. I hoped to access the new within-chain parallelization and other functionality that is reputed to speed up the sampling of complex models dramatically.

Result: I can no longer fit even a simple intercept-only model.

nullmod <- brm(dep.var ~ 1, family = categorical, data = d, prior = prior(normal(0,4), class = Intercept))

And I get:

Compiling Stan program...
Error in open.connection(con, open = mode) : 
  Could not resolve host: github.com
In addition: Warning messages:
1: Specifying global priors for regression coefficients in categorical models is deprecated. Please specify priors separately for each response category. 
2: In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
  '-E' not found
make cmd is
  make -f "C:/PROGRA~1/R/R-40~1.3/etc/x64/Makeconf" -f "C:/PROGRA~1/R/R-40~1.3/share/make/winshlib.mk" CXX='$(CXX14) $(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB="file21d872f22ea8.dll" WIN=64 TCLBIN=64 OBJECTS="file21d872f22ea8.o"

make would use
if test "zfile21d872f22ea8.o" != "z"; then \
  if test -e "file21d872f22ea8-win.def"; then \
    echo "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o file21d872f22ea8.dll file21d872f22ea8-win.def file21d872f22ea8.o   "C:/Users/Folio 1040/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a" -L"C:/Users/Folio 1040/Documents/R/win-library/4.0/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/Folio 1040/Documents/R/win-library/4.0/RcppParallel/lib/x64" -ltbb  -L"C:/PROGRA~1/R/R-40~1.3/bin/x64" -lR ; \
    "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o file21d872f22ea8.dll file21d872f22ea8-win.def file21d872f22ea8.o   "C:/Users/Folio 1040/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a" -L"C:/Users/Folio 1040/Documents/R/win-library/4.0/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/Folio 1040/Documents/R/win-library/4.0/RcppParallel/lib/x64" -ltbb  -L"C:/PROGRA~1/R/R-40~1.3/bin/x64" -lR ; \
  else \
    echo EXPORTS > tmp.def; \
    "C:/rtools40/mingw64/bin/"nm file21d872f22ea8.o | sed -n 's/^.* [BCDRT] / /p' | sed -e '/[.]refptr[.]/d' -e '/[.]weak[.]/d' | sed 's/[^ ][^ ]*/"&"/g'  >> tmp.def; \
    echo "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o file21d872f22ea8.dll tmp.def file21d872f22ea8.o   "C:/Users/Folio 1040/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a" -L"C:/Users/Folio 1040/Documents/R/win-library/4.0/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/Folio 1040/Documents/R/win-library/4.0/RcppParallel/lib/x64" -ltbb  -L"C:/PROGRA~1/R/R-40~1.3/bin/x64" -lR ; \
    "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o file21d872f22ea8.dll tmp.def file21d872f22ea8.o   "C:/Users/Folio 1040/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a" -L"C:/Users/Folio 1040/Documents/R/win-library/4.0/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/Folio 1040/Documents/R/win-library/4.0/RcppParallel/lib/x64" -ltbb  -L"C:/PROGRA~1/R/R-40~1.3/bin/x64" -lR ; \
    rm -f tmp.def; \
  fi \
fi
Error in compileCode(f, code, language = language, verbose = verbose) : 
  C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:/Users/Folio 1040/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a(stan_fit.o):stan_fit.cpp:(.data$_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1[_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1]+0x0): multiple definition of `boost::math::detail::bessel_j0<long double>(long double)::P1'; file21d872f22ea8.o:file21d872f22ea8.cpp:(.rdata$_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1[_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1]+0x0): first defined hereC:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:/Users/Folio 1040/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a(stan_fit.o):stan_fit.cpp:(.data$_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2QS[_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2QS]+0x0): multiple definition of `boost::math::detail::bessel_j0<long double>(long double)::QS'; file21d872f22ea8.o:file
Error in sink(type = "output") : invalid connection

R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

other attached packages:
[1] brms_2.14.4 Rcpp_1.0.6

Any ideas?

2

Do you have an open connection to a GitHub repository?

There are several suggestions in this thread for addressing Windows issues.

3

This is caused by RStan testing whether your code will work with the new compiler (which is hosted on GitHub), but your network/firewall is blocking the connection.

