autoreconf: Entering directory `.' autoreconf: configure.ac: not using Gettext autoreconf: running: aclocal --force autoreconf: configure.ac: tracing autoreconf: configure.ac: not using Libtool autoreconf: running: /usr/bin/autoconf --force autoreconf: running: /usr/bin/autoheader --force autoreconf: running: automake --add-missing --copy --force-missing configure.ac:16: installing './compile' configure.ac:14: installing './config.guess' configure.ac:14: installing './config.sub' configure.ac:5: installing './install-sh' configure.ac:5: installing './missing' src/Makefile.am: installing './depcomp' autoreconf: Leaving directory `.' 21/configure.ac phyml-3.3.20200621/doc/ phyml-3.3.20200621/doc/Makefile.am phyml-3.3.20200621/doc/fig/ phyml-3.3.20200621/doc/fig/phyrexlog.pdf phyml-3.3.20200621/doc/fig/phytimetrace.pdf phyml-3.3.20200621/doc/naturemag.bst phyml-3.3.20200621/doc/phyml-manual.pdf phyml-3.3.20200621/doc/phyml-manual.tex phyml-3.3.20200621/doc/ref.bib phyml-3.3.20200621/examples/ phyml-3.3.20200621/examples/lg4x/ phyml-3.3.20200621/examples/lg4x/X1.mat phyml-3.3.20200621/examples/lg4x/X2.mat phyml-3.3.20200621/examples/lg4x/X3.mat phyml-3.3.20200621/examples/lg4x/X4.mat phyml-3.3.20200621/examples/lg4x/lg4x.xml phyml-3.3.20200621/examples/nexus_example.nxs phyml-3.3.20200621/examples/nucleic phyml-3.3.20200621/examples/phyrex/ phyml-3.3.20200621/examples/phyrex/flu.xml phyml-3.3.20200621/examples/phyrex/h1n1.nxs phyml-3.3.20200621/examples/phyrex/usa_coord.txt phyml-3.3.20200621/examples/phytime/ phyml-3.3.20200621/examples/phytime/dating_example.xml phyml-3.3.20200621/examples/phytime/seq.txt phyml-3.3.20200621/examples/proteic phyml-3.3.20200621/src/ phyml-3.3.20200621/src/Makefile.am phyml-3.3.20200621/src/Makefile_mc.am phyml-3.3.20200621/src/Makefile_r.am phyml-3.3.20200621/src/alrt.c phyml-3.3.20200621/src/alrt.h phyml-3.3.20200621/src/ancestral.c phyml-3.3.20200621/src/ancestral.h phyml-3.3.20200621/src/avx.c phyml-3.3.20200621/src/avx.h phyml-3.3.20200621/src/beagle_utils.c phyml-3.3.20200621/src/beagle_utils.h phyml-3.3.20200621/src/bionj.c phyml-3.3.20200621/src/bionj.h phyml-3.3.20200621/src/checkpoint.c phyml-3.3.20200621/src/checkpoint.h phyml-3.3.20200621/src/cl.c phyml-3.3.20200621/src/cl.h phyml-3.3.20200621/src/date.c phyml-3.3.20200621/src/date.h phyml-3.3.20200621/src/draw.c phyml-3.3.20200621/src/draw.h phyml-3.3.20200621/src/eigen.c phyml-3.3.20200621/src/eigen.h phyml-3.3.20200621/src/free.c phyml-3.3.20200621/src/free.h phyml-3.3.20200621/src/geo.c phyml-3.3.20200621/src/geo.h phyml-3.3.20200621/src/help.c phyml-3.3.20200621/src/help.h phyml-3.3.20200621/src/init.c phyml-3.3.20200621/src/init.h phyml-3.3.20200621/src/interface.c phyml-3.3.20200621/src/interface.h phyml-3.3.20200621/src/invitee.c phyml-3.3.20200621/src/invitee.h phyml-3.3.20200621/src/io.c phyml-3.3.20200621/src/io.h phyml-3.3.20200621/src/lk.c phyml-3.3.20200621/src/lk.h phyml-3.3.20200621/src/m4.c phyml-3.3.20200621/src/m4.h phyml-3.3.20200621/src/main.c phyml-3.3.20200621/src/make.c phyml-3.3.20200621/src/make.h phyml-3.3.20200621/src/mcmc.c phyml-3.3.20200621/src/mcmc.h phyml-3.3.20200621/src/mg.c phyml-3.3.20200621/src/mg.h phyml-3.3.20200621/src/mixt.c phyml-3.3.20200621/src/mixt.h phyml-3.3.20200621/src/models.c phyml-3.3.20200621/src/models.h phyml-3.3.20200621/src/mpi_boot.c phyml-3.3.20200621/src/mpi_boot.h phyml-3.3.20200621/src/mxml.h phyml-3.3.20200621/src/nexus.c phyml-3.3.20200621/src/nexus.h phyml-3.3.20200621/src/optimiz.c phyml-3.3.20200621/src/optimiz.h phyml-3.3.20200621/src/pars.c phyml-3.3.20200621/src/pars.h phyml-3.3.20200621/src/phyrex.c phyml-3.3.20200621/src/phyrex.h phyml-3.3.20200621/src/rates.c phyml-3.3.20200621/src/rates.h phyml-3.3.20200621/src/rrw.c phyml-3.3.20200621/src/rrw.h phyml-3.3.20200621/src/rw.c phyml-3.3.20200621/src/rw.h phyml-3.3.20200621/src/rwrapper.c phyml-3.3.20200621/src/rwrapper.h phyml-3.3.20200621/src/simu.c phyml-3.3.20200621/src/simu.h phyml-3.3.20200621/src/slfv.c phyml-3.3.20200621/src/slfv.h phyml-3.3.20200621/src/spr.c phyml-3.3.20200621/src/spr.h phyml-3.3.20200621/src/sse.c phyml-3.3.20200621/src/sse.h phyml-3.3.20200621/src/stats.c phyml-3.3.20200621/src/stats.h phyml-3.3.20200621/src/tbe.c phyml-3.3.20200621/src/tbe.h phyml-3.3.20200621/src/times.c phyml-3.3.20200621/src/times.h