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CRAN Package Check Results for Package rbmiUtils

Last updated on 2026-09-22 07:50:42 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.3.0 5.54 745.21 750.75 OK
r-devel-linux-x86_64-debian-gcc 0.3.0 3.85 741.87 745.72 OK
r-devel-linux-x86_64-fedora-clang 0.3.0 341.52 OK
r-devel-linux-x86_64-fedora-gcc 0.3.0 534.57 OK
r-devel-windows-x86_64 0.3.0 12.00 437.00 449.00 ERROR
r-patched-linux-x86_64 0.3.0 6.74 838.06 844.80 OK
r-release-linux-x86_64 0.3.0 5.08 858.45 863.53 OK
r-release-macos-arm64 0.3.0 2.00 140.00 142.00 OK
r-release-macos-x86_64 0.3.0 5.00 794.00 799.00 OK
r-release-windows-x86_64 0.3.0 11.00 393.00 404.00 ERROR
r-oldrel-macos-arm64 0.3.0 2.00 138.00 140.00 OK
r-oldrel-macos-x86_64 0.3.0 6.00 1404.00 1410.00 OK
r-oldrel-windows-x86_64 0.3.0 16.00 517.00 533.00 ERROR

Check Details

Version: 0.3.0
Check: tests
Result: ERROR Running 'spelling.R' [0s] Running 'testthat.R' [139s] Running the tests in 'tests/testthat.R' failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(rbmiUtils) > > test_check("rbmiUtils") Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union v All outcome values are complete -- no missing data to impute. i You may not need `data_ice` for `rbmi::draws()`. v All outcome values are complete -- no missing data to impute. i You may not need `data_ice` for `rbmi::draws()`. v All outcome values are complete -- no missing data to impute. i You may not need `data_ice` for `rbmi::draws()`. v All outcome values are complete -- no missing data to impute. i You may not need `data_ice` for `rbmi::draws()`. 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="file49d801e9678c7.dll" WIN=64 TCLBIN= OBJECTS="file49d801e9678c7.o" make would use make[1]: Entering directory '/d/temp/2026_09_17_01_50_00_14611/Rtmp2z9liX' 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_17_01_50_00_14611/Rtmpc7adEt/RLIBS_570f4506372e2/RcppEigen/include/" -I"D:/temp/2026_09_17_01_50_00_14611/Rtmpc7adEt/RLIBS_570f4506372e2/RcppEigen/include/unsupported" -I"D:/temp/2026_09_17_01_50_00_14611/Rtmpc7adEt/RLIBS_570f4506372e2/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 file49d801e9678c7.cpp -o file49d801e9678c7.o if test "zfile49d801e9678c7.o" != "z"; then \ if test -e "file49d801e9678c7-win.def"; then \ echo g++ -shared -s -static-libgcc -o file49d801e9678c7.dll file49d801e9678c7-win.def file49d801e9678c7.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 file49d801e9678c7.dll file49d801e9678c7-win.def file49d801e9678c7.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 file49d801e9678c7.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 file49d801e9678c7.dll tmp.def file49d801e9678c7.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 file49d801e9678c7.dll tmp.def file49d801e9678c7.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_17_01_50_00_14611/Rtmp2z9liX' Saving _problems/test-utils-44.R [ FAIL 2 | WARN 16 | SKIP 2 | PASS 1024 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • Stanfit mock requires real Stan compilation - tested via integration (1): 'test-describe.R:273:3' • rbmi::pool() returned empty results for g-computation (df = NA not supported) (1): 'test-integration.R:279:5' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-utils.R:39:3'): positive test get_imputed_data (from vignettes) ── Error in `compileCode(f, code, language = language, verbose = verbose)`: ault_namespace::model49d806085089_rbmi_MMRM_us_default; BaseRNG = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >]' 22 | return 0.5 * z.p.transpose() * z.inv_e_metric_ * z.p; D:/RCompile/CRANpkg/lib/4.7/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:0: required from here 21 | double T(dense_e_point& z) { D:/RCompile/CRANpkg/lib/4.7/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits<double>::type' {aka '__m128d'} [-Wignored-attributes] 654 | return internal::first_aligned<int(unpacket_traits<DefaultPacketType>::alignment),Derived>(m); | ^~~~~~~~~ make[1]: *** [D:/RCompile/recent/R/etc/x64/Makeconf:304: file49d801e9678c7.o] Error 1 Backtrace: ▆ 1. ├─rbmi::draws(data = dat, vars = vars, method = method, quiet = TRUE) at test-utils.R:39:3 2. └─rbmi:::draws.bayes(...) 3. └─rbmi:::fit_mcmc(...) 4. └─rbmi:::get_stan_model(covariance = method$covariance, prior_cov = method$prior_cov) 5. └─rstan::stan_model(...) 6. └─rstan:::cxxfunctionplus(...) 