* installing *source* package ‘phylocomr’ ...
** package ‘phylocomr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘clang version 19.1.3’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/phylocomr/src'
rm -Rf phylocomr.so nothing.o register.o libphylocom/io.o libphylocom/new2fy.o libphylocom/traits.o libphylocom/comstruct.o libphylocom/nrutil.o libphylocom/fy2new.o libphylocom/bladj.o libphylocom/comnode.o libphylocom/prune.o libphylocom/comtrait.o libphylocom/stats.o libphylocom/combase.o libphylocom/libphylocom.a phylocom ecovolve phylomatic
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c libphylocom/io.c -o libphylocom/io.o
libphylocom/io.c:133:7: warning: variable 'linesread' set but not used [-Wunused-but-set-variable]
133 | int linesread = 0;
| ^
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c libphylocom/new2fy.c -o libphylocom/new2fy.o
1 warning generated.
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c libphylocom/traits.c -o libphylocom/traits.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c libphylocom/comstruct.c -o libphylocom/comstruct.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c libphylocom/nrutil.c -o libphylocom/nrutil.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c libphylocom/fy2new.c -o libphylocom/fy2new.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c libphylocom/bladj.c -o libphylocom/bladj.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c libphylocom/comnode.c -o libphylocom/comnode.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c libphylocom/prune.c -o libphylocom/prune.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c libphylocom/comtrait.c -o libphylocom/comtrait.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c libphylocom/stats.c -o libphylocom/stats.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c libphylocom/combase.c -o libphylocom/combase.o
libphylocom/combase.c:1909:10: warning: variable 'sumDist' set but not used [-Wunused-but-set-variable]
1909 | double sumDist = 0.0;
| ^
libphylocom/combase.c:1912:8: warning: variable 'countDist' set but not used [-Wunused-but-set-variable]
1912 | long countDist = 0;
| ^
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c libphylocom/main.c -o libphylocom/main.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c libphylocom/ecomain.c -o libphylocom/ecomain.o
libphylocom/ecomain.c:676:13: warning: variable 'k' set but not used [-Wunused-but-set-variable]
676 | int i, j, k, nterm;
| ^
1 warning generated.
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c libphylocom/phylomatic.c -o libphylocom/phylomatic.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c nothing.c -o nothing.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c register.c -o register.o
/usr/local/clang19/bin/clang -shared -L/usr/local/clang/lib64 -L/usr/local/clang19/lib -L/usr/local/clang19/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o phylocomr.so nothing.o register.o
2 warnings generated.
mkdir -p ../inst/bin
ar rcs libphylocom/libphylocom.a libphylocom/io.o libphylocom/new2fy.o libphylocom/traits.o libphylocom/comstruct.o libphylocom/nrutil.o libphylocom/fy2new.o libphylocom/bladj.o libphylocom/comnode.o libphylocom/prune.o libphylocom/comtrait.o libphylocom/stats.o libphylocom/combase.o
/usr/local/clang19/bin/clang -isystem /usr/local/clang19/include -I/usr/local/clang/include -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -o phylocom libphylocom/main.o -Llibphylocom -lphylocom -lm
cp -f phylocom ../inst/bin
/usr/local/clang19/bin/clang -isystem /usr/local/clang19/include -I/usr/local/clang/include -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -o ecovolve libphylocom/ecomain.o -Llibphylocom -lphylocom -lm
cp -f ecovolve ../inst/bin
/usr/local/clang19/bin/clang -isystem /usr/local/clang19/include -I/usr/local/clang/include -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -o phylomatic libphylocom/phylomatic.o -Llibphylocom -lphylocom -lm
cp -f phylomatic ../inst/bin
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/phylocomr/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/phylocomr/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/phylocomr/src'
installing to /data/gannet/ripley/R/packages/tests-clang/phylocomr.Rcheck/00LOCK-phylocomr/00new/phylocomr/libs
** R
** 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
* DONE (phylocomr)