* installing *source* package ‘diversitree’ ... ** using staged installation checking for gcc... clang-16 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 we are using the GNU C compiler... yes checking whether clang-16 accepts -g... yes checking for clang-16 option to accept ISO C89... none needed checking how to run the C preprocessor... clang-16 -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking fftw3.h usability... yes checking fftw3.h presence... yes checking for fftw3.h... yes Using fftw for QuaSSE FFT calculations checking for gsl-config... /usr/bin/gsl-config checking if GSL version >= 1.15... yes configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/config.h ** libs using C compiler: ‘Debian clang version 16.0.6 (11)’ using Fortran compiler: ‘GNU Fortran (Debian 13.2.0-2) 13.2.0’ using C++ compiler: ‘Debian clang version 16.0.6 (11)’ clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/include -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c GslOdeBase.cpp -o GslOdeBase.o clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/include -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c GslOdeCompiled.cpp -o GslOdeCompiled.o clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/include -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c GslOdeR.cpp -o GslOdeR.o clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/include -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c GslOdeTime.cpp -o GslOdeTime.o clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/include -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c Spline.cpp -o Spline.o clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/include -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c TimeMachine.cpp -o TimeMachine.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/include -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c asr-joint.c -o asr-joint.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/include -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c bd-eqs.c -o bd-eqs.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/include -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c bisse-eqs.c -o bisse-eqs.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/include -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c bisseness-eqs.c -o bisseness-eqs.o gfortran -fpic -g -O2 -Wall -mtune=native -c bucexp.f -o bucexp.o bucexp.f:79:63: 79 | double precision tol, anorm, v(nmax), wsp(lwsp), a(nzmax) | 1 Warning: Array ‘a’ at (1) is larger than limit set by ‘-fmax-stack-var-size=’, moved from stack to static storage. This makes the procedure unsafe when called recursively, or concurrently from multiple threads. Consider increasing the ‘-fmax-stack-var-size=’ limit (or use ‘-frecursive’, which implies unlimited ‘-fmax-stack-var-size’) - or change the code to use an ALLOCATABLE array. If the variable is never accessed concurrently, this warning can be ignored, and the variable could also be declared with the SAVE attribute. [-Wsurprising] bucexp.f:80:43: 80 | complex(kind=kind(0.0d0)) cwsp(lcwsp) | 1 Warning: Array ‘cwsp’ at (1) is larger than limit set by ‘-fmax-stack-var-size=’, moved from stack to static storage. This makes the procedure unsafe when called recursively, or concurrently from multiple threads. Consider increasing the ‘-fmax-stack-var-size=’ limit (or use ‘-frecursive’, which implies unlimited ‘-fmax-stack-var-size’) - or change the code to use an ALLOCATABLE array. If the variable is never accessed concurrently, this warning can be ignored, and the variable could also be declared with the SAVE attribute. [-Wsurprising] bucexp.f:78:23: 78 | integer ia(nzmax), ja(nzmax), iwsp(liwsp) | 1 Warning: Array ‘ia’ at (1) is larger than limit set by ‘-fmax-stack-var-size=’, moved from stack to static storage. This makes the procedure unsafe when called recursively, or concurrently from multiple threads. Consider increasing the ‘-fmax-stack-var-size=’ limit (or use ‘-frecursive’, which implies unlimited ‘-fmax-stack-var-size’) - or change the code to use an ALLOCATABLE array. If the variable is never accessed concurrently, this warning can be ignored, and the variable could also be declared with the SAVE attribute. [-Wsurprising] bucexp.f:78:47: 78 | integer ia(nzmax), ja(nzmax), iwsp(liwsp) | 1 Warning: Array ‘iwsp’ at (1) is larger than limit set by ‘-fmax-stack-var-size=’, moved from stack to static storage. This makes the procedure unsafe when called recursively, or concurrently from multiple threads. Consider increasing the ‘-fmax-stack-var-size=’ limit (or use ‘-frecursive’, which implies unlimited ‘-fmax-stack-var-size’) - or change the code to use an ALLOCATABLE array. If the variable is never accessed concurrently, this warning can be ignored, and the variable could also be declared with the SAVE attribute. [-Wsurprising] bucexp.f:78:34: 78 | integer ia(nzmax), ja(nzmax), iwsp(liwsp) | 1 Warning: Array ‘ja’ at (1) is larger than limit set by ‘-fmax-stack-var-size=’, moved from stack to static storage. This makes the procedure unsafe when called recursively, or concurrently from multiple threads. Consider increasing the ‘-fmax-stack-var-size=’ limit (or use ‘-frecursive’, which implies unlimited ‘-fmax-stack-var-size’) - or change the code to use an ALLOCATABLE array. If the variable is never accessed concurrently, this warning can be ignored, and the variable could also be declared with the SAVE attribute. [-Wsurprising] bucexp.f:79:42: 79 | double precision tol, anorm, v(nmax), wsp(lwsp), a(nzmax) | 1 Warning: Array ‘v’ at (1) is larger than limit set by ‘-fmax-stack-var-size=’, moved from stack to static storage. This makes the procedure unsafe when called recursively, or concurrently from multiple threads. Consider increasing the ‘-fmax-stack-var-size=’ limit (or use ‘-frecursive’, which implies unlimited ‘-fmax-stack-var-size’) - or change the code to use an ALLOCATABLE array. If the variable is never accessed concurrently, this warning can be ignored, and the variable could also be declared with the SAVE attribute. [-Wsurprising] bucexp.f:79:53: 79 | double precision tol, anorm, v(nmax), wsp(lwsp), a(nzmax) | 1 Warning: Array ‘wsp’ at (1) is larger than limit set by ‘-fmax-stack-var-size=’, moved from stack to static storage. This makes the procedure unsafe when called recursively, or concurrently from multiple threads. Consider increasing the ‘-fmax-stack-var-size=’ limit (or use ‘-frecursive’, which implies unlimited ‘-fmax-stack-var-size’) - or change the code to use an ALLOCATABLE array. If the variable is never accessed concurrently, this warning can be ignored, and the variable could also be declared with the SAVE attribute. [-Wsurprising] clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/include -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c classe-eqs.c -o classe-eqs.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/include -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c continuous.c -o continuous.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/include -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c derivs.c -o derivs.o gfortran -fpic -g -O2 -Wall -mtune=native -c dgcoov.f -o dgcoov.o gfortran -fpic -g -O2 -Wall -mtune=native -c dgexpvi.f -o dgexpvi.o gfortran -fpic -g -O2 -Wall -mtune=native -c dgpadm.f -o dgpadm.o gfortran -fpic -g -O2 -Wall -mtune=native -c dmexpv.f -o dmexpv.o gfortran -fpic -g -O2 -Wall -mtune=native -c dnchbv.f -o dnchbv.o gfortran -fpic -g -O2 -Wall -mtune=native -c dsexpv.f -o dsexpv.o gfortran -fpic -g -O2 -Wall -mtune=native -c dsexpvi.f -o dsexpvi.o gfortran -fpic -g -O2 -Wall -mtune=native -c expm.f -o expm.o expm.f:25:43: 25 | complex(kind=kind(0.0d0)) cwsp(lcwsp) | 1 Warning: Array ‘cwsp’ at (1) is larger than limit set by ‘-fmax-stack-var-size=’, moved from stack to static storage. This makes the procedure unsafe when called recursively, or concurrently from multiple threads. Consider increasing the ‘-fmax-stack-var-size=’ limit (or use ‘-frecursive’, which implies unlimited ‘-fmax-stack-var-size’) - or change the code to use an ALLOCATABLE array. If the variable is never accessed concurrently, this warning can be ignored, and the variable could also be declared with the SAVE attribute. [-Wsurprising] expm.f:24:37: 24 | double precision tol, wsp(lwsp), scal | 1 Warning: Array ‘wsp’ at (1) is larger than limit set by ‘-fmax-stack-var-size=’, moved from stack to static storage. This makes the procedure unsafe when called recursively, or concurrently from multiple threads. Consider increasing the ‘-fmax-stack-var-size=’ limit (or use ‘-frecursive’, which implies unlimited ‘-fmax-stack-var-size’) - or change the code to use an ALLOCATABLE array. If the variable is never accessed concurrently, this warning can be ignored, and the variable could also be declared with the SAVE attribute. [-Wsurprising] expm.f:58:32: 58 | double precision wsp(lwsp) | 1 Warning: Array ‘wsp’ at (1) is larger than limit set by ‘-fmax-stack-var-size=’, moved from stack to static storage. This makes the procedure unsafe when called recursively, or concurrently from multiple threads. Consider increasing the ‘-fmax-stack-var-size=’ limit (or use ‘-frecursive’, which implies unlimited ‘-fmax-stack-var-size’) - or change the code to use an ALLOCATABLE array. If the variable is never accessed concurrently, this warning can be ignored, and the variable could also be declared with the SAVE attribute. [-Wsurprising] expm.f:81:32: 81 | double precision wsp(lwsp) | 1 Warning: Array ‘wsp’ at (1) is larger than limit set by ‘-fmax-stack-var-size=’, moved from stack to static storage. This makes the procedure unsafe when called recursively, or concurrently from multiple threads. Consider increasing the ‘-fmax-stack-var-size=’ limit (or use ‘-frecursive’, which implies unlimited ‘-fmax-stack-var-size’) - or