* using log directory 'd:/Rcompile/CRANpkg/local/4.6/MUGS.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 03:19:45 UTC * checking for file 'MUGS/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'MUGS' version '0.1.0' * 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 'MUGS' can be installed ... OK * 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 ... [3s] OK * checking whether the package can be loaded with stated dependencies ... [2s] OK * checking whether the package can be unloaded cleanly ... [2s] OK * checking whether the namespace can be loaded with stated dependencies ... [2s] OK * checking whether the namespace can be unloaded cleanly ... [3s] OK * checking loading without being on the library search path ... [3s] 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 ... [8s] 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 ... NONE * checking for unstated dependencies in 'tests' ... OK * checking tests ... [25s] ERROR Running 'testthat.R' [24s] 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(MUGS) > > test_check("MUGS") Loading required package: foreach Loading required package: iterators Loading required package: snow Attaching package: 'snow' The following objects are masked from 'package:parallel': closeNode, clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, clusterSplit, makeCluster, parApply, parCapply, parLapply, parRapply, parSapply, recvData, recvOneData, sendData, splitIndices, stopCluster Attaching package: 'inline' The following object is masked from 'package:Rcpp': registerPlugin ERROR(s) during compilation: source code errors or compiler configuration errors! make cmd is make -f "D:/RCompile/recent/R/etc/x64/Makeconf" -f "D:/RCompile/recent/R/share/make/winshlib.mk" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="file10ff42bc1b95.dll" WIN=64 TCLBIN= OBJECTS="file10ff42bc1b95.o" make would use make[1]: Entering directory '/d/temp/2026_04_17_01_50_00_1722/RtmpwLi9Tl' g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I../inst/include -fopenmp -I"D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include" -I"D:/RCompile/CRANpkg/lib/4.6/Rcpp/include" -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c file10ff42bc1b95.cpp -o file10ff42bc1b95.o if test "zfile10ff42bc1b95.o" != "z"; then \ if test -e "file10ff42bc1b95-win.def"; then \ echo g++ -std=gnu++20 -shared -s -static-libgcc -o file10ff42bc1b95.dll file10ff42bc1b95-win.def file10ff42bc1b95.o -fopenmp -L"D:/RCompile/recent/R/bin/x64" -lRlapack -L"D:/RCompile/recent/R/bin/x64" -lRblas -lgfortran -lquadmath -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++ -std=gnu++20 -shared -s -static-libgcc -o file10ff42bc1b95.dll file10ff42bc1b95-win.def file10ff42bc1b95.o -fopenmp -L"D:/RCompile/recent/R/bin/x64" -lRlapack -L"D:/RCompile/recent/R/bin/x64" -lRblas -lgfortran -lquadmath -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 file10ff42bc1b95.o | sed -n 's/^.* [BCDRT] / /p' | sed -e '/[.]refptr[.]/d' -e '/[.]weak[.]/d' | sed 's/[^ ][^ ]*/"&"/g' >> tmp.def; \ echo g++ -std=gnu++20 -shared -s -static-libgcc -o file10ff42bc1b95.dll tmp.def file10ff42bc1b95.o -fopenmp -L"D:/RCompile/recent/R/bin/x64" -lRlapack -L"D:/RCompile/recent/R/bin/x64" -lRblas -lgfortran -lquadmath -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++ -std=gnu++20 -shared -s -static-libgcc -o file10ff42bc1b95.dll tmp.def file10ff42bc1b95.o -fopenmp -L"D:/RCompile/recent/R/bin/x64" -lRlapack -L"D:/RCompile/recent/R/bin/x64" -lRblas -lgfortran -lquadmath -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/RtmpwLi9Tl' Program source: 1: 2: // includes