Error in compileCode(f, code, language = language, verbose = verbose)

[hemantgujar]

Hi

Can you please help with the following error. thanks.

BITFAM_res <- BITFAM(data = data_matrix_normalized, species = "mouse", scATAC_obj = NA, 
                      iter = 8, ncores = 1)

Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
rstan (Version 2.21.8, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
Do not specify '-march=native' in 'LOCAL_CPPFLAGS' or a Makevars file
make cmd is
make -f "C:/PROGRA1/R/R-421.3/etc/x64/Makeconf" -f "C:/PROGRA1/R/R-421.3/share/make/winshlib.mk" CXX='$(CXX14) $(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB="file4dfc22eb2c08.dll" WIN=64 TCLBIN= OBJECTS="file4dfc22eb2c08.o"

make would use
g++ -std=gnu++14 -I"C:/PROGRA1/R/R-421.3/include" -DNDEBUG -I"C:/Users/Hemant Gujar/AppData/Local/R/win-library/4.2/Rcpp/include/" -I"C:/Users/Hemant Gujar/AppData/Local/R/win-library/4.2/RcppEigen/include/" -I"C:/Users/Hemant Gujar/AppData/Local/R/win-library/4.2/RcppEigen/include/unsupported" -I"C:/Users/Hemant Gujar/AppData/Local/R/win-library/4.2/BH/include" -I"C:/Users/Hemant Gujar/AppData/Local/R/win-library/4.2/StanHeaders/include/src/" -I"C:/Users/Hemant Gujar/AppData/Local/R/win-library/4.2/StanHeaders/include/" -I"C:/Users/Hemant Gujar/AppData/Local/R/win-library/4.2/RcppParallel/include/" -I"C:/Users/Hemant Gujar/AppData/Local/R/win-library/4.2/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include "C:/Users/Hemant Gujar/AppData/Local/R/win-library/4.2/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp" -std=c++1y -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c file4dfc22eb2c08.cpp -o file4dfc22eb2c08.o
if test "zfile4dfc22eb2c08.o" != "z"; then
if test -e "file4dfc22eb2c08-win.def"; then
echo g++ -shared -s -static-libgcc -o file4dfc22eb2c08.dll file4dfc22eb2c08-win.def file4dfc22eb2c08.o -L"c:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64" -L"c:/rtools42/x86_64-w64-mingw32.static.posix/lib" -L"C:/PROGRA1/R/R-421.3/bin/x64" -lR ;
g++ -shared -s -static-libgcc -o file4dfc22eb2c08.dll file4dfc22eb2c08-win.def file4dfc22eb2c08.o -L"c:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64" -L"c:/rtools42/x86_64-w64-mingw32.static.posix/lib" -L"C:/PROGRA1/R/R-421.3/bin/x64" -lR ;
else
echo EXPORTS > tmp.def;
nm file4dfc22eb2c08.o | sed -n 's/^.* [BCDRT] / /p' | sed -e '/[.]refptr[.]/d' -e '/[.]weak[.]/d' | sed 's/[^ ][^ ]*/"&"/g' >> tmp.def;
echo g++ -shared -s -static-libgcc -o file4dfc22eb2c08.dll tmp.def file4dfc22eb2c08.o -L"c:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64" -L"c:/rtools42/x86_64-w64-mingw32.static.posix/lib" -L"C:/PROGRA1/R/R-421.3/bin/x64" -lR ;
g++ -shared -s -static-libgcc -o file4dfc22eb2c08.dll tmp.def file4dfc22eb2c08.o -L"c:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64" -L"c:/rtools42/x86_64-w64-mingw32.static.posix/lib" -L"C:/PROGRA1/R/R-421.3/bin/x64" -lR ;
rm -f tmp.def;
fi
fi
Error in compileCode(f, code, language = language, verbose = verbose) :
from C:/Users/Hemant Gujar/AppData/Local/R/win-library/4.2/StanHeaders/include/src/stan/model/model_header.hpp:4, from file4dfc22eb2c08.cpp:14:C:/Users/Hemant Gujar/AppData/Local/R/win-library/4.2/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:/PROGRA1/R/R-421.3/etc/x64/Makeconf:260: file4dfc22eb2c08.o] Error 1
Error in sink(type = "output") : invalid connection

[sgao30]

Hi,
Thank you for using our tool!
BITFAM is developed and tested on Linux system. It seems like you are trying it on windows. I believe the error is related to the rstan in windows. We will have a investigation on that. Currently, the easy solution is to switch to a Linux machine and try it again.