* installing *source* package ‘babelmixr2’ ...
** this is package ‘babelmixr2’ version ‘0.1.6’
** package ‘babelmixr2’ successfully unpacked and MD5 sums checked
** using staged installation
--------[begin src/Makevars]--------
# -*- mode: makefile-gmake -*-
ARMA=`"$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e 'cat(file.path(find.package("RcppArmadillo"),"include"))'`
RCPP=`"$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e 'cat(file.path(find.package("Rcpp"),"include"))'`
EG=`"$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e 'cat(file.path(find.package("RcppEigen"),"include"))'`
RXAPI=`"$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e 'cat(length(rxode2::.rxode2ptrs()))'`
PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
PKG_CXXFLAGS = -Id -I"$(EG)" -I"$(RCPP)" -I"$(ARMA)" -DRXAPI=$(RXAPI)
SHLIB_LDFLAGS = $(SHLIB_CXXLDFLAGS)
SHLIB_LD = $(SHLIB_CXXLD)
--------[end src/Makevars]--------
** libs
using C compiler: ‘clang version 19.1.7’
using C++ compiler: ‘clang version 19.1.7’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/babelmixr2/src'
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/rxode2/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -Id -I"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppEigen"),"include"))'`" -I"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("Rcpp"),"include"))'`" -I"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppArmadillo"),"include"))'`" -DRXAPI=`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(length(rxode2::.rxode2ptrs()))'` -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
273 | Index count = 0;
| ^
In file included from RcppExports.cpp:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
| ^
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree
| ^
In file included from RcppExports.cpp:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
72 | Index replacements = 0;
| ^
In file included from RcppExports.cpp:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
246 | int count = 0;
| ^
5 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/rxode2/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -Id -I"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppEigen"),"include"))'`" -I"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("Rcpp"),"include"))'`" -I"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppArmadillo"),"include"))'`" -DRXAPI=`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(length(rxode2::.rxode2ptrs()))'` -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c classicReverse.cpp -o classicReverse.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/rxode2/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c init.c -o init.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/rxode2/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -Id -I"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppEigen"),"include"))'`" -I"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("Rcpp"),"include"))'`" -I"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppArmadillo"),"include"))'`" -DRXAPI=`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(length(rxode2::.rxode2ptrs()))'` -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c poped.cpp -o poped.o
In file included from poped.cpp:13:
In file included from /data/gannet/ripley/R/test-clang/rxode2/include/rxode2ptr.h:4:
In file included from /data/gannet/ripley/R/test-clang/rxode2/include/rxode2.h:45:
In file included from /data/gannet/ripley/R/test-clang/rxode2/include/rxode2_RcppExports.h:9:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
273 | Index count = 0;
| ^
In file included from poped.cpp:13:
In file included from /data/gannet/ripley/R/test-clang/rxode2/include/rxode2ptr.h:4:
In file included from /data/gannet/ripley/R/test-clang/rxode2/include/rxode2.h:45:
In file included from /data/gannet/ripley/R/test-clang/rxode2/include/rxode2_RcppExports.h:9:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
| ^
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree
| ^
In file included from poped.cpp:13:
In file included from /data/gannet/ripley/R/test-clang/rxode2/include/rxode2ptr.h:4:
In file included from /data/gannet/ripley/R/test-clang/rxode2/include/rxode2.h:45:
In file included from /data/gannet/ripley/R/test-clang/rxode2/include/rxode2_RcppExports.h:9:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
72 | Index replacements = 0;
| ^
In file included from poped.cpp:13:
In file included from /data/gannet/ripley/R/test-clang/rxode2/include/rxode2ptr.h:4:
In file included from /data/gannet/ripley/R/test-clang/rxode2/include/rxode2.h:45:
In file included from /data/gannet/ripley/R/test-clang/rxode2/include/rxode2_RcppExports.h:9:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
246 | int count = 0;
| ^
poped.cpp:498:19: warning: unused function 'getSafeId' [-Wunused-function]
498 | static inline int getSafeId(int id) {
| ^~~~~~~~~
6 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/rxode2/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -Id -I"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppEigen"),"include"))'`" -I"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("Rcpp"),"include"))'`" -I"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppArmadillo"),"include"))'`" -DRXAPI=`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(length(rxode2::.rxode2ptrs()))'` -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c transform.cpp -o transform.o
In file included from transform.cpp:12:
In file included from /data/gannet/ripley/R/test-clang/rxode2/include/rxode2.h:45:
In file included from /data/gannet/ripley/R/test-clang/rxode2/include/rxode2_RcppExports.h:9:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
273 | Index count = 0;
| ^
In file included from transform.cpp:12:
In file included from /data/gannet/ripley/R/test-clang/rxode2/include/rxode2.h:45:
In file included from /data/gannet/ripley/R/test-clang/rxode2/include/rxode2_RcppExports.h:9:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
| ^
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree
| ^
In file included from transform.cpp:12:
In file included from /data/gannet/ripley/R/test-clang/rxode2/include/rxode2.h:45:
In file included from /data/gannet/ripley/R/test-clang/rxode2/include/rxode2_RcppExports.h:9:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
72 | Index replacements = 0;
| ^
In file included from transform.cpp:12:
In file included from /data/gannet/ripley/R/test-clang/rxode2/include/rxode2.h:45:
In file included from /data/gannet/ripley/R/test-clang/rxode2/include/rxode2_RcppExports.h:9:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
246 | int count = 0;
| ^
5 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang19/lib -L/usr/local/clang19/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -o babelmixr2.so RcppExports.o classicReverse.o init.o poped.o transform.o -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lFortranRuntime -lFortranDecimal -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/babelmixr2/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/babelmixr2/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/babelmixr2/src'
installing to /data/gannet/ripley/R/packages/tests-clang/babelmixr2.Rcheck/00LOCK-babelmixr2/00new/babelmixr2/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (babelmixr2)