failure to compile models on Win 10
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Description
Summary:
Please provide a short summary (no more than a sentence or two).
failure to compile brms models
Description:
Describe the issue as clearly as possible.
Reproducible Steps:
Please report steps to reproduce the issue. If it's not possible to reproduce, please include a description of how you discovered the issue.
Hi I ran a simple model using brms, with the following code and I copied the output in the console:
intercept_mdl <- brm(F0 ~ 1, data=pitch)
If you have a reproducible example, please include it.
Current Output:
If applicable, any relevant output from RStan.
Compiling Stan program...
make cmd is
make -f "C:/PROGRA1/R/R-4.0.3/etc/x64/Makeconf" -f "C:/PROGRA1/R/R-4.0.3/share/make/winshlib.mk" -f "C:/Users/Veronica/Documents/.R/Makevars.win" CXX='$(CXX14) $(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB="file61085bab729c.dll" WIN=64 TCLBIN=64 OBJECTS="file61085bab729c.o"
make would use
"C:/rtools40/mingw64/bin/"g++ -std=gnu++14 -I"C:/PROGRA1/R/R-4.0.3/include" -DNDEBUG -I"C:/Users/Veronica/Documents/R/win-library/4.0/Rcpp/include/" -I"C:/Users/Veronica/Documents/R/win-library/4.0/RcppEigen/include/" -I"C:/Users/Veronica/Documents/R/win-library/4.0/RcppEigen/include/unsupported" -I"C:/Users/Veronica/Documents/R/win-library/4.0/BH/include" -I"C:/Users/Veronica/Documents/R/win-library/4.0/StanHeaders/include/src/" -I"C:/Users/Veronica/Documents/R/win-library/4.0/StanHeaders/include/" -I"C:/Users/Veronica/Documents/R/win-library/4.0/RcppParallel/include/" -I"C:/Users/Veronica/Documents/R/win-library/4.0/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include "C:/Users/Veronica/Documents/R/win-library/4.0/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp" -std=c++1y -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c file61085bab729c.cpp -o file61085bab729c.o1/R/R-4.0.3/bin/x64" -lR ;
if test "zfile61085bab729c.o" != "z"; then
if test -e "file61085bab729c-win.def"; then
echo "C:/rtools40/mingw64/bin/"g++ -shared -s -static-libgcc -o file61085bab729c.dll file61085bab729c-win.def file61085bab729c.o "C:/Users/Veronica/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a" -L"C:/Users/Veronica/Documents/R/win-library/4.0/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/Veronica/Documents/R/win-library/4.0/RcppParallel/lib/x64" -ltbb -L"C:/PROGRA
"C:/rtools40/mingw64/bin/"g++ -shared -s -static-libgcc -o file61085bab729c.dll file61085bab729c-win.def file61085bab729c.o "C:/Users/Veronica/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a" -L"C:/Users/Veronica/Documents/R/win-library/4.0/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/Veronica/Documents/R/win-library/4.0/RcppParallel/lib/x64" -ltbb -L"C:/PROGRA1/R/R-4.0.3/bin/x64" -lR ; 1/R/R-4.0.3/bin/x64" -lR ;
else
echo EXPORTS > tmp.def;
"C:/rtools40/mingw64/bin/"nm file61085bab729c.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 file61085bab729c.dll tmp.def file61085bab729c.o "C:/Users/Veronica/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a" -L"C:/Users/Veronica/Documents/R/win-library/4.0/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/Veronica/Documents/R/win-library/4.0/RcppParallel/lib/x64" -ltbb -L"C:/PROGRA
"C:/rtools40/mingw64/bin/"g++ -shared -s -static-libgcc -o file61085bab729c.dll tmp.def file61085bab729c.o "C:/Users/Veronica/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a" -L"C:/Users/Veronica/Documents/R/win-library/4.0/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/Veronica/Documents/R/win-library/4.0/RcppParallel/lib/x64" -ltbb -L"C:/PROGRA1/R/R-4.0.3/bin/x64" -lR ; 1/R/R-4.0.3/etc/x64/Makeconf:229: file61085bab729c.o] Error 1
rm -f tmp.def;
fi
fi
Error in compileCode(f, code, language = language, verbose = verbose) :
from C:/Users/Veronica/Documents/R/win-library/4.0/StanHeaders/include/src/stan/model/model_header.hpp:4, from file61085bab729c.cpp:14:C:/Users/Veronica/Documents/R/win-library/4.0/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: 'void stan::math::set_zero_all_adjoints()' defined but not used [-Wunused-function] static void set_zero_all_adjoints() { ^~~~~~~~~~~~~~~~~~~~~make: *** [C:/PROGRA
In addition: Warning message:
In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
'C:/rtools40/usr/mingw_/bin/g++' not found
Error in sink(type = "output") : invalid connection
Expected Output:
If applicable, the output you expected from RStan.