from the plugin 3: #include 4: #include 5: 6: 7: #ifndef BEGIN_RCPP 8: #define BEGIN_RCPP 9: #endif 10: 11: #ifndef END_RCPP 12: #define END_RCPP 13: #endif 14: 15: using namespace Rcpp; 16: 17: // user includes 18: 19: 20: // declarations 21: extern "C" { 22: SEXP file10ff42bc1b95( SEXP n_, SEXP mu_, SEXP sigma_) ; 23: } 24: 25: // definition 26: SEXP file10ff42bc1b95(SEXP n_, SEXP mu_, SEXP sigma_) { 27: BEGIN_RCPP 28: 29: using namespace Rcpp; 30: int n = as(n_); 31: arma::vec mu = as(mu_); 32: arma::mat sigma = as(sigma_); 33: int ncols = sigma.n_cols; // Corrected syntax 34: arma::mat Y = arma::randn(n, ncols); 35: return wrap(arma::repmat(mu, 1, n).t() + Y * arma::chol(sigma)); 36: 37: END_RCPP 38: } Compilation ERROR, function(s)/method(s) not created! Loaded glmnet 4.1-10 Attaching package: 'dplyr' The following object is masked from 'package:MASS': select The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Type 'citation("pROC")' for a citation. Attaching package: 'pROC' The following objects are masked from 'package:stats': cov, smooth, var Setting levels: control = 0, case = 1 Setting direction: controls > cases Setting levels: control = 0, case = 1 Setting direction: controls > cases [ FAIL 1 | WARN 0 | SKIP 0 | PASS 48 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-DataGen_rare_group.R:25:3'): DataGen_rare_group returns correct output structure and dimensions ── Error in `compileCode(f, code, language = language, verbose = verbose)`: using C++ compiler: 'g++.exe (GCC) 14.3.0' In file included from D:/RCompile/CRANpkg/lib/4.6/Rcpp/include/Rcpp.h:49, from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/RcppArmadillo.h:35, from file10ff42bc1b95.cpp:3: D:/RCompile/CRANpkg/lib/4.6/Rcpp/include/Rcpp/Function.h: In constructor 'Rcpp::Function_Impl::Function_Impl(const std::string&, const std::string&)': D:/RCompile/CRANpkg/lib/4.6/Rcpp/include/Rcpp/Function.h:75:65: error: 'R_NamespaceRegistry' was not declared in this scope 75 | Shield env(R_getVarEx(Rf_install(ns.c_str()), R_NamespaceRegistry, FALSE, R_UnboundValue)); | ^~~~~~~~~~~~~~~~~~~ make[1]: *** [D:/RCompile/recent/R/etc/x64/Makeconf:304: file10ff42bc1b95.o] Error 1 Backtrace: ▆ 1. └─MUGS::DataGen_rare_group(...) at test-DataGen_rare_group.R:25:3 2. └─inline::cxxfunction(...) 3. └─inline:::compileCode(f, code, language = language, verbose = verbose) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 48 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [37s] ERROR Error(s) in re-building vignettes: --- re-building 'CodeEff_Matrix_usage.Rmd' using rmarkdown --- finished re-building 'CodeEff_Matrix_usage.Rmd' --- re-building 'CodeSiteEff_I2_par_usage.Rmd' using rmarkdown --- finished re-building 'CodeSiteEff_I2_par_usage.Rmd' --- re-building 'DataGen_rare_group_usage.Rmd' using rmarkdown make cmd is make -f "D:/RCompile/recent/R/etc/x64/Makeconf" -f "D:/RCompile/recent/R/share/make/winshlib.mk" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="file140a43735e9f.dll" WIN=64 TCLBIN= OBJECTS="file140a43735e9f.o" make would use make[1]: Entering directory '/d/temp/2026_04_17_01_50_00_1722/Rtmpo9o9E1' g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I../inst/include -fopenmp -I"D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include" -I"D:/RCompile/CRANpkg/lib/4.6/Rcpp/include" -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c file140a43735e9f.cpp -o file140a43735e9f.o if test "zfile140a43735e9f.o" != "z"; then \ if test -e "file140a43735e9f-win.def"; then \ echo g++ -std=gnu++20 -shared -s -static-libgcc -o file140a43735e9f.dll file140a43735e9f-win.def file140a43735e9f.o -fopenmp -L"D:/RCompile/recent/R/bin/x64" -lRlapack -L"D:/RCompile/recent/R/bin/x64" -lRblas -lgfortran -lquadmath -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++ -std=gnu++20 -shared -s -static-libgcc -o file140a43735e9f.dll file140a43735e9f-win.def file140a43735e9f.o -fopenmp -L"D:/RCompile/recent/R/bin/x64" -lRlapack -L"D:/RCompile/recent/R/bin/x64" -lRblas -lgfortran -lquadmath -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 file140a43735e9f.o | sed -n 's/^.