* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘phylocomr’ ...
** package ‘phylocomr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.2.0-8) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpO9vSbm/R.INSTALL2d2971172f02f3/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-14 -I"/home/hornik/tmp/R.check/r-patched-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
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-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-14 -I"/home/hornik/tmp/R.check/r-patched-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-14 -I"/home/hornik/tmp/R.check/r-patched-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-14 -I"/home/hornik/tmp/R.check/r-patched-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-14 -I"/home/hornik/tmp/R.check/r-patched-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-14 -I"/home/hornik/tmp/R.check/r-patched-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-14 -I"/home/hornik/tmp/R.check/r-patched-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-14 -I"/home/hornik/tmp/R.check/r-patched-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-14 -I"/home/hornik/tmp/R.check/r-patched-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-14 -I"/home/hornik/tmp/R.check/r-patched-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-14 -I"/home/hornik/tmp/R.check/r-patched-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
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-14 -I"/home/hornik/tmp/R.check/r-patched-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-14 -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-14 -I"/home/hornik/tmp/R.check/r-patched-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
gcc-14 -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-14 -I"/home/hornik/tmp/R.check/r-patched-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-14 -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-14 -I"/home/hornik/tmp/R.check/r-patched-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-14 -I"/home/hornik/tmp/R.check/r-patched-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-14 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o phylocomr.so nothing.o register.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpO9vSbm/R.INSTALL2d2971172f02f3/phylocomr/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpO9vSbm/R.INSTALL2d2971172f02f3/phylocomr/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpO9vSbm/R.INSTALL2d2971172f02f3/phylocomr/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-phylocomr/00new/phylocomr/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘phylocomr’
finding HTML links ... done
executables html
ph_aot html
ph_bladj html
ph_comdist html
ph_comstruct html
ph_comtrait html
ph_ecovolve html
ph_pd html
ph_phylomatic html
ph_rao html
phylocomr-inputs html
phylocomr-package html
*** 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)