7. ├─pkgbuild::with_build_tools(...) 8. │ └─pkgbuild:::withr_with_path(rtools_path(), code) 9. │ └─base::force(code) 10. └─inline::cxxfunction(...) 11. └─inline:::compileCode(f, code, language = language, verbose = verbose) ── Error ('test-utils.R:39:3'): positive test get_imputed_data (from vignettes) ── Error in `sink(type = "output")`: invalid connection Backtrace: ▆ 1. ├─rbmi::draws(data = dat, vars = vars, method = method, quiet = TRUE) at test-utils.R:39:3 2. └─rbmi:::draws.bayes(...) 3. └─rbmi:::fit_mcmc(...) 4. └─rbmi:::get_stan_model(covariance = method$covariance, prior_cov = method$prior_cov) 5. └─rstan::stan_model(...) 6. └─rstan:::cxxfunctionplus(...) 7. └─base::sink(type = "output") [ FAIL 2 | WARN 16 | SKIP 2 | PASS 1024 ] Error: ! Test failures. Execution halted Flavor: r-devel-windows-x86_64

Version: 0.3.0
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building 'analyse2.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="file31a789586dfc.dll" WIN=64 TCLBIN= OBJECTS="file31a789586dfc.o" make would use make[1]: Entering directory '/d/temp/2026_09_17_01_50_00_14611/RtmpSmt37X' 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_17_01_50_00_14611/Rtmpc7adEt/RLIBS_570f4506372e2/RcppEigen/include/" -I"D:/temp/2026_09_17_01_50_00_14611/Rtmpc7adEt/RLIBS_570f4506372e2/RcppEigen/include/unsupported" -I"D:/temp/2026_09_17_01_50_00_14611/Rtmpc7adEt/RLIBS_570f4506372e2/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 file31a789586dfc.cpp -o file31a789586dfc.o if test "zfile31a789586dfc.o" != "z"; then \ if test -e "file31a789586dfc-win.def"; then \ echo g++ -shared -s -static-libgcc -o file31a789586dfc.dll file31a789586dfc-win.def file31a789586dfc.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 file31a789586dfc.dll file31a789586dfc-win.def file31a789586dfc.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 file31a789586dfc.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 file31a789586dfc.dll tmp.def file31a789586dfc.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 file31a789586dfc.dll tmp.def file31a789586dfc.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_17_01_50_00_14611/RtmpSmt37X' Quitting from analyse2.Rmd:98-107 [impute] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `sink()`: ! invalid connection --- Backtrace: ▆ 1. ├─rbmi::draws(data = dat, vars = vars, method = method) 2. └─rbmi:::draws.bayes(data = dat, vars = vars, method = method) 3. └─rbmi:::fit_mcmc(...) 4. └─rbmi:::get_stan_model(covariance = method$covariance, prior_cov = method$prior_cov) 5. └─rstan::stan_model(...) 6. └─rstan:::cxxfunctionplus(...) 7. └─base::sink(type = "output") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'analyse2.Rmd' failed with diagnostics: invalid connection --- failed re-building 'analyse2.Rmd' --- re-building 'data-preparation.Rmd' using rmarkdown --- finished re-building 'data-preparation.Rmd' --- re-building 'deriving-endpoints.Rmd' using rmarkdown --- finished re-building 'deriving-endpoints.Rmd' --- re-building 'diagnostics.Rmd' using rmarkdown --- finished re-building 'diagnostics.Rmd' --- re-building 'efficient-storage.Rmd' using rmarkdown --- finished re-building 'efficient-storage.Rmd' --- re-building 'pipeline.Rmd' using rmarkdown specified C++17 make cmd is make -f "D:/RCompile/recent/R/etc/x64/Makeconf" -f "D:/RCompile/recent/R/share/make/winshlib.mk" CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB="file3e52c9647a9c.dll" WIN=64 TCLBIN= OBJECTS="file3e52c9647a9c.o" make would use make[1]: Entering directory '/d/temp/2026_09_17_01_50_00_14611/RtmpCovBrp' 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_17_01_50_00_14611/Rtmpc7adEt/RLIBS_570f4506372e2/RcppEigen/include/" -I"D:/temp/2026_09_17_01_50_00_14611/Rtmpc7adEt/RLIBS_570f4506372e2/RcppEigen/include/unsupported" -I"D:/temp/2026_09_17_01_50_00_14611/Rtmpc7adEt/RLIBS_570f4506372e2/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 file3e52c9647a9c.cpp -o file3e52c9647a9c.o if test "zfile3e52c9647a9c.o" != "z"; then \ if test -e "file3e52c9647a9c-win.def"; then \ echo g++ -shared -s -static-libgcc -o file3e52c9647a9c.dll file3e52c9647a9c-win.def file3e52c9647a9c.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 file3e52c9647a9c.dll file3e52c9647a9c-win.def file3e52c9647a9c.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 file3e52c9647a9c.