* using log directory 'd:/Rcompile/CRANpkg/local/4.6/CLRtools.Rcheck' * using R version 4.6.0 beta (2026-04-16 r89899 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.3.0 GNU Fortran (GCC) 14.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * current time: 2026-04-17 08:03:40 UTC * checking for file 'CLRtools/DESCRIPTION' ... OK * this is package 'CLRtools' version '0.1.1' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'CLRtools' can be installed ... OK * checking installed package size ... INFO installed size is 5.3Mb sub-directories of 1Mb or more: extdata 4.3Mb * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [6s] OK * checking whether the package can be loaded with stated dependencies ... [5s] OK * checking whether the package can be unloaded cleanly ... [6s] OK * checking whether the namespace can be loaded with stated dependencies ... [6s] OK * checking whether the namespace can be unloaded cleanly ... [6s] OK * checking loading without being on the library search path ... [10s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [16s] OK * checking Rd files ... [1s] OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... [0s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [19s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [96s] ERROR Error(s) in re-building vignettes: --- re-building 'Bayesian_Logistic_regression.Rmd' using rmarkdown specified C++17 make cmd is make -f "D:/RCompile/recent/R/etc/x64/Makeconf" -f "D:/RCompile/recent/R/share/make/winshlib.mk" CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB="file72e466106248.dll" WIN=64 TCLBIN= OBJECTS="file72e466106248.o" make would use make[1]: Entering directory '/d/temp/2026_04_17_01_50_00_1722/RtmpUTaWRH' g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I"D:/RCompile/CRANpkg/lib/4.6/Rcpp/include/" -I"D:/temp/2026_04_17_01_50_00_1722/RtmpaMtupr/RLIBS_81304eac695c/RcppEigen/include/" -I"D:/temp/2026_04_17_01_50_00_1722/RtmpaMtupr/RLIBS_81304eac695c/RcppEigen/include/unsupported" -I"D:/temp/2026_04_17_01_50_00_1722/RtmpaMtupr/RLIBS_81304eac695c/BH/include" -I"D:/RCompile/CRANpkg/lib/4.6/StanHeaders/include/src/" -I"D:/RCompile/CRANpkg/lib/4.6/StanHeaders/include/" -I"D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/" -DRCPP_PARALLEL_USE_TBB=1 -I"D:/RCompile/CRANpkg/lib/4.6/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include "D:/RCompile/CRANpkg/lib/4.6/StanHeaders/include/stan/math/prim/fun/Eigen.hpp" -std=c++1y -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c file72e466106248.cpp -o file72e466106248.o if test "zfile72e466106248.o" != "z"; then \ if test -e "file72e466106248-win.def"; then \ echo g++ -shared -s -static-libgcc -o file72e466106248.dll file72e466106248-win.def file72e466106248.o "D:/RCompile/CRANpkg/lib/4.6/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.6/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.6/RcppParallel/lib/x64" -ltbb -L"D:/RCompile/CRANpkg/lib/4.6/RcppParallel/libs/x64" -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.6/RcppParallel/lib/x64 -ltbb -ltbbmalloc -L"d:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64" -L"d:/rtools45/x86_64-w64-mingw32.static.posix/lib" -L"D:/RCompile/recent/R/bin/x64" -lR ; \ g++ -shared -s -static-libgcc -o file72e466106248.dll file72e466106248-win.def file72e466106248.o "D:/RCompile/CRANpkg/lib/4.6/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.6/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.6/RcppParallel/lib/x64" -ltbb -L"D:/RCompile/CRANpkg/lib/4.6/RcppParallel/libs/x64" -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.6/RcppParallel/lib/x64 -ltbb -ltbbmalloc -L"d:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64" -L"d:/rtools45/x86_64-w64-mingw32.static.posix/lib" -L"D:/RCompile/recent/R/bin/x64" -lR ; \ else \ echo EXPORTS > tmp.def; \ nm file72e466106248.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 file72e466106248.dll tmp.def file72e466106248.o "D:/RCompile/CRANpkg/lib/4.6/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.6/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.6/RcppParallel/lib/x64" -ltbb -L"D:/RCompile/CRANpkg/lib/4.6/RcppParallel/libs/x64" -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.6/RcppParallel/lib/x64 -ltbb -ltbbmalloc -L"d:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64" -L"d:/rtools45/x86_64-w64-mingw32.static.posix/lib" -L"D:/RCompile/recent/R/bin/x64" -lR ; \ g++ -shared -s -static-libgcc -o file72e466106248.dll tmp.def file72e466106248.o "D:/RCompile/CRANpkg/lib/4.6/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.6/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.6/RcppParallel/lib/x64" -ltbb -L"D:/RCompile/CRANpkg/lib/4.6/RcppParallel/libs/x64" -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.6/RcppParallel/lib/x64 -ltbb -ltbbmalloc -L"d:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64" -L"d:/rtools45/x86_64-w64-mingw32.static.posix/lib" -L"D:/RCompile/recent/R/bin/x64" -lR ; \ rm -f tmp.def; \ fi \ fi make[1]: Leaving directory '/d/temp/2026_04_17_01_50_00_1722/RtmpUTaWRH' Quitting from Bayesian_Logistic_regression.Rmd:268-348 [unnamed-chunk-7] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `sink()`: ! invalid connection --- Backtrace: ▆ 1. └─rstan::stan(...) 2. └─rstan::stan_model(...) 3. └─rstan:::cxxfunctionplus(...) 4. └─base::sink(type = "output") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Bayesian_Logistic_regression.Rmd' failed with diagnostics: invalid connection --- failed re-building 'Bayesian_Logistic_regression.Rmd' --- re-building 'Conditional_Logistic_Regression.Rmd' using rmarkdown --- finished re-building 'Conditional_Logistic_Regression.Rmd' --- re-building 'Logistic_Regression.Rmd' using rmarkdown --- finished re-building 'Logistic_Regression.Rmd' SUMMARY: processing the following file failed: 'Bayesian_Logistic_regression.Rmd' Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [21s] OK * checking HTML version of manual ... [7s] OK * DONE Status: 1 ERROR