* using log directory 'd:/Rcompile/CRANpkg/local/4.6/rtk.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 14:55:54 UTC * checking for file 'rtk/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'rtk' version '0.2.7' * 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 'rtk' can be installed ... ERROR Installation failed. See 'd:/Rcompile/CRANpkg/local/4.6/rtk.Rcheck/00install.out' for details. * DONE The installation logfile: * installing *source* package 'rtk' ... ** this is package 'rtk' version '0.2.7' ** package 'rtk' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 14.3.0' using C++ compiler: 'g++.exe (GCC) 14.3.0' make[1]: Entering directory '/d/temp/2026_04_17_01_50_00_1722/RtmpGWMIrR/R.INSTALL19e782b1638f/rtk/src' g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -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 ClStr2Mat.cpp -o ClStr2Mat.o In file included from Matrix.h:2, from ClStr2Mat.h:2, from ClStr2Mat.cpp:1: IO.h:28: warning: ignoring '#pragma warning ' [-Wunknown-pragmas] 28 | #pragma warning(disable:4996) g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -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 IO.cpp -o IO.o In file included from IO.cpp:1: IO.h:28: warning: ignoring '#pragma warning ' [-Wunknown-pragmas] 28 | #pragma warning(disable:4996) IO.cpp: In function 'void lineCntOut(options*)': IO.cpp:74:19: warning: 'in' may be used uninitialized [-Wmaybe-uninitialized] 74 | while (getline((*in), line, '\n')) { | ~~~~~~~^~~~~~~~~~~~~~~~~~~ IO.cpp:21:18: note: 'in' was declared here 21 | istream* in; | ^~ g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -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 Math.cpp -o Math.o g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -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 Matrix.cpp -o Matrix.o In file included from Matrix.h:2, from Matrix.cpp:1: IO.h:28: warning: ignoring '#pragma warning ' [-Wunknown-pragmas] 28 | #pragma warning(disable:4996) Matrix.cpp: In constructor 'Matrix::Matrix(std::string, std::string, std::vector, std::vector >)': Matrix.cpp:672:13: warning: unused variable 'ini_ColPerRow' [-Wunused-variable] 672 | int ini_ColPerRow = iniCols(in); | ^~~~~~~~~~~~~ Matrix.cpp: In constructor 'Matrix::Matrix(std::string, std::string, std::vector, std::vector >)': Matrix.cpp:672:36: warning: 'in' may be used uninitialized [-Wmaybe-uninitialized] 672 | int ini_ColPerRow = iniCols(in); | ~~~~~~~^~~~ Matrix.cpp:646:18: note: 'in' was declared here 646 | istream* in; | ^~ Matrix.cpp: In constructor 'Matrix::Matrix(std::string, std::string, std::string, std::vector >&, bool, bool, bool)': Matrix.cpp:797:36: warning: 'in' may be used uninitialized [-Wmaybe-uninitialized] 797 | int ini_ColPerRow = iniCols(in); | ~~~~~~~^~~~ Matrix.cpp:771:18: note: 'in' was declared here 771 | istream* in; | ^~ Matrix.cpp: In constructor 'Matrix::Matrix(std::string, std::string, bool)': Matrix.cpp:980:36: warning: 'in' may be used uninitialized [-Wmaybe-uninitialized] 980 | int ini_ColPerRow = iniCols(in); | ~~~~~~~^~~~ Matrix.cpp:958:18: note: 'in' was declared here 958 | istream* in; | ^~ g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -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 RRare.cpp -o RRare.o In file included from Matrix.h:2, from ClStr2Mat.h:2, from RRare.h:2, from RRare.cpp:1: IO.h:28: warning: ignoring '#pragma warning ' [-Wunknown-pragmas] 28 | #pragma warning(disable:4996) RRare.cpp: In function 'int rarefyMain(options*, std::string, std::vector >, std::vector >, std::vector >, std::vector&, std::vector > > >&, std::vector > >&, std::vector >&, std::vector >&, std::vector >&, std::vector >&, std::vector >&, bool)': RRare.cpp:307:14: warning: unused variable 'writeFiles' [-Wunused-variable] 307 | bool writeFiles = false; | ^~~~~~~~~~ g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -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 RcppExports.cpp -o RcppExports.o In file included from D:/RCompile/CRANpkg/lib/4.6/Rcpp/include/Rcpp.h:49, from RcppExports.cpp:4: 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: RcppExports.o] Error 1 make[1]: Leaving directory '/d/temp/2026_04_17_01_50_00_1722/RtmpGWMIrR/R.INSTALL19e782b1638f/rtk/src' ERROR: compilation failed for package 'rtk' * removing 'd:/Rcompile/CRANpkg/lib/4.6/rtk' * restoring previous 'd:/Rcompile/CRANpkg/lib/4.6/rtk'