phyml-3.3.20200621/src/tiporder.c phyml-3.3.20200621/src/tiporder.h phyml-3.3.20200621/src/utilities.c phyml-3.3.20200621/src/utilities.h phyml-3.3.20200621/src/xml.c phyml-3.3.20200621/src/xml.h checking for a BSD-compatible install... /usr/bin/ginstall -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking build system type... i586-slackware-linux-gnu checking host system type... i586-slackware-linux-gnu checking for gcc... gcc 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 gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... gcc3 checking dependency style of gcc... (cached) gcc3 checking for log in -lm... yes checking how to run the C preprocessor... gcc -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 float.h usability... yes checking float.h presence... yes checking for float.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking for pdflatex... pdflatex checking for latex... latex checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for vprintf... yes checking for _doprnt... no checking for floor... yes checking for pow... yes checking for rint... yes checking for sqrt... yes checking for strchr... yes checking for strstr... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating doc/Makefile config.status: creating config.h config.status: executing depfiles commands make all-recursive make[1]: Entering directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621' Making all in src make[2]: Entering directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621/src' .: Building [phyml]. Version 3.3.20200621 :. gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.c mv -f .deps/main.Tpo .deps/main.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT utilities.o -MD -MP -MF .deps/utilities.Tpo -c -o utilities.o utilities.c mv -f .deps/utilities.Tpo .deps/utilities.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 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-Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT interface.o -MD -MP -MF .deps/interface.Tpo -c -o interface.o interface.c mv -f .deps/interface.Tpo .deps/interface.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT cl.o -MD -MP -MF .deps/cl.Tpo -c -o cl.o cl.c mv -f .deps/cl.Tpo .deps/cl.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall 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-fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT rates.o -MD -MP -MF .deps/rates.Tpo -c -o rates.o rates.c mv -f .deps/rates.Tpo .deps/rates.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT mcmc.o -MD -MP -MF .deps/mcmc.Tpo -c -o mcmc.o mcmc.c mv -f .deps/mcmc.Tpo .deps/mcmc.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT times.o -MD -MP -MF .deps/times.Tpo -c -o times.o times.c mv -f .deps/times.Tpo .deps/times.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT tiporder.o -MD -MP -MF .deps/tiporder.Tpo -c -o tiporder.o tiporder.c mv -f .deps/tiporder.Tpo .deps/tiporder.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT io.o -MD -MP -MF .deps/io.Tpo -c -o io.o io.c io.c: In function ‘Print_Fp_Out’: io.c:2315:47: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 6 [-Wformat-truncation=] 2315 | if (precision > 0) snprintf (format, 8, "%%.%df", precision); | ^~ io.c:2315:43: note: directive argument in the range [1, 2147483647] 2315 | if (precision > 0) snprintf (format, 8, "%%.%df", precision); | ^~~~~~~~ io.c:2315:22: note: ‘snprintf’ output between 5 and 14 bytes into a destination of size 8 2315 | if (precision > 0) snprintf (format, 8, "%%.%df", precision); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/io.Tpo .deps/io.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT make.o -MD -MP -MF .deps/make.Tpo -c -o make.o make.c mv -f .deps/make.Tpo .deps/make.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT nexus.o -MD -MP -MF .deps/nexus.Tpo -c -o nexus.o nexus.c mv -f .deps/nexus.Tpo .deps/nexus.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT init.o -MD -MP -MF .deps/init.Tpo -c -o init.o init.c mv -f .deps/init.Tpo .deps/init.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT xml.o -MD -MP -MF .deps/xml.Tpo -c -o xml.o xml.c mv -f .deps/xml.Tpo .deps/xml.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT date.o -MD -MP -MF .deps/date.Tpo -c -o date.o date.c mv -f .deps/date.Tpo .deps/date.