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 file3e52c9647a9c.dll tmp.def file3e52c9647a9c.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 file3e52c9647a9c.dll tmp.def file3e52c9647a9c.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_17_01_50_00_14611/RtmpCovBrp' Quitting from pipeline.Rmd:160-165 [draws] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `sink()`: ! invalid connection --- Backtrace: ▆ 1. ├─rbmi::draws(data = dat, vars = vars, method = method) 2. └─rbmi:::draws.bayes(data = dat, vars = vars, method = method) 3. └─rbmi:::fit_mcmc(...) 4. └─rbmi:::get_stan_model(covariance = method$covariance, prior_cov = method$prior_cov) 5. └─rstan::stan_model(...) 6. └─rstan:::cxxfunctionplus(...) 7. └─base::sink(type = "output") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'pipeline.Rmd' failed with diagnostics: invalid connection --- failed re-building 'pipeline.Rmd' SUMMARY: processing the following files failed: 'analyse2.Rmd' 'pipeline.Rmd' Error: Vignette re-building failed. Execution halted Flavor: r-devel-windows-x86_64

Version: 0.3.0
Check: tests
Result: ERROR Running 'spelling.R' [0s] Running 'testthat.R' [122s] Running the tests in 'tests/testthat.R' failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(rbmiUtils) > > test_check("rbmiUtils") Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union v All outcome values are complete -- no missing data to impute. i You may not need `data_ice` for `rbmi::draws()`. v All outcome values are complete -- no missing data to impute. i You may not need `data_ice` for `rbmi::draws()`. v All outcome values are complete -- no missing data to impute. i You may not need `data_ice` for `rbmi::draws()`. v All outcome values are complete -- no missing data to impute. i You may not need `data_ice` for `rbmi::draws()`. specified C++17 make cmd is make -f "D:/RCompile/recent/R-4.6.1/etc/x64/Makeconf" -f "D:/RCompile/recent/R-4.6.1/share/make/winshlib.mk" CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB="fileb7486f273ed.dll" WIN=64 TCLBIN= OBJECTS="fileb7486f273ed.o" make would use make[1]: Entering directory '/d/temp/2026_09_09_01_50_00_18435/RtmpGWKXMT' g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.6.1/include" -DNDEBUG -I"D:/RCompile/CRANpkg/lib/4.6/Rcpp/include/" -I"D:/temp/2026_09_09_01_50_00_18435/RtmpkhSaTd/RLIBS_37a5c75462633/RcppEigen/include/" -I"D:/temp/2026_09_09_01_50_00_18435/RtmpkhSaTd/RLIBS_37a5c75462633/RcppEigen/include/unsupported" -I"D:/temp/2026_09_09_01_50_00_18435/RtmpkhSaTd/RLIBS_37a5c75462633/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 -DTBB_INTERFACE_NEW -ID:/RCompile/CRANpkg/lib/4.6/RcppParallel/include -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 fileb7486f273ed.cpp -o fileb7486f273ed.o if test "zfileb7486f273ed.o" != "z"; then \ if test -e "fileb7486f273ed-win.def"; then \ echo g++ -shared -s -static-libgcc -o fileb7486f273ed.dll fileb7486f273ed-win.def fileb7486f273ed.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 -LD:/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-4.6.1/bin/x64" -lR ; \ g++ -shared -s -static-libgcc -o fileb7486f273ed.dll fileb7486f273ed-win.def fileb7486f273ed.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 -LD:/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-4.6.1/bin/x64" -lR ; \ else \ echo EXPORTS > tmp.def; \ nm fileb7486f273ed.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 fileb7486f273ed.dll tmp.def fileb7486f273ed.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 -LD:/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-4.6.1/bin/x64" -lR ; \ g++ -shared -s -static-libgcc -o fileb7486f273ed.dll tmp.def fileb7486f273ed.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 -LD:/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-4.6.1/bin/x64" -lR ; \ rm -f tmp.def; \ fi \ fi make[1]: Leaving directory '/d/temp/2026_09_09_01_50_00_18435/RtmpGWKXMT' Saving _problems/test-utils-44.R [ FAIL 2 | WARN 16 | SKIP 2 | PASS 1024 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • Stanfit mock requires real Stan compilation - tested via integration (1): 'test-describe.R:273:3' • rbmi::pool() returned empty results for g-computation (df = NA not supported) (1): 'test-integration.R:279:5' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-utils.R:39:3'): positive test get_imputed_data (from vignettes) ── Error in `compileCode(f, code, language = language, verbose = verbose)`: _namespace::modelb748116476c7_rbmi_MMRM_us_default; BaseRNG = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >]' 22 | return 0.5 * z.p.transpose() * z.inv_e_metric_ * z.p; D:/RCompile/CRANpkg/lib/4.6/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:0: required from here 21 | double T(dense_e_point& z) { D:/RCompile/CRANpkg/lib/4.6/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits<double>::type' {aka '__m128d'} [-Wignored-attributes] 654 | return internal::first_aligned<int(unpacket_traits<DefaultPacketType>::alignment),Derived>(m); | ^~~~~~~~~ make[1]: *** [D:/RCompile/recent/R-4.6.1/etc/x64/Makeconf:304: fileb7486f273ed.o] Error 1 Backtrace: ▆ 1. ├─rbmi::draws(data = dat, vars = vars, method = method, quiet = TRUE) at test-utils.R:39:3 2. └─rbmi:::draws.bayes(...) 3. └─rbmi:::fit_mcmc(...) 4. └─rbmi:::get_stan_model(covariance = method$covariance, prior_cov = method$prior_cov) 5. └─rstan::stan_model(...) 6. └─rstan:::cxxfunctionplus(...) 7. ├─pkgbuild::with_build_tools(...) 8. │ └─pkgbuild:::withr_with_path(rtools_path(), code) 9. │ └─base::force(code) 10. └─inline::cxxfunction(...) 11. └─inline:::compileCode(f, code, language = language, verbose = verbose) ── Error ('test-utils.R:39:3'): positive test get_imputed_data (from vignettes) ── Error in `sink(type = "output")`: invalid connection Backtrace: ▆ 1. ├─rbmi::draws(data = dat, vars = vars, method = method, quiet = TRUE) at test-utils.R:39:3 2. └─rbmi:::draws.bayes(...) 3. └─rbmi:::fit_mcmc(...) 4. └─rbmi:::get_stan_model(covariance = method$covariance, prior_cov = method$prior_cov) 5. └─rstan::stan_model(...) 6. └─rstan:::cxxfunctionplus(...) 7. └─base::sink(type = "output") [ FAIL 2 | WARN 16 | SKIP 2 | PASS 1024 ] Error: ! Test failures. Execution halted Flavor: r-release-windows-x86_64

Version: 0.3.0
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building 'analyse2.Rmd' using rmarkdown specified C++17 make cmd is make -f "D:/RCompile/recent/R-4.6.1/etc/x64/Makeconf" -f "D:/RCompile/recent/R-4.6.1/share/make/winshlib.mk" CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB="file5506410d75f75.dll" WIN=64 TCLBIN= OBJECTS="file5506410d75f75.o" make would use make[1]: Entering directory '/d/temp/2026_09_09_01_50_00_18435/RtmpiES7QR' g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.6.1/include" -DNDEBUG -I"D:/RCompile/CRANpkg/lib/4.6/Rcpp/include/" -I"D:/temp/2026_09_09_01_50_00_18435/RtmpkhSaTd/RLIBS_37a5c75462633/RcppEigen/include/" -I"D:/temp/2026_09_09_01_50_00_18435/RtmpkhSaTd/RLIBS_37a5c75462633/RcppEigen/include/unsupported" -I"D:/temp/2026_09_09_01_50_00_18435/RtmpkhSaTd/RLIBS_37a5c75462633/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 -DTBB_INTERFACE_NEW -ID:/RCompile/CRANpkg/lib/4.6/RcppParallel/include -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 file5506410d75f75.cpp -o file5506410d75f75.o if test "zfile5506410d75f75.o" != "z"; then \ if test -e "file5506410d75f75-win.def"; then \ echo g++ -shared -s -static-libgcc -o file5506410d75f75.dll file5506410d75f75-win.def file5506410d75f75.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 -LD:/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-4.6.1/bin/x64" -lR ; \ g++ -shared -s -static-libgcc -o file5506410d75f75.dll file5506410d75f75-win.def file5506410d75f75.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 -LD:/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-4.6.1/bin/x64" -lR ; \ else \ echo EXPORTS > tmp.def; \ nm file5506410d75f75.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 file5506410d75f75.dll tmp.def file5506410d75f75.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 -LD:/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-4.6.1/bin/x64" -lR ; \ g++ -shared -s -static-libgcc -o file5506410d75f75.dll tmp.def file5506410d75f75.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 -LD:/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-4.6.1/bin/x64" -lR ; \ rm -f tmp.def; \ fi \ fi make[1]: Leaving directory '/d/temp/2026_09_09_01_50_00_18435/RtmpiES7QR' Quitting from analyse2.Rmd:98-107 [impute] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `sink()`: ! invalid connection --- Backtrace: ▆ 1. ├─rbmi::draws(data = dat, vars = vars, method = method) 2. └─rbmi:::draws.bayes(data = dat, vars = vars, method = method) 3. └─rbmi:::fit_mcmc(...) 