* [BCDRT] / /p' | sed -e '/[.]refptr[.]/d' -e '/[.]weak[.]/d' | sed 's/[^ ][^ ]*/"&"/g' >> tmp.def; \ echo g++ -std=gnu++20 -shared -s -static-libgcc -o file140a43735e9f.dll tmp.def file140a43735e9f.o -fopenmp -L"D:/RCompile/recent/R/bin/x64" -lRlapack -L"D:/RCompile/recent/R/bin/x64" -lRblas -lgfortran -lquadmath -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++ -std=gnu++20 -shared -s -static-libgcc -o file140a43735e9f.dll tmp.def file140a43735e9f.o -fopenmp -L"D:/RCompile/recent/R/bin/x64" -lRlapack -L"D:/RCompile/recent/R/bin/x64" -lRblas -lgfortran -lquadmath -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/Rtmpo9o9E1' Quitting from DataGen_rare_group_usage.Rmd:37-57 [generate_data] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `compileCode()`: ! using C++ compiler: 'g++.exe (GCC) 14.3.0' In file included from D:/RCompile/CRANpkg/lib/4.6/Rcpp/include/Rcpp.h:49, from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/RcppArmadillo.h:35, from file140a43735e9f.cpp:3: D:/RCompile/CRANpkg/lib/4.6/Rcpp/include/Rcpp/Function.h: In constructor 'Rcpp::Function_Impl::Function_Impl(const std::string&, const std::string&)': D:/RCompile/CRANpkg/lib/4.6/Rcpp/include/Rcpp/Function.h:75:65: error: 'R_NamespaceRegistry' was not declared in this scope 75 | Shield env(R_getVarEx(Rf_install(ns.c_str()), R_NamespaceRegistry, FALSE, R_UnboundValue)); | ^~~~~~~~~~~~~~~~~~~ make[1]: *** [D:/RCompile/recent/R/etc/x64/Makeconf:304: file140a43735e9f.o] Error 1 --- Backtrace: ▆ 1. └─MUGS::DataGen_rare_group(...) 2. └─inline::cxxfunction(...) 3. └─inline:::compileCode(f, code, language = language, verbose = verbose) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'DataGen_rare_group_usage.Rmd' failed with diagnostics: using C++ compiler: 'g++.exe (GCC) 14.3.0' In file included from D:/RCompile/CRANpkg/lib/4.6/Rcpp/include/Rcpp.h:49, from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/RcppArmadillo.h:35, from file140a43735e9f.cpp:3: D:/RCompile/CRANpkg/lib/4.6/Rcpp/include/Rcpp/Function.h: In constructor 'Rcpp::Function_Impl::Function_Impl(const std::string&, const std::string&)': D:/RCompile/CRANpkg/lib/4.6/Rcpp/include/Rcpp/Function.h:75:65: error: 'R_NamespaceRegistry' was not declared in this scope 75 | Shield env(R_getVarEx(Rf_install(ns.c_str()), R_NamespaceRegistry, FALSE, R_UnboundValue)); | ^~~~~~~~~~~~~~~~~~~ make[1]: *** [D:/RCompile/recent/R/etc/x64/Makeconf:304: file140a43735e9f.o] Error 1 --- failed re-building 'DataGen_rare_group_usage.Rmd' --- re-building 'Evaluation_sim_usage.Rmd' using rmarkdown --- finished re-building 'Evaluation_sim_usage.Rmd' --- re-building 'GroupEff_par_usage.Rmd' using rmarkdown --- finished re-building 'GroupEff_par_usage.Rmd' --- re-building 'get_embed_usage.Rmd' using rmarkdown --- finished re-building 'get_embed_usage.Rmd' --- re-building 'main-steps.Rmd' using rmarkdown --- finished re-building 'main-steps.Rmd' SUMMARY: processing the following file failed: 'DataGen_rare_group_usage.Rmd' Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [20s] OK * checking HTML version of manual ... [4s] OK * DONE Status: 2 ERRORs