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT sse.o -MD -MP -MF .deps/sse.Tpo -c -o sse.o sse.c mv -f .deps/sse.Tpo .deps/sse.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT avx.o -MD -MP -MF .deps/avx.Tpo -c -o avx.o avx.c mv -f .deps/avx.Tpo .deps/avx.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT tbe.o -MD -MP -MF .deps/tbe.Tpo -c -o tbe.o tbe.c mv -f .deps/tbe.Tpo .deps/tbe.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT ancestral.o -MD -MP -MF .deps/ancestral.Tpo -c -o ancestral.o ancestral.c mv -f .deps/ancestral.Tpo .deps/ancestral.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT mixt.o -MD -MP -MF .deps/mixt.Tpo -c -o mixt.o mixt.c mv -f .deps/mixt.Tpo .deps/mixt.Po gcc -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -o phyml main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o draw.o stats.o rates.o mcmc.o times.o tiporder.o io.o make.o nexus.o init.o xml.o date.o sse.o avx.o tbe.o ancestral.o mixt.o -lm -lm Done. make[2]: Leaving directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621/src' make[2]: Entering directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621' make[2]: Leaving directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621' make[1]: Leaving directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621' Making install in src make[1]: Entering directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621/src' .: Building [phyml]. Version 3.3.20200621 :. Done. make[2]: Entering directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621/src' /usr/bin/mkdir -p '/usr/src/slapt-src/academic/PhyML/package-PhyML/usr/bin' /usr/bin/ginstall -c phyml '/usr/src/slapt-src/academic/PhyML/package-PhyML/usr/bin' make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621/src' make[1]: Leaving directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621/src' make[1]: Entering directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621' make[2]: Entering directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621' make[1]: Leaving directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621' autoreconf: Entering directory `.' autoreconf: configure.ac: not using Gettext autoreconf: running: aclocal --force autoreconf: configure.ac: tracing autoreconf: configure.ac: not using Libtool autoreconf: running: /usr/bin/autoconf --force autoreconf: running: /usr/bin/autoheader --force autoreconf: running: automake --add-missing --copy --force-missing autoreconf: Leaving directory `.' checking for a BSD-compatible install... /usr/bin/ginstall -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking build system type... i586-slackware-linux-gnu checking host system type... i586-slackware-linux-gnu checking for gcc... gcc 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 gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... gcc3 checking dependency style of gcc... (cached) gcc3 checking for log in -lm... yes checking how to run the C preprocessor... gcc -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 float.h usability... yes checking float.h presence... yes checking for float.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking for pdflatex... pdflatex checking for latex... latex checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for vprintf... yes checking for _doprnt... no checking for floor... yes checking for pow... yes checking for rint... yes checking for sqrt... yes checking for strchr... yes checking for strstr... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating doc/Makefile config.status: creating config.h config.status: executing depfiles commands make all-recursive make[1]: Entering directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621' Making all in src make[2]: Entering directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621/src' .: Building [phyml-mpi]. Version 3.3.20200621 :. mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.c mv -f .deps/main.Tpo .deps/main.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT utilities.o -MD -MP -MF .deps/utilities.Tpo -c -o utilities.o utilities.c mv -f .deps/utilities.Tpo .deps/utilities.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT optimiz.o -MD -MP -MF .deps/optimiz.Tpo -c -o optimiz.o optimiz.c mv -f .deps/optimiz.Tpo .deps/optimiz.