* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’
* installing *source* package ‘phylocomr’ ...
** this is package ‘phylocomr’ version ‘0.3.4’
** package ‘phylocomr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-16 (Debian 16-20260425-1) 16.0.1 20260425 (prerelease) [gcc-16 r16-8812-gd9c07462a22]’
make[1]: Entering directory '/tmp/RtmpTNy17i/R.INSTALLbbccb32cc757c/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
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c libphylocom/io.c -o libphylocom/io.o
libphylocom/io.c: In function ‘ReadMeans’:
libphylocom/io.c:133:7: warning: variable ‘linesread’ set but not used [-Wunused-but-set-variable=]
133 | int linesread = 0;
| ^~~~~~~~~
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c libphylocom/new2fy.c -o libphylocom/new2fy.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c libphylocom/traits.c -o libphylocom/traits.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c libphylocom/comstruct.c -o libphylocom/comstruct.o
libphylocom/comstruct.c: In function ‘NodeSig’:
libphylocom/comstruct.c:1241:34: warning: ‘*test_r[<unknown>]’ may be used uninitialized [-Wmaybe-uninitialized]
1241 | (int) test_r[(int) ((float) RUNS * 0.5)], ordHI,
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
libphylocom/comstruct.c:1255:34: warning: ‘*test_r[<unknown>]’ may be used uninitialized [-Wmaybe-uninitialized]
1255 | (int) test_r[(int) ((float) RUNS * 0.5)], ordHI,
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
libphylocom/comstruct.c:1262:32: warning: ‘*test_r[<unknown>]’ may be used uninitialized [-Wmaybe-uninitialized]
1262 | (int) test_r[(int) ((float) RUNS * 0.5)], ordHI,
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c libphylocom/nrutil.c -o libphylocom/nrutil.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c libphylocom/fy2new.c -o libphylocom/fy2new.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c libphylocom/bladj.c -o libphylocom/bladj.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c libphylocom/comnode.c -o libphylocom/comnode.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c libphylocom/prune.c -o libphylocom/prune.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c libphylocom/comtrait.c -o libphylocom/comtrait.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c libphylocom/stats.c -o libphylocom/stats.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c libphylocom/combase.c -o libphylocom/combase.o
libphylocom/combase.c: In function ‘RaoDiversity’:
libphylocom/combase.c:1912:8: warning: variable ‘countDist’ set but not used [-Wunused-but-set-variable=]
1912 | long countDist = 0;
| ^~~~~~~~~
libphylocom/combase.c:1909:10: warning: variable ‘sumDist’ set but not used [-Wunused-but-set-variable=]
1909 | double sumDist = 0.0;
| ^~~~~~~
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
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c libphylocom/main.c -o libphylocom/main.o
gcc-16 -I/usr/local/include -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -o phylocom libphylocom/main.o -Llibphylocom -lphylocom -lm
cp -f phylocom ../inst/bin
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c libphylocom/ecomain.c -o libphylocom/ecomain.o
libphylocom/ecomain.c: In function ‘Balance’:
libphylocom/ecomain.c:676:13: warning: variable ‘k’ set but not used [-Wunused-but-set-variable=]
676 | int i, j, k, nterm;
| ^
gcc-16 -I/usr/local/include -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -o ecovolve libphylocom/ecomain.o -Llibphylocom -lphylocom -lm
cp -f ecovolve ../inst/bin
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c libphylocom/phylomatic.c -o libphylocom/phylomatic.o
gcc-16 -I/usr/local/include -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -o phylomatic libphylocom/phylomatic.o -Llibphylocom -lphylocom -lm
cp -f phylomatic ../inst/bin
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c nothing.c -o nothing.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c register.c -o register.o
gcc-16 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -o phylocomr.so nothing.o register.o -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpTNy17i/R.INSTALLbbccb32cc757c/phylocomr/src'
make[1]: Entering directory '/tmp/RtmpTNy17i/R.INSTALLbbccb32cc757c/phylocomr/src'
make[1]: Leaving directory '/tmp/RtmpTNy17i/R.INSTALLbbccb32cc757c/phylocomr/src'
installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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)