4. └─rbmi:::get_stan_model(covariance = method$covariance, prior_cov = method$prior_cov) 5. └─rstan::stan_model(...) 6. └─rstan:::cxxfunctionplus(...) 7. └─base::sink(type = "output") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'analyse2.Rmd' failed with diagnostics: invalid connection --- failed re-building 'analyse2.Rmd' --- re-building 'data-preparation.Rmd' using rmarkdown --- finished re-building 'data-preparation.Rmd' --- re-building 'deriving-endpoints.Rmd' using rmarkdown --- finished re-building 'deriving-endpoints.Rmd' --- re-building 'diagnostics.Rmd' using rmarkdown --- finished re-building 'diagnostics.Rmd' --- re-building 'efficient-storage.Rmd' using rmarkdown --- finished re-building 'efficient-storage.Rmd' --- re-building 'pipeline.Rmd' using rmarkdown specified C++17 make cmd is make -f "D:/RCompile/recent/R-4.6.1/etc/x64/Makeconf" -f "D:/RCompile/recent/R-4.6.1/share/make/winshlib.mk" CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB="file204f054836891.dll" WIN=64 TCLBIN= OBJECTS="file204f054836891.o" make would use make[1]: Entering directory '/d/temp/2026_09_09_01_50_00_18435/RtmpQjsCPX' g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.6.1/include" -DNDEBUG -I"D:/RCompile/CRANpkg/lib/4.6/Rcpp/include/" -I"D:/temp/2026_09_09_01_50_00_18435/RtmpkhSaTd/RLIBS_37a5c75462633/RcppEigen/include/" -I"D:/temp/2026_09_09_01_50_00_18435/RtmpkhSaTd/RLIBS_37a5c75462633/RcppEigen/include/unsupported" -I"D:/temp/2026_09_09_01_50_00_18435/RtmpkhSaTd/RLIBS_37a5c75462633/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 -DTBB_INTERFACE_NEW -ID:/RCompile/CRANpkg/lib/4.6/RcppParallel/include -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 file204f054836891.cpp -o file204f054836891.o if test "zfile204f054836891.o" != "z"; then \ if test -e "file204f054836891-win.def"; then \ echo g++ -shared -s -static-libgcc -o file204f054836891.dll file204f054836891-win.def file204f054836891.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 -LD:/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-4.6.1/bin/x64" -lR ; \ g++ -shared -s -static-libgcc -o file204f054836891.dll file204f054836891-win.def file204f054836891.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 -LD:/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-4.6.1/bin/x64" -lR ; \ else \ echo EXPORTS > tmp.def; \ nm file204f054836891.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 file204f054836891.dll tmp.def file204f054836891.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 -LD:/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-4.6.1/bin/x64" -lR ; \ g++ -shared -s -static-libgcc -o file204f054836891.dll tmp.def file204f054836891.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 -LD:/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-4.6.1/bin/x64" -lR ; \ rm -f tmp.def; \ fi \ fi make[1]: Leaving directory '/d/temp/2026_09_09_01_50_00_18435/RtmpQjsCPX' Quitting from pipeline.Rmd:160-165 [draws] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `sink()`: ! invalid connection --- Backtrace: ▆ 1. ├─rbmi::draws(data = dat, vars = vars, method = method) 2. └─rbmi:::draws.bayes(data = dat, vars = vars, method = method) 3. └─rbmi:::fit_mcmc(...) 4. └─rbmi:::get_stan_model(covariance = method$covariance, prior_cov = method$prior_cov) 5. └─rstan::stan_model(...) 6. └─rstan:::cxxfunctionplus(...) 7. └─base::sink(type = "output") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'pipeline.Rmd' failed with diagnostics: invalid connection --- failed re-building 'pipeline.Rmd' SUMMARY: processing the following files failed: 'analyse2.Rmd' 'pipeline.Rmd' Error: Vignette re-building failed. Execution halted Flavor: r-release-windows-x86_64

Version: 0.3.0
Check: tests
Result: ERROR Running 'spelling.R' [0s] Running 'testthat.R' [171s] Running the tests in 'tests/testthat.R' failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(rbmiUtils) > > test_check("rbmiUtils") Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union v All outcome values are complete -- no missing data to impute. i You may not need `data_ice` for `rbmi::draws()`. v All outcome values are complete -- no missing data to impute. i You may not need `data_ice` for `rbmi::draws()`. v All outcome values are complete -- no missing data to impute. i You may not need `data_ice` for `rbmi::draws()`. v All outcome values are complete -- no missing data to impute. i You may not need `data_ice` for `rbmi::draws()`. make cmd is make -f "D:/RCompile/recent/R-4.5.3/etc/x64/Makeconf" -f "D:/RCompile/recent/R-4.5.3/share/make/winshlib.mk" CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB="file4157c36f317ab.dll" WIN=64 TCLBIN= OBJECTS="file4157c36f317ab.o" make would use make[1]: Entering directory '/d/temp/2026_09_15_23_03_36_27542/RtmpOoeWQ0' g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.3/include" -DNDEBUG -I"D:/RCompile/CRANpkg/lib/4.5/Rcpp/include/" -I"D:/temp/2026_09_15_23_03_36_27542/RtmpExYuBg/RLIBS_357c8612574b9/RcppEigen/include/" -I"D:/temp/2026_09_15_23_03_36_27542/RtmpExYuBg/RLIBS_357c8612574b9/RcppEigen/include/unsupported" -I"D:/temp/2026_09_15_23_03_36_27542/RtmpExYuBg/RLIBS_357c8612574b9/BH/include" -I"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/include/src/" -I"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/include/" -I"D:/RCompile/CRANpkg/lib/4.5/RcppParallel/include/" -DRCPP_PARALLEL_USE_TBB=1 -DTBB_INTERFACE_NEW -ID:/RCompile/CRANpkg/lib/4.5/RcppParallel/include -I"D:/RCompile/CRANpkg/lib/4.5/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/4.5/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 file4157c36f317ab.cpp -o file4157c36f317ab.o if test "zfile4157c36f317ab.o" != "z"; then \ if test -e "file4157c36f317ab-win.def"; then \ echo g++ -shared -s -static-libgcc -o file4157c36f317ab.dll file4157c36f317ab-win.def file4157c36f317ab.o "D:/RCompile/CRANpkg/lib/4.5/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.5/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.5/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.5/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-4.5.3/bin/x64" -lR ; \ g++ -shared -s -static-libgcc -o file4157c36f317ab.dll file4157c36f317ab-win.def file4157c36f317ab.o "D:/RCompile/CRANpkg/lib/4.5/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.5/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.5/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.5/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-4.5.3/bin/x64" -lR ; \ else \ echo EXPORTS > tmp.def; \ nm file4157c36f317ab.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 file4157c36f317ab.dll tmp.def file4157c36f317ab.o "D:/RCompile/CRANpkg/lib/4.5/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.5/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.5/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.5/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-4.5.3/bin/x64" -lR ; \ g++ -shared -s -static-libgcc -o file4157c36f317ab.dll tmp.def file4157c36f317ab.o "D:/RCompile/CRANpkg/lib/4.5/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.5/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.5/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.5/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-4.5.3/bin/x64" -lR ; \ rm -f tmp.def; \ fi \ fi make[1]: Leaving directory '/d/temp/2026_09_15_23_03_36_27542/RtmpOoeWQ0' Saving _problems/test-utils-44.R [ FAIL 2 | WARN 16 | SKIP 2 | PASS 1024 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • Stanfit mock requires real Stan compilation - tested via integration (1): 'test-describe.R:273:3' • rbmi::pool() returned empty results for g-computation (df = NA not supported) (1): 'test-integration.R:279:5' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-utils.R:39:3'): positive test get_imputed_data (from vignettes) ── Error in `compileCode(f, code, language = language, verbose = verbose)`: amespace::model4157c5775d22_rbmi_MMRM_us_default; BaseRNG = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >]' 22 | return 0.5 * z.p.transpose() * z.inv_e_metric_ * z.p; D:/RCompile/CRANpkg/lib/4.5/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:0: required from here 21 | double T(dense_e_point& z) { D:/RCompile/CRANpkg/lib/4.5/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits<double>::type' {aka '__m128d'} [-Wignored-attributes] 654 | return internal::first_aligned<int(unpacket_traits<DefaultPacketType>::alignment),Derived>(m); | ^~~~~~~~~ make[1]: *** [D:/RCompile/recent/R-4.5.3/etc/x64/Makeconf:302: file4157c36f317ab.o] Error 1 Backtrace: ▆ 1. ├─rbmi::draws(data = dat, vars = vars, method = method, quiet = TRUE) at test-utils.R:39:3 2. └─rbmi:::draws.bayes(...) 3. └─rbmi:::fit_mcmc(...) 4. └─rbmi:::get_stan_model(covariance = method$covariance, prior_cov = method$prior_cov) 5. └─rstan::stan_model(...) 