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT lk.o -MD -MP -MF .deps/lk.Tpo -c -o lk.o lk.c In file included from lk.h:18, from lk.c:14: utilities.h:18: warning: "_POSIX_C_SOURCE" redefined 18 | #define _POSIX_C_SOURCE 200112L | In file included from /usr/include/assert.h:35, from lk.c:13: /usr/include/features.h:310: note: this is the location of the previous definition 310 | # define _POSIX_C_SOURCE 199506L | mv -f .deps/lk.Tpo .deps/lk.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT bionj.o -MD -MP -MF .deps/bionj.Tpo -c -o bionj.o bionj.c mv -f .deps/bionj.Tpo .deps/bionj.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT models.o -MD -MP -MF .deps/models.Tpo -c -o models.o models.c mv -f .deps/models.Tpo .deps/models.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT free.o -MD -MP -MF .deps/free.Tpo -c -o free.o free.c mv -f .deps/free.Tpo .deps/free.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT help.o -MD -MP -MF .deps/help.Tpo -c -o help.o help.c mv -f .deps/help.Tpo .deps/help.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT simu.o -MD -MP -MF .deps/simu.Tpo -c -o simu.o simu.c mv -f .deps/simu.Tpo .deps/simu.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT eigen.o -MD -MP -MF .deps/eigen.Tpo -c -o eigen.o eigen.c mv -f .deps/eigen.Tpo .deps/eigen.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT pars.o -MD -MP -MF .deps/pars.Tpo -c -o pars.o pars.c mv -f .deps/pars.Tpo .deps/pars.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT alrt.o -MD -MP -MF .deps/alrt.Tpo -c -o alrt.o alrt.c mv -f .deps/alrt.Tpo .deps/alrt.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT interface.o -MD -MP -MF .deps/interface.Tpo -c -o interface.o interface.c mv -f .deps/interface.Tpo .deps/interface.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT cl.o -MD -MP -MF .deps/cl.Tpo -c -o cl.o cl.c In file included from cl.h:21, from cl.c:13: utilities.h:18: warning: "_POSIX_C_SOURCE" redefined 18 | #define _POSIX_C_SOURCE 200112L | In file included from /usr/include/unistd.h:25, from cl.h:19, from cl.c:13: /usr/include/features.h:310: note: this is the location of the previous definition 310 | # define _POSIX_C_SOURCE 199506L | mv -f .deps/cl.Tpo .deps/cl.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT spr.o -MD -MP -MF .deps/spr.Tpo -c -o spr.o spr.c mv -f .deps/spr.Tpo .deps/spr.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT draw.o -MD -MP -MF .deps/draw.Tpo -c -o draw.o draw.c mv -f .deps/draw.Tpo .deps/draw.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT stats.o -MD -MP -MF .deps/stats.Tpo -c -o stats.o stats.c mv -f .deps/stats.Tpo .deps/stats.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT rates.o -MD -MP -MF .deps/rates.Tpo -c -o rates.o rates.c mv -f .deps/rates.Tpo .deps/rates.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT mcmc.o -MD -MP -MF .deps/mcmc.Tpo -c -o mcmc.o mcmc.c mv -f .deps/mcmc.Tpo .deps/mcmc.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT times.o -MD -MP -MF .deps/times.Tpo -c -o times.o times.c mv -f .deps/times.Tpo .deps/times.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT tiporder.o -MD -MP -MF .deps/tiporder.Tpo -c -o tiporder.o tiporder.c mv -f .deps/tiporder.Tpo .deps/tiporder.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT mg.o -MD -MP -MF .deps/mg.Tpo -c -o mg.o mg.c mv -f .deps/mg.Tpo .deps/mg.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT io.o -MD -MP -MF .deps/io.Tpo -c -o io.o io.c io.c: In function ‘Print_Fp_Out’: io.c:2315:47: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 6 [-Wformat-truncation=] 2315 | if (precision > 0) snprintf (format, 8, "%%.%df", precision); | ^~ io.c:2315:43: note: directive argument in the range [1, 2147483647] 2315 | if (precision > 0) snprintf (format, 8, "%%.%df", precision); | ^~~~~~~~ io.c:2315:22: note: ‘snprintf’ output between 5 and 14 bytes into a destination of size 8 2315 | if (precision > 0) snprintf (format, 8, "%%.%df", precision); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/io.Tpo .deps/io.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT make.o -MD -MP -MF .deps/make.Tpo -c -o make.o make.c mv -f .deps/make.Tpo .deps/make.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT nexus.o -MD -MP -MF .deps/nexus.Tpo -c -o nexus.o nexus.c mv -f .deps/nexus.Tpo .deps/nexus.