Install log for 'ape'

* installing *source* package ‘ape’ ...
** package ‘ape’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c BIONJ.c -o BIONJ.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c NNI.c -o NNI.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c SPR.c -o SPR.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c additive.c -o additive.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ape.c -o ape.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bNNI.c -o bNNI.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bionjs.c -o bionjs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bipartition.c -o bipartition.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bitsplits.c -o bitsplits.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c delta_plot.c -o delta_plot.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c dist_dna.c -o dist_dna.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c dist_nodes.c -o dist_nodes.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ewLasso.c -o ewLasso.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c heap.c -o heap.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c mat_expo.c -o mat_expo.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c me.c -o me.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c me_balanced.c -o me_balanced.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c me_ols.c -o me_ols.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c mvr.c -o mvr.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c mvrs.c -o mvrs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c nj.c -o nj.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c njs.c -o njs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pic.c -o pic.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c plot_phylo.c -o plot_phylo.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c prop_part.cpp -o prop_part.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rTrait.c -o rTrait.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c read_dna.c -o read_dna.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c reorder_Rcpp.cpp -o reorder_Rcpp.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c reorder_phylo.c -o reorder_phylo.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c treePop.c -o treePop.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c tree_build.c -o tree_build.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c tree_phylo.c -o tree_phylo.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c triangMtd.c -o triangMtd.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c triangMtds.c -o triangMtds.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ultrametric.c -o ultrametric.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o ape.so BIONJ.o NNI.o RcppExports.o SPR.o additive.o ape.o bNNI.o bionjs.o bipartition.o bitsplits.o delta_plot.o dist_dna.o dist_nodes.o ewLasso.o heap.o mat_expo.o me.o me_balanced.o me_ols.o mvr.o mvrs.o nj.o njs.o pic.o plot_phylo.o prop_part.o rTrait.o read_dna.o reorder_Rcpp.o reorder_phylo.o treePop.o tree_build.o tree_phylo.o triangMtd.o triangMtds.o ultrametric.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame
installing to /Volumes/Builds/packages/big-sur-arm64/results/4.3/ape.Rcheck/00LOCK-ape/00new/ape/libs
** generating debug symbols (dSYM)
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (ape)