6. └─rstan:::cxxfunctionplus(...) 7. ├─pkgbuild::with_build_tools(...) 8. │ └─pkgbuild:::withr_with_path(rtools_path(), code) 9. │ └─base::force(code) 10. └─inline::cxxfunction(...) 11. └─inline:::compileCode(f, code, language = language, verbose = verbose) ── Error ('test-utils.R:39:3'): positive test get_imputed_data (from vignettes) ── Error in `sink(type = "output")`: invalid connection Backtrace: ▆ 1. ├─rbmi::draws(data = dat, vars = vars, method = method, quiet = TRUE) at test-utils.R:39:3 2. └─rbmi:::draws.bayes(...) 3. └─rbmi:::fit_mcmc(...) 4. └─rbmi:::get_stan_model(covariance = method$covariance, prior_cov = method$prior_cov) 5. └─rstan::stan_model(...) 6. └─rstan:::cxxfunctionplus(...) 7. └─base::sink(type = "output") [ FAIL 2 | WARN 16 | SKIP 2 | PASS 1024 ] Error: ! Test failures. Execution halted Flavor: r-oldrel-windows-x86_64

Version: 0.3.0
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building 'analyse2.Rmd' using rmarkdown make cmd is make -f "D:/RCompile/recent/R-4.5.3/etc/x64/Makeconf" -f "D:/RCompile/recent/R-4.5.3/share/make/winshlib.mk" CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB="file43c8424346c7a.dll" WIN=64 TCLBIN= OBJECTS="file43c8424346c7a.o" make would use make[1]: Entering directory '/d/temp/2026_09_15_23_03_36_27542/RtmpANA0RS' g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.3/include" -DNDEBUG -I"D:/RCompile/CRANpkg/lib/4.5/Rcpp/include/" -I"D:/temp/2026_09_15_23_03_36_27542/RtmpExYuBg/RLIBS_357c8612574b9/RcppEigen/include/" -I"D:/temp/2026_09_15_23_03_36_27542/RtmpExYuBg/RLIBS_357c8612574b9/RcppEigen/include/unsupported" -I"D:/temp/2026_09_15_23_03_36_27542/RtmpExYuBg/RLIBS_357c8612574b9/BH/include" -I"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/include/src/" -I"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/include/" -I"D:/RCompile/CRANpkg/lib/4.5/RcppParallel/include/" -DRCPP_PARALLEL_USE_TBB=1 -DTBB_INTERFACE_NEW -ID:/RCompile/CRANpkg/lib/4.5/RcppParallel/include -I"D:/RCompile/CRANpkg/lib/4.5/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/4.5/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 file43c8424346c7a.cpp -o file43c8424346c7a.o if test "zfile43c8424346c7a.o" != "z"; then \ if test -e "file43c8424346c7a-win.def"; then \ echo g++ -shared -s -static-libgcc -o file43c8424346c7a.dll file43c8424346c7a-win.def file43c8424346c7a.o "D:/RCompile/CRANpkg/lib/4.5/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.5/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.5/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.5/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-4.5.3/bin/x64" -lR ; \ g++ -shared -s -static-libgcc -o file43c8424346c7a.dll file43c8424346c7a-win.def file43c8424346c7a.o "D:/RCompile/CRANpkg/lib/4.5/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.5/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.5/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.5/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-4.5.3/bin/x64" -lR ; \ else \ echo EXPORTS > tmp.def; \ nm file43c8424346c7a.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 file43c8424346c7a.dll tmp.def file43c8424346c7a.o "D:/RCompile/CRANpkg/lib/4.5/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.5/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.5/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.5/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-4.5.3/bin/x64" -lR ; \ g++ -shared -s -static-libgcc -o file43c8424346c7a.dll tmp.def file43c8424346c7a.o "D:/RCompile/CRANpkg/lib/4.5/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.5/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.5/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.5/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-4.5.3/bin/x64" -lR ; \ rm -f tmp.def; \ fi \ fi make[1]: Leaving directory '/d/temp/2026_09_15_23_03_36_27542/RtmpANA0RS' Quitting from analyse2.Rmd:98-107 [impute] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `sink()`: ! invalid connection --- Backtrace: ▆ 1. ├─rbmi::draws(data = dat, vars = vars, method = method) 2. └─rbmi:::draws.bayes(data = dat, vars = vars, method = method) 3. └─rbmi:::fit_mcmc(...) 4. └─rbmi:::get_stan_model(covariance = method$covariance, prior_cov = method$prior_cov) 5. └─rstan::stan_model(...) 6. └─rstan:::cxxfunctionplus(...) 