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT init.o -MD -MP -MF .deps/init.Tpo -c -o init.o init.c mv -f .deps/init.Tpo .deps/init.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT xml.o -MD -MP -MF .deps/xml.Tpo -c -o xml.o xml.c mv -f .deps/xml.Tpo .deps/xml.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT mixt.o -MD -MP -MF .deps/mixt.Tpo -c -o mixt.o mixt.c mv -f .deps/mixt.Tpo .deps/mixt.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT tbe.o -MD -MP -MF .deps/tbe.Tpo -c -o tbe.o tbe.c mv -f .deps/tbe.Tpo .deps/tbe.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT date.o -MD -MP -MF .deps/date.Tpo -c -o date.o date.c mv -f .deps/date.Tpo .deps/date.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT sse.o -MD -MP -MF .deps/sse.Tpo -c -o sse.o sse.c In file included from sse.h:18, from sse.c:14: utilities.h:18: warning: "_POSIX_C_SOURCE" redefined 18 | #define _POSIX_C_SOURCE 200112L | In file included from /usr/include/assert.h:35, from sse.c:13: /usr/include/features.h:310: note: this is the location of the previous definition 310 | # define _POSIX_C_SOURCE 199506L | mv -f .deps/sse.Tpo .deps/sse.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT avx.o -MD -MP -MF .deps/avx.Tpo -c -o avx.o avx.c In file included from avx.h:18, from avx.c:14: utilities.h:18: warning: "_POSIX_C_SOURCE" redefined 18 | #define _POSIX_C_SOURCE 200112L | In file included from /usr/include/assert.h:35, from avx.c:13: /usr/include/features.h:310: note: this is the location of the previous definition 310 | # define _POSIX_C_SOURCE 199506L | mv -f .deps/avx.Tpo .deps/avx.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT ancestral.o -MD -MP -MF .deps/ancestral.Tpo -c -o ancestral.o ancestral.c mv -f .deps/ancestral.Tpo .deps/ancestral.Po mpicc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT mpi_boot.o -MD -MP -MF .deps/mpi_boot.Tpo -c -o mpi_boot.o mpi_boot.c mv -f .deps/mpi_boot.Tpo .deps/mpi_boot.Po mpicc -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -o phyml-mpi main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o draw.o stats.o rates.o mcmc.o times.o tiporder.o mg.o io.o make.o nexus.o init.o xml.o mixt.o tbe.o date.o sse.o avx.o ancestral.o mpi_boot.o -lm -lm Done. make[2]: Leaving directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621/src' make[2]: Entering directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621' make[2]: Leaving directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621' make[1]: Leaving directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621' Making install in src make[1]: Entering directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621/src' .: Building [phyml-mpi]. Version 3.3.20200621 :. Done. make[2]: Entering directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621/src' /usr/bin/mkdir -p '/usr/src/slapt-src/academic/PhyML/package-PhyML/usr/bin' /usr/bin/ginstall -c phyml-mpi '/usr/src/slapt-src/academic/PhyML/package-PhyML/usr/bin' make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621/src' make[1]: Leaving directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621/src' make[1]: Entering directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621' make[2]: Entering directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621' make[1]: Leaving directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621' autoreconf: Entering directory `.' autoreconf: configure.ac: not using Gettext autoreconf: running: aclocal --force autoreconf: configure.ac: tracing autoreconf: configure.ac: not using Libtool autoreconf: running: /usr/bin/autoconf --force autoreconf: running: /usr/bin/autoheader --force autoreconf: running: automake --add-missing --copy --force-missing autoreconf: Leaving directory `.' checking for a BSD-compatible install... /usr/bin/ginstall -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking build system type... i586-slackware-linux-gnu checking host system type... i586-slackware-linux-gnu checking for gcc... gcc 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 gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... gcc3 checking dependency style of gcc... (cached) gcc3 checking for log in -lm... yes checking how to run the C preprocessor... gcc -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 float.h usability... yes checking float.h presence... yes checking for float.