The simple fix is to run:

rstan_options(javascript=FALSE)

When you first load RStan. This will disable that check.

4

Additionally I just noticed there’s a second error in the output, you’ll also need to reinstall rstan and StanHeaders from source:


# Compile packages using all cores
Sys.setenv(MAKEFLAGS = paste0("-j",parallel::detectCores()))

install.packages(c("StanHeaders","rstan"),type="source")
5

I did the two things suggested by @andrjohns, and now I seem to have graduated to the next error message:

make cmd is
  make -f "C:/PROGRA~1/R/R-40~1.3/etc/x64/Makeconf" -f "C:/PROGRA~1/R/R-40~1.3/share/make/winshlib.mk" CXX='$(CXX14) $(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB="file20a41fa52aa4.dll" WIN=64 TCLBIN=64 OBJECTS="file20a41fa52aa4.o"

make would use
if test "zfile20a41fa52aa4.o" != "z"; then \
  if test -e "file20a41fa52aa4-win.def"; then \
    echo "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o file20a41fa52aa4.dll file20a41fa52aa4-win.def file20a41fa52aa4.o   "C:/Users/Folio 1040/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a" -L"C:/Users/Folio 1040/Documents/R/win-library/4.0/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/Folio 1040/Documents/R/win-library/4.0/RcppParallel/lib/x64" -ltbb  -L"C:/PROGRA~1/R/R-40~1.3/bin/x64" -lR ; \
    "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o file20a41fa52aa4.dll file20a41fa52aa4-win.def file20a41fa52aa4.o   "C:/Users/Folio 1040/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a" -L"C:/Users/Folio 1040/Documents/R/win-library/4.0/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/Folio 1040/Documents/R/win-library/4.0/RcppParallel/lib/x64" -ltbb  -L"C:/PROGRA~1/R/R-40~1.3/bin/x64" -lR ; \
  else \
    echo EXPORTS > tmp.def; \
    "C:/rtools40/mingw64/bin/"nm file20a41fa52aa4.o | sed -n 's/^.* [BCDRT] / /p' | sed -e '/[.]refptr[.]/d' -e '/[.]weak[.]/d' | sed 's/[^ ][^ ]*/"&"/g'  >> tmp.def; \
    echo "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o file20a41fa52aa4.dll tmp.def file20a41fa52aa4.o   "C:/Users/Folio 1040/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a" -L"C:/Users/Folio 1040/Documents/R/win-library/4.0/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/Folio 1040/Documents/R/win-library/4.0/RcppParallel/lib/x64" -ltbb  -L"C:/PROGRA~1/R/R-40~1.3/bin/x64" -lR ; \
    "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o file20a41fa52aa4.dll tmp.def file20a41fa52aa4.o   "C:/Users/Folio 1040/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a" -L"C:/Users/Folio 1040/Documents/R/win-library/4.0/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/Folio 1040/Documents/R/win-library/4.0/RcppParallel/lib/x64" -ltbb  -L"C:/PROGRA~1/R/R-40~1.3/bin/x64" -lR ; \
    rm -f tmp.def; \
  fi \
fi
Error in compileCode(f, code, language = language, verbose = verbose) : 
  C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:/Users/Folio 1040/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a(stan_fit.o):stan_fit.cpp:(.data$_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1[_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1]+0x0): multiple definition of `boost::math::detail::bessel_j0<long double>(long double)::P1'; file20a41fa52aa4.o:file20a41fa52aa4.cpp:(.rdata$_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1[_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1]+0x0): first defined hereC:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:/Users/Folio 1040/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a(stan_fit.o):stan_fit.cpp:(.data$_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2QS[_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2QS]+0x0): multiple definition of `boost::math::detail::bessel_j0<long double>(long double)::QS'; file20a41fa52aa4.o:file
In addition: Warning message:
Specifying global priors for regression coefficients in categorical models is deprecated. Please specify priors separately for each response category. 
Error in sink(type = "output") : invalid connection

I wonder if that stuff about ‘multiple definitions’ is significant.

6

It doesn’t look like the re-install happened properly. Can you restart R and then do the reinstall from source again?

7

Thank you for your patience. That seems to have done the trick.

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