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jaleesr / BITFAM

BITFAM is a Bayesian approach and platform to infer transcription factor activities within individual cells using single cell RNA-sequencing data. Please see Gao S et al., Genome Research (2021) https://genome.cshlp.org/content/31/7/1296 for details.
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Error in compileCode(f, code, language = language, verbose = verbose) #8

Closed beetlejuice007 closed 1 year ago

beetlejuice007 commented 1 year ago

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:/PROGRA~1/R/R-42~1.3/etc/x64/Makeconf" -f "C:/PROGRA~1/R/R-42~1.3/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:/PROGRA~1/R/R-42~1.3/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:/PROGRA~1/R/R-42~1.3/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:/PROGRA~1/R/R-42~1.3/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:/PROGRA~1/R/R-42~1.3/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:/PROGRA~1/R/R-42~1.3/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:/PROGRA~1/R/R-42~1.3/etc/x64/Makeconf:260: file4dfc22eb2c08.o] Error 1 Error in sink(type = "output") : invalid connection

sgao30 commented 1 year ago

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.