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking for pdflatex... pdflatex checking for latex... latex checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for vprintf... yes checking for _doprnt... no checking for floor... yes checking for pow... yes checking for rint... yes checking for sqrt... yes checking for strchr... yes checking for strstr... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating doc/Makefile config.status: creating config.h config.status: executing depfiles commands make all-recursive make[1]: Entering directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621' Making all in src make[2]: Entering directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621/src' .: Building [phyrex]. Version 3.3.20200621 :. gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.c mv -f .deps/main.Tpo .deps/main.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT utilities.o -MD -MP -MF .deps/utilities.Tpo -c -o utilities.o utilities.c mv -f .deps/utilities.Tpo .deps/utilities.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT optimiz.o -MD -MP -MF .deps/optimiz.Tpo -c -o optimiz.o optimiz.c mv -f .deps/optimiz.Tpo .deps/optimiz.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT lk.o -MD -MP -MF .deps/lk.Tpo -c -o lk.o lk.c mv -f .deps/lk.Tpo .deps/lk.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT bionj.o -MD -MP -MF .deps/bionj.Tpo -c -o bionj.o bionj.c mv -f .deps/bionj.Tpo .deps/bionj.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT models.o -MD -MP -MF .deps/models.Tpo -c -o models.o models.c mv -f .deps/models.Tpo .deps/models.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT free.o -MD -MP -MF .deps/free.Tpo -c -o free.o free.c mv -f .deps/free.Tpo .deps/free.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT help.o -MD -MP -MF .deps/help.Tpo -c -o help.o help.c mv -f .deps/help.Tpo .deps/help.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT simu.o -MD -MP -MF .deps/simu.Tpo -c -o simu.o simu.c mv -f .deps/simu.Tpo .deps/simu.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT eigen.o -MD -MP -MF .deps/eigen.Tpo -c -o eigen.o eigen.c mv -f .deps/eigen.Tpo .deps/eigen.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT pars.o -MD -MP -MF .deps/pars.Tpo -c -o pars.o pars.c mv -f .deps/pars.Tpo .deps/pars.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT alrt.o -MD -MP -MF .deps/alrt.Tpo -c -o alrt.o alrt.c mv -f .deps/alrt.Tpo .deps/alrt.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT interface.o -MD -MP -MF .deps/interface.Tpo -c -o interface.o interface.c mv -f .deps/interface.Tpo .deps/interface.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT cl.o -MD -MP -MF .deps/cl.Tpo -c -o cl.o cl.c mv -f .deps/cl.Tpo .deps/cl.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT spr.o -MD -MP -MF .deps/spr.Tpo -c -o spr.o spr.c mv -f .deps/spr.Tpo .deps/spr.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT draw.o -MD -MP -MF .deps/draw.Tpo -c -o draw.o draw.c mv -f .deps/draw.Tpo .deps/draw.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT stats.o -MD -MP -MF .deps/stats.Tpo -c -o stats.o stats.c mv -f .deps/stats.Tpo .deps/stats.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT rates.o -MD -MP -MF .deps/rates.Tpo -c -o rates.o rates.c mv -f .deps/rates.Tpo .deps/rates.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT mcmc.o -MD -MP -MF .deps/mcmc.Tpo -c -o mcmc.o mcmc.c mv -f .deps/mcmc.Tpo .deps/mcmc.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT times.o -MD -MP -MF .deps/times.Tpo -c -o times.o times.c mv -f .deps/times.Tpo .deps/times.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT tiporder.o -MD -MP -MF .deps/tiporder.Tpo -c -o tiporder.o tiporder.c mv -f .deps/tiporder.Tpo .deps/tiporder.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT mg.o -MD -MP -MF .deps/mg.Tpo -c -o mg.o mg.c mv -f .deps/mg.Tpo .deps/mg.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT io.o -MD -MP -MF .deps/io.Tpo -c -o io.o io.c io.c: In function ‘Print_Fp_Out’: io.c:2315:47: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 6 [-Wformat-truncation=] 2315 | if (precision > 0) snprintf (format, 8, "%%.