change the code to use an ALLOCATABLE array. If the variable is never accessed concurrently, this warning can be ignored, and the variable could also be declared with the SAVE attribute. [-Wsurprising] expm.f:108:43: 108 | complex(kind=kind(0.0d0)) cwsp(lcwsp) | 1 Warning: Array ‘cwsp’ at (1) is larger than limit set by ‘-fmax-stack-var-size=’, moved from stack to static storage. This makes the procedure unsafe when called recursively, or concurrently from multiple threads. Consider increasing the ‘-fmax-stack-var-size=’ limit (or use ‘-frecursive’, which implies unlimited ‘-fmax-stack-var-size’) - or change the code to use an ALLOCATABLE array. If the variable is never accessed concurrently, this warning can be ignored, and the variable could also be declared with the SAVE attribute. [-Wsurprising] expm.f:107:37: 107 | double precision tol, wsp(lwsp), scal | 1 Warning: Array ‘wsp’ at (1) is larger than limit set by ‘-fmax-stack-var-size=’, moved from stack to static storage. This makes the procedure unsafe when called recursively, or concurrently from multiple threads. Consider increasing the ‘-fmax-stack-var-size=’ limit (or use ‘-frecursive’, which implies unlimited ‘-fmax-stack-var-size’) - or change the code to use an ALLOCATABLE array. If the variable is never accessed concurrently, this warning can be ignored, and the variable could also be declared with the SAVE attribute. [-Wsurprising] clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/include -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c geosse-eqs.c -o geosse-eqs.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/include -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c hdr.c -o hdr.o gfortran -fpic -g -O2 -Wall -mtune=native -c hyperg.f -o hyperg.o clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/include -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c interface.cpp -o interface.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/include -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c mkn-eqs.c -o mkn-eqs.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/include -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c mkn-expokit.c -o mkn-expokit.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/include -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c mkn-meristic-eqs.c -o mkn-meristic-eqs.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/include -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c mkn-pij.c -o mkn-pij.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/include -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c musse-eqs.c -o musse-eqs.o gfortran -fpic -g -O2 -Wall -mtune=native -c nucexp.f -o nucexp.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/include -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c quasse-eqs-fftC.c -o quasse-eqs-fftC.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/include -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c quasse-eqs-mol.c -o quasse-eqs-mol.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/include -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c rfftw.c -o rfftw.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/include -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c scm-mkn.c -o scm-mkn.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/include -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c simulate-bisse.c -o simulate-bisse.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/include -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c util-matrix.c -o util-matrix.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/include -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c util-splines.c -o util-splines.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/include -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c util.c -o util.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I/usr/include -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c zzz.c -o zzz.o clang++-16 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o diversitree.so GslOdeBase.o GslOdeCompiled.o GslOdeR.o GslOdeTime.o Spline.o TimeMachine.o asr-joint.o bd-eqs.o bisse-eqs.o bisseness-eqs.o bucexp.o classe-eqs.o continuous.o derivs.o dgcoov.o dgexpvi.o dgpadm.o dmexpv.o dnchbv.o dsexpv.o dsexpvi.o expm.o geosse-eqs.o hdr.o hyperg.o interface.o mkn-eqs.o mkn-expokit.o mkn-meristic-eqs.o mkn-pij.o musse-eqs.o nucexp.o quasse-eqs-fftC.o quasse-eqs-mol.o rfftw.o scm-mkn.o simulate-bisse.o util-matrix.o util-splines.o util.o zzz.o -lfftw3 -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm -llapack -L/home/hornik/tmp/R/lib -lRblas -lgfortran -lm -lquadmath -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm -lgfortran -lm -lquadmath -L/home/hornik/tmp/R/lib -lR installing to /srv/hornik/tmp/CRAN/diversitree.Rcheck/00LOCK-diversitree/00new/diversitree/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 (diversitree)