* using log directory 'd:/Rcompile/CRANpkg/local/4.7/alien.Rcheck'
* using R Under development (unstable) (2026-10-24 r90762 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: 2026-10-25 14:54:22 UTC
* checking for file 'alien/DESCRIPTION' ... OK
* this is package 'alien' version '1.0.2'
* 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 'alien' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
  Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'lambda_functions.R' 'likelihood-space.R' 'snc.R'
* 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 ... [1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s] OK
* checking whether the package can be unloaded cleanly ... [1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s] OK
* checking loading without being on the library search path ... [1s] 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 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 ... [1s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [123s] OK
  Running 'testthat.R' [122s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [135s] ERROR
Error(s) in re-building vignettes:
--- re-building 'basic_usage.Rmd' using rmarkdown
--- finished re-building 'basic_usage.Rmd'

--- re-building 'native_discoveries.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="file51fe0411f74ab.dll" WIN=64 TCLBIN= OBJECTS="file51fe0411f74ab.o"

make would use
make[1]: Entering directory '/d/temp/2026_10_25_01_50_00_21025/RtmpkFZL7G'
g++  -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG   -I"D:/RCompile/CRANpkg/lib/4.7/Rcpp/include/"  -I"D:/temp/2026_10_25_01_50_00_21025/Rtmpszwwz3/RLIBS_5cc7851a362ac/RcppEigen/include/"  -I"D:/temp/2026_10_25_01_50_00_21025/Rtmpszwwz3/RLIBS_5cc7851a362ac/RcppEigen/include/unsupported"  -I"D:/temp/2026_10_25_01_50_00_21025/Rtmpszwwz3/RLIBS_5cc7851a362ac/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 file51fe0411f74ab.cpp -o file51fe0411f74ab.o
if test "zfile51fe0411f74ab.o" != "z"; then \
  if test -e "file51fe0411f74ab-win.def"; then \
    echo g++   -shared  -s -static-libgcc -o file51fe0411f74ab.dll file51fe0411f74ab-win.def file51fe0411f74ab.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 file51fe0411f74ab.dll file51fe0411f74ab-win.def file51fe0411f74ab.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 file51fe0411f74ab.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 file51fe0411f74ab.dll tmp.def file51fe0411f74ab.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 file51fe0411f74ab.dll tmp.def file51fe0411f74ab.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_10_25_01_50_00_21025/RtmpkFZL7G'

Quitting from native_discoveries.Rmd:71-73 [setting_model]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `sink()`:
! invalid connection
---
Backtrace:
    ▆
 1. └─rstan::stan_model(model_file)
 2.   └─rstan:::cxxfunctionplus(...)
 3.     └─base::sink(type = "output")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'native_discoveries.Rmd' failed with diagnostics:
invalid connection
--- failed re-building 'native_discoveries.Rmd'

--- re-building 'simulations.Rmd' using rmarkdown
--- finished re-building 'simulations.Rmd'

SUMMARY: processing the following file failed:
  'native_discoveries.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [19s] OK
* checking HTML version of manual ... [1s] OK
* DONE
Status: 1 ERROR, 1 NOTE