%df", precision); | ^~ io.c:2315:43: note: directive argument in the range [1, 2147483647] 2315 | if (precision > 0) snprintf (format, 8, "%%.%df", precision); | ^~~~~~~~ io.c:2315:22: note: ‘snprintf’ output between 5 and 14 bytes into a destination of size 8 2315 | if (precision > 0) snprintf (format, 8, "%%.%df", precision); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/io.Tpo .deps/io.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT make.o -MD -MP -MF .deps/make.Tpo -c -o make.o make.c mv -f .deps/make.Tpo .deps/make.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT nexus.o -MD -MP -MF .deps/nexus.Tpo -c -o nexus.o nexus.c mv -f .deps/nexus.Tpo .deps/nexus.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT init.o -MD -MP -MF .deps/init.Tpo -c -o init.o init.c mv -f .deps/init.Tpo .deps/init.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT xml.o -MD -MP -MF .deps/xml.Tpo -c -o xml.o xml.c mv -f .deps/xml.Tpo .deps/xml.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT mixt.o -MD -MP -MF .deps/mixt.Tpo -c -o mixt.o mixt.c mv -f .deps/mixt.Tpo .deps/mixt.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT date.o -MD -MP -MF .deps/date.Tpo -c -o date.o date.c mv -f .deps/date.Tpo .deps/date.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT tbe.o -MD -MP -MF .deps/tbe.Tpo -c -o tbe.o tbe.c mv -f .deps/tbe.Tpo .deps/tbe.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT sse.o -MD -MP -MF .deps/sse.Tpo -c -o sse.o sse.c mv -f .deps/sse.Tpo .deps/sse.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT avx.o -MD -MP -MF .deps/avx.Tpo -c -o avx.o avx.c mv -f .deps/avx.Tpo .deps/avx.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT ancestral.o -MD -MP -MF .deps/ancestral.Tpo -c -o ancestral.o ancestral.c mv -f .deps/ancestral.Tpo .deps/ancestral.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT phyrex.o -MD -MP -MF .deps/phyrex.Tpo -c -o phyrex.o phyrex.c mv -f .deps/phyrex.Tpo .deps/phyrex.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT slfv.o -MD -MP -MF .deps/slfv.Tpo -c -o slfv.o slfv.c mv -f .deps/slfv.Tpo .deps/slfv.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT rw.o -MD -MP -MF .deps/rw.Tpo -c -o rw.o rw.c mv -f .deps/rw.Tpo .deps/rw.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT rrw.o -MD -MP -MF .deps/rrw.Tpo -c -o rrw.o rrw.c rrw.c: In function ‘RRW_Lk’: rrw.c:20:16: warning: variable ‘d_ic’ set but not used [-Wunused-but-set-variable] 20 | phydbl d_fwd,d_ic,d_coal,d_sigsq_scale; | ^~~~ mv -f .deps/rrw.Tpo .deps/rrw.Po gcc -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -o phyrex main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o draw.o stats.o rates.o mcmc.o times.o tiporder.o mg.o io.o make.o nexus.o init.o xml.o mixt.o date.o tbe.o sse.o avx.o ancestral.o phyrex.o slfv.o rw.o rrw.o -lm -lm Done. make[2]: Leaving directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621/src' make[2]: Entering directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621' make[2]: Leaving directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621' make[1]: Leaving directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621' Making install in src make[1]: Entering directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621/src' .: Building [phyrex]. Version 3.3.20200621 :. Done. make[2]: Entering directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621/src' /usr/bin/mkdir -p '/usr/src/slapt-src/academic/PhyML/package-PhyML/usr/bin' /usr/bin/ginstall -c phyrex '/usr/src/slapt-src/academic/PhyML/package-PhyML/usr/bin' make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621/src' make[1]: Leaving directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621/src' make[1]: Entering directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621' make[2]: Entering directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621' make[1]: Leaving directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621' autoreconf: Entering directory `.' autoreconf: configure.ac: not using Gettext autoreconf: running: aclocal --force autoreconf: configure.ac: tracing autoreconf: configure.ac: not using Libtool autoreconf: running: /usr/bin/autoconf --force autoreconf: running: /usr/bin/autoheader --force autoreconf: running: automake --add-missing --copy --force-missing autoreconf: Leaving directory `.' checking for a BSD-compatible install... /usr/bin/ginstall -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking build system type... i586-slackware-linux-gnu checking host system type... i586-slackware-linux-gnu checking for gcc... gcc 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 gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... gcc3 checking dependency style of gcc... (cached) gcc3 checking for log in -lm... yes checking how to run the C preprocessor... gcc -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 float.h usability... yes checking float.h presence... yes checking for float.