=> Bootstrap dependency digest>=20211023: found digest-20220214 ===> Skipping vulnerability checks. WARNING: No /usr/pkg/pkgdb/pkg-vulnerabilities file found. WARNING: To fix run: `/usr/sbin/pkg_admin -K /usr/pkg/pkgdb fetch-pkg-vulnerabilities'. ===> Installing for R-nimble-1.3.0 => Generating pre-install file lists => Creating installation directories * installing *source* package 'nimble' ... ** this is package 'nimble' version '1.3.0' ** package 'nimble' successfully unpacked and MD5 sums checked ** using staged installation checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether c++ -std=gnu++20 accepts -g... yes checking for c++ -std=gnu++20 option to enable C++11 features... none needed working on eigen checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for Eigen/Dense... no Using the version of Eigen provided with NIMBLE ENABLE_LIB=false configure: creating ./config.status config.status: creating inst/make/Makevars config.status: creating inst/make/Makevars_lib config.status: creating R/config.R config.status: creating src/Makevars config.status: creating inst/CppCode/Makevars removing debugging flags /usr/pkg/lib/R/bin/Rscript --vanilla ./customizeMakeconf.R Building libnimble.a c++ -std=gnu++20 -I"/usr/pkg/lib/R/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/glib-2.0 -I/usr/pkg/include/gio-unix-2.0 -I/usr/pkg/lib/glib-2.0/include -I/usr/X11R7/include -I/usr/pkg/include/freetype2 -I/usr/pkg/include/harfbuzz -I/usr/pkg/include/libxml2 -fpic -O2 -march=i586 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/glib-2.0 -I/usr/pkg/include/gio-unix-2.0 -I/usr/pkg/lib/glib-2.0/include -I/usr/X11R7/include -I/usr/pkg/include/freetype2 -I/usr/pkg/include/harfbuzz -I/usr/pkg/include/libxml2 -c nimOptim.cpp -o nimOptim.o In file included from ../include/nimble/Utils.h:27, from ../include/nimble/NimArr.h:27, from ../include/nimble/nimOptim.h:25, from nimOptim.cpp:23: ../include/nimble/accessorClasses.h: In member function 'void NodeVectorClassNew_derivs::populateDerivsInfo(SEXP)': ../include/nimble/accessorClasses.h:936:13: error: 'Rf_findVarInFrame' was not declared in this scope; did you mean 'R_existsVarInFrame'? 936 | Rf_findVarInFrame(PROTECT(GET_SLOT(SderivsInfo, SpxData)), | ^~~~~~~~~~~~~~~~~ /pbulk/work/math/R-nimble/work/.buildlink/lib/R/include/Rinternals.h:357:36: note: in definition of macro 'PROTECT' 357 | #define PROTECT(s) Rf_protect(s) | ^ ../include/nimble/nimOptim.h: In member function 'virtual void NimOptimProblem_Fun_Grad_Hess::hessian_callback()': ../include/nimble/nimOptim.h:249:40: warning: top-level comma expression in array subscript is deprecated [-Wcomma-subscript] 249 | NimOptimProblem::ans_hessian_[i,j] *= parscale[i] * parscale[j]; | ^ nimOptim.cpp: In member function 'nimSmartPtr NimOptimProblem::solve(NimArr<1, double>&)': nimOptim.cpp:292:41: error: 'Rf_findVar' was not declared in this scope; did you mean 'Rf_findFun'? 292 | PROTECT(Rf_eval(PROTECT(Rf_findVar(Rf_install("nimbleInternalFunctions"), | ^~~~~~~~~~ /pbulk/work/math/R-nimble/work/.buildlink/lib/R/include/Rinternals.h:357:36: note: in definition of macro 'PROTECT' 357 | #define PROTECT(s) Rf_protect(s) | ^ nimOptim.cpp:292:33: note: in expansion of macro 'PROTECT' 292 | PROTECT(Rf_eval(PROTECT(Rf_findVar(Rf_install("nimbleInternalFunctions"), | ^~~~~~~ make: *** [Makeconf:197: nimOptim.o] Error 1 rm -f Makeconf ** libs using C++ compiler: 'g++ (nb1 20250721) 12.5.0' c++ -std=gnu++20 -I"/usr/pkg/lib/R/include" -DNDEBUG -DR_NO_REMAP -I../inst/include -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/glib-2.0 -I/usr/pkg/include/gio-unix-2.0 -I/usr/pkg/lib/glib-2.0/include -I/usr/X11R7/include -I/usr/pkg/include/freetype2 -I/usr/pkg/include/harfbuzz -I/usr/pkg/include/libxml2 -fpic -O2 -march=i586 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/glib-2.0 -I/usr/pkg/include/gio-unix-2.0 -I/usr/pkg/lib/glib-2.0/include -I/usr/X11R7/include -I/usr/pkg/include/freetype2 -I/usr/pkg/include/harfbuzz -I/usr/pkg/include/libxml2 -c RcppUtils.cpp -o RcppUtils.o In file included from ../inst/include/nimble/Utils.h:27, from ../inst/include/nimble/RcppUtils.h:31, from RcppUtils.cpp:22: RcppUtils.cpp: In function 'SEXPREC* makeNewNimbleList(SEXP)': RcppUtils.cpp:906:29: error: 'Rf_findVar' was not declared in this scope; did you mean 'Rf_findFun'? 906 | PROTECT(Rf_eval(PROTECT(Rf_findVar(Rf_install("nimbleInternalFunctions"), R_GlobalEnv)), R_GlobalEnv)); | ^~~~~~~~~~ /pbulk/work/math/R-nimble/work/.buildlink/lib/R/include/Rinternals.h:357:36: note: in definition of macro 'PROTECT' 357 | #define PROTECT(s) Rf_protect(s) | ^ RcppUtils.cpp:906:21: note: in expansion of macro 'PROTECT' 906 | PROTECT(Rf_eval(PROTECT(Rf_findVar(Rf_install("nimbleInternalFunctions"), R_GlobalEnv)), R_GlobalEnv)); | ^~~~~~~ make: *** [/usr/pkg/lib/R/etc/Makeconf:197: RcppUtils.o] Error 1 ERROR: compilation failed for package 'nimble' * removing '/pbulk/work/math/R-nimble/work/.destdir/usr/pkg/lib/R/library/nimble' *** Error code 1 Stop. make[1]: stopped making "stage-install" in /usr/pkgsrc/math/R-nimble *** Error code 1 Stop. make: stopped making "stage-install" in /usr/pkgsrc/math/R-nimble