- using R Under development (unstable) (2026-08-31 r90457 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: 2026-09-01 12:58:58 UTC
- checking for file 'cdtmbnma/DESCRIPTION' ... OK
- checking extension type ... Package
- this is package 'cdtmbnma' version '0.2.1'
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... INFO
Package suggested but not available for checking: 'cmdstanr'
- 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 'cdtmbnma' can be installed ... OK
See the install log for details.
- checking installed package size ... OK
- 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 ... [0s] OK
- checking whether the package can be loaded with stated dependencies ... [0s] OK
- checking whether the package can be unloaded cleanly ... [0s] OK
- checking whether the namespace can be loaded with stated dependencies ... [0s] OK
- checking whether the namespace can be unloaded cleanly ... [0s] OK
- checking loading without being on the library search path ... [0s] 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 ... [4s] 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 installed files from 'inst/doc' ... OK
- checking files in 'vignettes' ... OK
- checking examples ... [1s] OK
- checking for unstated dependencies in 'tests' ... OK
- checking tests ... [2s] OK
Running 'testthat.R' [2s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [64s] ERROR
Error(s) in re-building vignettes:
--- re-building 'cdtmbnma.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="file1f46021eb74ba.dll" WIN=64 TCLBIN= OBJECTS="file1f46021eb74ba.o"
make would use
make[1]: Entering directory '/d/temp/2026_09_01_01_50_00_22259/Rtmp2Dh7mb'
g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I"D:/RCompile/CRANpkg/lib/4.7/Rcpp/include/" -I"D:/temp/2026_09_01_01_50_00_22259/RtmpGgbWIM/RLIBS_4653816727eeb/RcppEigen/include/" -I"D:/temp/2026_09_01_01_50_00_22259/RtmpGgbWIM/RLIBS_4653816727eeb/RcppEigen/include/unsupported" -I"D:/temp/2026_09_01_01_50_00_22259/RtmpGgbWIM/RLIBS_4653816727eeb/BH/include" -I"D:/RCompile/CRANpkg/lib/4.7/StanHeaders/include/src/" -I"D:/RCompile/CRANpkg/lib/4.7/StanHeaders/include/" -I"D:/RCompile/CRANpkg/lib/4.7/RcppParallel/include/" -DRCPP_PARALLEL_USE_TBB=1 -DTBB_INTERFACE_NEW -ID:/RCompile/CRANpkg/lib/4.7/RcppParallel/include -I"D:/RCompile/CRANpkg/lib/4.7/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/4.7/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 file1f46021eb74ba.cpp -o file1f46021eb74ba.o
if test "zfile1f46021eb74ba.o" != "z"; then \
if test -e "file1f46021eb74ba-win.def"; then \
echo g++ -shared -s -static-libgcc -o file1f46021eb74ba.dll file1f46021eb74ba-win.def file1f46021eb74ba.o "D:/RCompile/CRANpkg/lib/4.7/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.7/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.7/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.7/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.7/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 file1f46021eb74ba.dll file1f46021eb74ba-win.def file1f46021eb74ba.o "D:/RCompile/CRANpkg/lib/4.7/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.7/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.7/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.7/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.7/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 file1f46021eb74ba.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 file1f46021eb74ba.dll tmp.def file1f46021eb74ba.o "D:/RCompile/CRANpkg/lib/4.7/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.7/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.7/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.7/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.7/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 file1f46021eb74ba.dll tmp.def file1f46021eb74ba.o "D:/RCompile/CRANpkg/lib/4.7/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.7/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.7/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.7/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.7/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_09_01_01_50_00_22259/Rtmp2Dh7mb'
Quitting from cdtmbnma.Rmd:53-63 [fit]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `sink()`:
! invalid connection
---
Backtrace:
▆
1. └─cdtmbnma::cdt_fit(...)
2. └─cdtmbnma:::.cdt_model(be, "cdtmbnma.stan")
3. └─rstan::stan_model(file = stan_file)
4. └─rstan:::cxxfunctionplus(...)
5. └─base::sink(type = "output")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'cdtmbnma.Rmd' failed with diagnostics:
invalid connection
--- failed re-building 'cdtmbnma.Rmd'
SUMMARY: processing the following file failed:
'cdtmbnma.Rmd'
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [20s] OK
- checking HTML version of manual ... [1s] OK
- DONE
Status: 1 ERROR