* installing *source* package ‘phylocomr’ ... ** package ‘phylocomr’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-13 (GCC) 13.2.0’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/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-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c libphylocom/io.c -o libphylocom/io.o gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c libphylocom/new2fy.c -o libphylocom/new2fy.o gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c libphylocom/traits.c -o libphylocom/traits.o gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c libphylocom/comstruct.c -o libphylocom/comstruct.o gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c libphylocom/nrutil.c -o libphylocom/nrutil.o gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c libphylocom/fy2new.c -o libphylocom/fy2new.o libphylocom/comstruct.c: In function 'NodeSig': libphylocom/comstruct.c:1241:34: warning: '*test_r[]' may be used uninitialized [-Wmaybe-uninitialized] 1241 | (int) test_r[(int) ((float) RUNS * 0.5)], ordHI, | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ libphylocom/comstruct.c:1255:34: warning: '*test_r[]' may be used uninitialized [-Wmaybe-uninitialized] 1255 | (int) test_r[(int) ((float) RUNS * 0.5)], ordHI, | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ libphylocom/comstruct.c:1262:32: warning: '*test_r[]' may be used uninitialized [-Wmaybe-uninitialized] 1262 | (int) test_r[(int) ((float) RUNS * 0.5)], ordHI, | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c libphylocom/bladj.c -o libphylocom/bladj.o gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c libphylocom/comnode.c -o libphylocom/comnode.o gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c libphylocom/prune.c -o libphylocom/prune.o gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c libphylocom/comtrait.c -o libphylocom/comtrait.o gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c libphylocom/stats.c -o libphylocom/stats.o gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c libphylocom/combase.c -o libphylocom/combase.o gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c libphylocom/main.c -o libphylocom/main.o gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c libphylocom/ecomain.c -o libphylocom/ecomain.o gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c libphylocom/phylomatic.c -o libphylocom/phylomatic.o gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c nothing.c -o nothing.o gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c register.c -o register.o mkdir -p ../inst/bin gcc-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-13 -shared -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -o phylocomr.so nothing.o register.o gcc-13 -I/usr/local/include -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -o phylocom libphylocom/main.o -Llibphylocom -lphylocom -lm cp -f phylocom ../inst/bin gcc-13 -I/usr/local/include -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -o ecovolve libphylocom/ecomain.o -Llibphylocom -lphylocom -lm cp -f ecovolve ../inst/bin gcc-13 -I/usr/local/include -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -o phylomatic libphylocom/phylomatic.o -Llibphylocom -lphylocom -lm cp -f phylomatic ../inst/bin make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/phylocomr/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/phylocomr/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/phylocomr/src' installing to /data/gannet/ripley/R/packages/tests-devel/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)