7. └─base::sink(type = "output") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'analyse2.Rmd' failed with diagnostics: invalid connection --- failed re-building 'analyse2.Rmd' --- re-building 'data-preparation.Rmd' using rmarkdown --- finished re-building 'data-preparation.Rmd' --- re-building 'deriving-endpoints.Rmd' using rmarkdown --- finished re-building 'deriving-endpoints.Rmd' --- re-building 'diagnostics.Rmd' using rmarkdown --- finished re-building 'diagnostics.Rmd' --- re-building 'efficient-storage.Rmd' using rmarkdown --- finished re-building 'efficient-storage.Rmd' --- re-building 'pipeline.Rmd' using rmarkdown make cmd is make -f "D:/RCompile/recent/R-4.5.3/etc/x64/Makeconf" -f "D:/RCompile/recent/R-4.5.3/share/make/winshlib.mk" CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB="file33a44a5a77d1.dll" WIN=64 TCLBIN= OBJECTS="file33a44a5a77d1.o" make would use make[1]: Entering directory '/d/temp/2026_09_15_23_03_36_27542/RtmpekNHwY' g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.3/include" -DNDEBUG -I"D:/RCompile/CRANpkg/lib/4.5/Rcpp/include/" -I"D:/temp/2026_09_15_23_03_36_27542/RtmpExYuBg/RLIBS_357c8612574b9/RcppEigen/include/" -I"D:/temp/2026_09_15_23_03_36_27542/RtmpExYuBg/RLIBS_357c8612574b9/RcppEigen/include/unsupported" -I"D:/temp/2026_09_15_23_03_36_27542/RtmpExYuBg/RLIBS_357c8612574b9/BH/include" -I"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/include/src/" -I"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/include/" -I"D:/RCompile/CRANpkg/lib/4.5/RcppParallel/include/" -DRCPP_PARALLEL_USE_TBB=1 -DTBB_INTERFACE_NEW -ID:/RCompile/CRANpkg/lib/4.5/RcppParallel/include -I"D:/RCompile/CRANpkg/lib/4.5/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/4.5/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 file33a44a5a77d1.cpp -o file33a44a5a77d1.o if test "zfile33a44a5a77d1.o" != "z"; then \ if test -e "file33a44a5a77d1-win.def"; then \ echo g++ -shared -s -static-libgcc -o file33a44a5a77d1.dll file33a44a5a77d1-win.def file33a44a5a77d1.o "D:/RCompile/CRANpkg/lib/4.5/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.5/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.5/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.5/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-4.5.3/bin/x64" -lR ; \ g++ -shared -s -static-libgcc -o file33a44a5a77d1.dll file33a44a5a77d1-win.def file33a44a5a77d1.o "D:/RCompile/CRANpkg/lib/4.5/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.5/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.5/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.5/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-4.5.3/bin/x64" -lR ; \ else \ echo EXPORTS > tmp.def; \ nm file33a44a5a77d1.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 file33a44a5a77d1.dll tmp.def file33a44a5a77d1.o "D:/RCompile/CRANpkg/lib/4.5/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.5/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.5/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.5/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-4.5.3/bin/x64" -lR ; \ g++ -shared -s -static-libgcc -o file33a44a5a77d1.dll tmp.def file33a44a5a77d1.o "D:/RCompile/CRANpkg/lib/4.5/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.5/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.5/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.5/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-4.5.3/bin/x64" -lR ; \ rm -f tmp.def; \ fi \ fi make[1]: Leaving directory '/d/temp/2026_09_15_23_03_36_27542/RtmpekNHwY' Quitting from pipeline.Rmd:160-165 [draws] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `sink()`: ! invalid connection --- Backtrace: ▆ 1. ├─rbmi::draws(data = dat, vars = vars, method = method) 2. └─rbmi:::draws.bayes(data = dat, vars = vars, method = method) 3. └─rbmi:::fit_mcmc(...) 4. └─rbmi:::get_stan_model(covariance = method$covariance, prior_cov = method$prior_cov) 5. └─rstan::stan_model(...) 6. └─rstan:::cxxfunctionplus(...) 7. └─base::sink(type = "output") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'pipeline.Rmd' failed with diagnostics: invalid connection --- failed re-building 'pipeline.Rmd' SUMMARY: processing the following files failed: 'analyse2.Rmd' 'pipeline.Rmd' Error: Vignette re-building failed. Execution halted Flavor: r-oldrel-windows-x86_64

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