compiled model
RStan Version:
The version of RStan you are running (e.g., from packageVersion("rstan"))
2.21.2
R Version:
The version of R you are running (e.g., from R.version.string)
4.0.3
Operating System:
Your operating system (e.g., OS X 10.11.3)
devtools::session_info("rstan")
-
Session info ------------------------------------------
setting value
version R version 4.0.3 (2020-10-10)
os Windows 10 x64
system x86_64, mingw32
ui RStudio
language (EN)
collate Chinese (Simplified)_China.936
ctype Chinese (Simplified)_China.936
tz Europe/London
date 2021-08-25 -
Packages ----------------------------------------------
! package * version date lib source
backports 1.2.0 2020-11-02 [1] CRAN (R 4.0.3)
BH 1.72.0-3 2020-01-08 [1] CRAN (R 4.0.0)
brio 1.1.0 2020-08-31 [1] CRAN (R 4.0.3)
callr 3.7.0 2021-04-20 [1] CRAN (R 4.0.5)
checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.0.0)
cli 2.5.0 2021-04-26 [1] CRAN (R 4.0.5)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.0)
crayon 1.4.1 2021-02-08 [1] CRAN (R 4.0.5)
curl 4.3 2019-12-02 [1] CRAN (R 4.0.0)
desc 1.3.0 2021-03-05 [1] CRAN (R 4.0.5)
diffobj 0.3.2 2020-10-05 [1] CRAN (R 4.0.3)
digest 0.6.27 2020-10-24 [1] CRAN (R 4.0.3)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.0.5)
evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.0)
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0)
farver 2.0.3 2020-01-16 [1] CRAN (R 4.0.0)
ggplot2 * 3.3.5 2021-06-25 [1] CRAN (R 4.0.5)
glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.3)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.0)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.0)
V inline 0.3.17 2021-05-31 [1] CRAN (R 4.0.5)
isoband 0.2.3 2020-12-01 [1] CRAN (R 4.0.3)
jsonlite 1.7.2 2020-12-09 [1] CRAN (R 4.0.5)
labeling 0.4.2 2020-10-20 [1] CRAN (R 4.0.3)
lattice 0.20-41 2020-04-02 [2] CRAN (R 4.0.3)
lifecycle 1.0.0 2021-02-15 [1] CRAN (R 4.0.5)
loo 2.4.1 2020-12-09 [1] CRAN (R 4.0.3)
magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.0.3)
MASS 7.3-53 2020-09-09 [2] CRAN (R 4.0.3)
Matrix 1.2-18 2019-11-27 [2] CRAN (R 4.0.3)
matrixStats 0.57.0 2020-09-25 [1] CRAN (R 4.0.3)
mgcv 1.8-33 2020-08-27 [2] CRAN (R 4.0.3)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.0)
nlme 3.1-149 2020-08-23 [2] CRAN (R 4.0.3)
pillar 1.6.1 2021-05-16 [1] CRAN (R 4.0.3)
pkgbuild 1.2.0 2020-12-15 [1] CRAN (R 4.0.3)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.0)
pkgload 1.2.1 2021-04-06 [1] CRAN (R 4.0.5)
praise 1.0.0 2015-08-11 [1] CRAN (R 4.0.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.0)
processx 3.5.2 2021-04-30 [1] CRAN (R 4.0.5)
ps 1.4.0 2020-10-07 [1] CRAN (R 4.0.3)
R6 2.5.0 2020-10-28 [1] CRAN (R 4.0.3)
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.0.0)
Rcpp * 1.0.7 2021-07-07 [1] CRAN (R 4.0.5)
RcppEigen 0.3.3.9.1 2020-12-17 [1] CRAN (R 4.0.3)
D RcppParallel 5.0.2 2020-06-24 [1] CRAN (R 4.0.3)
rematch2 2.1.2 2020-05-01 [1] CRAN (R 4.0.0)
rlang 0.4.11 2021-04-30 [1] CRAN (R 4.0.5)
rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.0.3)
rstan * 2.21.2 2020-07-27 [1] CRAN (R 4.0.3)
rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.0.3)
scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.0)
StanHeaders * 2.21.0-6 2020-08-16 [1] CRAN (R 4.0.3)
testthat 3.0.2 2021-02-14 [1] CRAN (R 4.0.5)
tibble * 3.1.1 2021-04-18 [1] CRAN (R 4.0.5)
utf8 1.1.4 2018-05-24 [1] CRAN (R 4.0.0)
V8 3.4.0 2020-11-04 [1] CRAN (R 4.0.3)
vctrs 0.3.8 2021-04-29 [1] CRAN (R 4.0.5)
viridisLite 0.3.0 2018-02-01 [1] CRAN (R 4.0.0)
waldo 0.2.5 2021-03-08 [1] CRAN (R 4.0.5)
withr 2.4.2 2021-04-18 [1] CRAN (R 4.0.5)
[1] C:/Users/Documents/R/win-library/4.0
[2] C:/Program Files/R/R-4.0.3/library
V -- Loaded and on-disk version mismatch.
D -- DLL MD5 mismatch, broken installation.
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Begin with the brm(F0 ~ 1, data=pitch) reproduction and the compiler output, especially the reported missing g++ path. Compare the R 4.0.3/RStan 2.21.2 Windows setup shown here with the project's supported toolchain; done means the same model compiles successfully.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- cpp, r
- Domain
- build-system, operating-systems
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100