* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’
* installing *source* package ‘phangorn’ ...
** package ‘phangorn’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘Debian clang version 18.1.4 (1)’
using C++ compiler: ‘Debian clang version 18.1.4 (1)’
using C++11
make[1]: Entering directory '/tmp/RtmpMW0aD2/R.INSTALL2d19c14f3ce74/phangorn/src'
clang++-18 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion  -c RcppExports.cpp -o RcppExports.o
clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c dist.c -o dist.o
clang++-18 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion  -c dupAtomMat.cpp -o dupAtomMat.o
clang++-18 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion  -c fitch64.cpp -o fitch64.o
clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c ml.c -o ml.o
clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c phangorn.c -o phangorn.o
clang++-18 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion  -c phangorn_utils.cpp -o phangorn_utils.o
clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c sankoff.c -o sankoff.o
clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c sprdist.c -o sprdist.o
clang++-18 -std=gnu++11 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o phangorn.so RcppExports.o dist.o dupAtomMat.o fitch64.o ml.o phangorn.o phangorn_utils.o sankoff.o sprdist.o -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lRblas -L/usr/lib/llvm-18/lib -lFortran_main -lFortranRuntime -lFortranDecimal -lm -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpMW0aD2/R.INSTALL2d19c14f3ce74/phangorn/src'
make[1]: Entering directory '/tmp/RtmpMW0aD2/R.INSTALL2d19c14f3ce74/phangorn/src'
make[1]: Leaving directory '/tmp/RtmpMW0aD2/R.INSTALL2d19c14f3ce74/phangorn/src'
installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-phangorn/00new/phangorn/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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
* creating tarball
packaged installation of ‘phangorn’ as ‘phangorn_2.11.1_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (phangorn)