* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’
* installing *source* package ‘dbarts’ ...
** package ‘dbarts’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... clang-18
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 clang-18 accepts -g... yes
checking for clang-18 option to enable C11 features... none needed
checking how to run the C preprocessor... clang-18 -E
checking whether the compiler supports GNU C++... yes
checking whether clang++-18 -std=gnu++17 accepts -g... yes
checking for clang++-18 -std=gnu++17 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... clang++-18 -std=gnu++17 -E
checking for C/C++ restrict keyword... no
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 whether byte ordering is bigendian... no
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for C compiler vendor... clang
checking whether C compiler accepts ... yes
checking whether C compiler accepts -msse2... yes
checking whether C compiler accepts -msse4.1... yes
checking whether C compiler accepts -mavx... yes
checking whether C compiler accepts -mavx2... yes
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking whether clang-18 is Clang... yes
checking whether pthreads work with "-pthread" and "-lpthread"... yes
checking whether Clang needs flag to prevent "argument unused" warning when linking with -pthread... unknown
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking whether more special flags are required for pthreads... no
checking for PTHREAD_PRIO_INHERIT... yes
checking for cstdint... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for malloc.h... yes
checking for int64_t... yes
checking for uint64_t... yes
checking size of size_t... 8
checking alignment of void*... 8
checking for gettimeofday... yes
checking for clock_gettime... yes
checking for ffs... yes
checking for size_t... yes
checking for working alloca.h... yes
checking for alloca... yes
checking for working posix_memalign... yes
checking for snprintf... yes
checking if g++ supports namespace std... yes
checking whether snprintf is in std::... yes
checking for log1p... yes
checking whether log1p is in std::... no
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/config.hpp
config.status: creating src/dbarts/config.hpp
config.status: creating src/misc/config.h
config.status: creating src/external/config.h
config.status: creating inst/include/dbarts/types.hpp
config.status: creating src/include/misc/types.h
** libs
using C compiler: ‘Debian clang version 18.1.8 (1+b1)’
using C++ compiler: ‘Debian clang version 18.1.8 (1+b1)’
make[1]: Entering directory '/tmp/RtmpiVnxsW/R.INSTALL6a82411f21d4f/dbarts/src'
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../inst/include -Iinclude -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic  -c R_C_interface.cpp -o R_C_interface.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../inst/include -Iinclude -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic  -c R_interface.cpp -o R_interface.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../inst/include -Iinclude -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic  -c R_interface_common.cpp -o R_interface_common.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../inst/include -Iinclude -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic  -c R_interface_crossvalidate.cpp -o R_interface_crossvalidate.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../inst/include -Iinclude -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic  -c R_interface_rbart.cpp -o R_interface_rbart.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../inst/include -Iinclude -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic  -c R_interface_sampler.cpp -o R_interface_sampler.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../inst/include -Iinclude -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic  -c crossvalidate.cpp -o crossvalidate.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../inst/include -Iinclude -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic  -c guessNumCores.cpp -o guessNumCores.o
clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../inst/include -Iinclude -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c makeModelMatrixFromDataFrame.c -o makeModelMatrixFromDataFrame.o
make[2]: Entering directory '/tmp/RtmpiVnxsW/R.INSTALL6a82411f21d4f/dbarts/src/dbarts'
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../../inst/include -I../include  -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -fpic  -c bartFit.cpp -o bartFit.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../../inst/include -I../include  -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -fpic  -c binaryIO.cpp -o binaryIO.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../../inst/include -I../include  -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -fpic  -c birthDeathRule.cpp -o birthDeathRule.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../../inst/include -I../include  -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -fpic  -c changeRule.cpp -o changeRule.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../../inst/include -I../include  -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -fpic  -c functions.cpp -o functions.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../../inst/include -I../include  -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -fpic  -c likelihood.cpp -o likelihood.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../../inst/include -I../include  -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -fpic  -c node.cpp -o node.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../../inst/include -I../include  -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -fpic  -c parameterPrior.cpp -o parameterPrior.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../../inst/include -I../include  -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -fpic  -c state.cpp -o state.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../../inst/include -I../include  -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -fpic  -c swapRule.cpp -o swapRule.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../../inst/include -I../include  -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -fpic  -c tree.cpp -o tree.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../../inst/include -I../include  -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -fpic  -c treePrior.cpp -o treePrior.o
ar rv ../dbarts.a bartFit.o binaryIO.o birthDeathRule.o changeRule.o functions.o likelihood.o node.o parameterPrior.o state.o swapRule.o tree.o treePrior.o
ar: creating ../dbarts.a
a - bartFit.o
a - binaryIO.o
a - birthDeathRule.o
a - changeRule.o
a - functions.o
a - likelihood.o
a - node.o
a - parameterPrior.o
a - state.o
a - swapRule.o
a - tree.o
a - treePrior.o
make[2]: Leaving directory '/tmp/RtmpiVnxsW/R.INSTALL6a82411f21d4f/dbarts/src/dbarts'
make[2]: Entering directory '/tmp/RtmpiVnxsW/R.INSTALL6a82411f21d4f/dbarts/src/external'
clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../include -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -fpic -c io.c -o io.o
clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../include -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -fpic -c randomBase.c -o randomBase.o
clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../include -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -fpic -c randomNorm.c -o randomNorm.o
clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../include -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -fpic -c random.c -o random.o
ar rv ../external.a io.o randomBase.o randomNorm.o random.o
ar: creating ../external.a
a - io.o
a - randomBase.o
a - randomNorm.o
a - random.o
make[2]: Leaving directory '/tmp/RtmpiVnxsW/R.INSTALL6a82411f21d4f/dbarts/src/external'
make[2]: Entering directory '/tmp/RtmpiVnxsW/R.INSTALL6a82411f21d4f/dbarts/src/misc'
clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../include -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -fpic -msse2 -c adaptiveRadixTree.c -o adaptiveRadixTree.o
clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../include -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -fpic -c binaryIO.c -o binaryIO.o
clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../include -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -fpic -c blockingThreadManager.c -o blockingThreadManager.o
clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../include -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -fpic -c hierarchicalThreadManager.c -o hierarchicalThreadManager.o
clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../include -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -fpic -c linearAlgebra.c -o linearAlgebra.o
clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../include -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -fpic -c moments.c -o moments.o
clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../include -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -fpic -c partition.c -o partition.o
clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../include -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -fpic -c simd.c -o simd.o
clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../include -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -fpic -c string.c -o string.o
clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../include -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -fpic -c thread.c -o thread.o
echo clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../include -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -fpic -c linearAlgebra_sse2.c -o linearAlgebra_sse2.c
clang-18 -I/home/hornik/tmp/R.check/r-devel-clang/Work/build/include -DNDEBUG -I../include -pthread -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -fpic -c linearAlgebra_sse2.c -o linearAlgebra_sse2.c
echo clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../include -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -fpic -c moments_sse2.c -o moments_sse2.o
clang-18 -I/home/hornik/tmp/R.check/r-devel-clang/Work/build/include -DNDEBUG -I../include -pthread -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -fpic -c moments_sse2.c -o moments_sse2.o
echo clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../include -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -fpic -c partition_sse2.c -o partition_sse2.o
clang-18 -I/home/hornik/tmp/R.check/r-devel-clang/Work/build/include -DNDEBUG -I../include -pthread -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -fpic -c partition_sse2.c -o partition_sse2.o
echo clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../include -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -fpic -c partition_sse4_1.c -o partition_sse4_1.o
clang-18 -I/home/hornik/tmp/R.check/r-devel-clang/Work/build/include -DNDEBUG -I../include -pthread -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -fpic -c partition_sse4_1.c -o partition_sse4_1.o
echo clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../include -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -fpic -c linearAlgebra_avx.c -o linearAlgebra_avx.c
clang-18 -I/home/hornik/tmp/R.check/r-devel-clang/Work/build/include -DNDEBUG -I../include -pthread -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -fpic -c linearAlgebra_avx.c -o linearAlgebra_avx.c
echo clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../include -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -fpic -c partition_avx2.c -o partition_avx2.o
clang-18 -I/home/hornik/tmp/R.check/r-devel-clang/Work/build/include -DNDEBUG -I../include -pthread -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -fpic -c partition_avx2.c -o partition_avx2.o
ar rv ../misc.a adaptiveRadixTree.o binaryIO.o blockingThreadManager.o hierarchicalThreadManager.o linearAlgebra.o moments.o partition.o simd.o string.o thread.o linearAlgebra_sse2.o moments_sse2.o partition_sse2.o partition_sse4_1.o linearAlgebra_avx.o partition_avx2.o
ar: creating ../misc.a
a - adaptiveRadixTree.o
a - binaryIO.o
a - blockingThreadManager.o
a - hierarchicalThreadManager.o
a - linearAlgebra.o
a - moments.o
a - partition.o
a - simd.o
a - string.o
a - thread.o
a - linearAlgebra_sse2.o
a - moments_sse2.o
a - partition_sse2.o
a - partition_sse4_1.o
a - linearAlgebra_avx.o
a - partition_avx2.o
make[2]: Leaving directory '/tmp/RtmpiVnxsW/R.INSTALL6a82411f21d4f/dbarts/src/misc'
make[2]: Entering directory '/tmp/RtmpiVnxsW/R.INSTALL6a82411f21d4f/dbarts/src/rc'
clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../include -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3  -g -O3 -Wall -pedantic -fpic -c bounds.c -o bounds.o
clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../include -pthread  -I/usr/local/include -D_FORTIFY_SOURCE=3  -g -O3 -Wall -pedantic -fpic -c util.c -o util.o
ar rv ../rc.a bounds.o util.o
ar: creating ../rc.a
a - bounds.o
a - util.o
make[2]: Leaving directory '/tmp/RtmpiVnxsW/R.INSTALL6a82411f21d4f/dbarts/src/rc'
clang++-18 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o dbarts.so R_C_interface.o R_interface.o R_interface_common.o R_interface_crossvalidate.o R_interface_rbart.o R_interface_sampler.o crossvalidate.o guessNumCores.o makeModelMatrixFromDataFrame.o dbarts.a external.a misc.a rc.a -pthread -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpiVnxsW/R.INSTALL6a82411f21d4f/dbarts/src'
make[1]: Entering directory '/tmp/RtmpiVnxsW/R.INSTALL6a82411f21d4f/dbarts/src'
make[1]: Leaving directory '/tmp/RtmpiVnxsW/R.INSTALL6a82411f21d4f/dbarts/src'
installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-dbarts/00new/dbarts/libs
** R
** 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 (dbarts)