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking for pdflatex... pdflatex checking for latex... latex checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for vprintf... yes checking for _doprnt... no checking for floor... yes checking for pow... yes checking for rint... yes checking for sqrt... yes checking for strchr... yes checking for strstr... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating doc/Makefile config.status: creating config.h config.status: executing depfiles commands make all-recursive make[1]: Entering directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621' Making all in src make[2]: Entering directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621/src' .: Building [phytime]. Version 3.3.20200621 :. gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.c mv -f .deps/main.Tpo .deps/main.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT utilities.o -MD -MP -MF .deps/utilities.Tpo -c -o utilities.o utilities.c mv -f .deps/utilities.Tpo .deps/utilities.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT optimiz.o -MD -MP -MF .deps/optimiz.Tpo -c -o optimiz.o optimiz.c mv -f .deps/optimiz.Tpo .deps/optimiz.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT lk.o -MD -MP -MF .deps/lk.Tpo -c -o lk.o lk.c mv -f .deps/lk.Tpo .deps/lk.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT bionj.o -MD -MP -MF .deps/bionj.Tpo -c -o bionj.o bionj.c mv -f .deps/bionj.Tpo .deps/bionj.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT models.o -MD -MP -MF .deps/models.Tpo -c -o models.o models.c mv -f .deps/models.Tpo .deps/models.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT free.o -MD -MP -MF .deps/free.Tpo -c -o free.o free.c mv -f .deps/free.Tpo .deps/free.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT help.o -MD -MP -MF .deps/help.Tpo -c -o help.o help.c mv -f .deps/help.Tpo .deps/help.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT simu.o -MD -MP -MF .deps/simu.Tpo -c -o simu.o simu.c mv -f .deps/simu.Tpo .deps/simu.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT eigen.o -MD -MP -MF .deps/eigen.Tpo -c -o eigen.o eigen.c mv -f .deps/eigen.Tpo .deps/eigen.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT pars.o -MD -MP -MF .deps/pars.Tpo -c -o pars.o pars.c mv -f .deps/pars.Tpo .deps/pars.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT alrt.o -MD -MP -MF .deps/alrt.Tpo -c -o alrt.o alrt.c mv -f .deps/alrt.Tpo .deps/alrt.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT interface.o -MD -MP -MF .deps/interface.Tpo -c -o interface.o interface.c mv -f .deps/interface.Tpo .deps/interface.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT cl.o -MD -MP -MF .deps/cl.Tpo -c -o cl.o cl.c mv -f .deps/cl.Tpo .deps/cl.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT spr.o -MD -MP -MF .deps/spr.Tpo -c -o spr.o spr.c mv -f .deps/spr.Tpo .deps/spr.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT times.o -MD -MP -MF .deps/times.Tpo -c -o times.o times.c mv -f .deps/times.Tpo .deps/times.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT draw.o -MD -MP -MF .deps/draw.Tpo -c -o draw.o draw.c mv -f .deps/draw.Tpo .deps/draw.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT rates.o -MD -MP -MF .deps/rates.Tpo -c -o rates.o rates.c mv -f .deps/rates.Tpo .deps/rates.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT mcmc.o -MD -MP -MF .deps/mcmc.Tpo -c -o mcmc.o mcmc.c mv -f .deps/mcmc.Tpo .deps/mcmc.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT stats.o -MD -MP -MF .deps/stats.Tpo -c -o stats.o stats.c mv -f .deps/stats.Tpo .deps/stats.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT mg.o -MD -MP -MF .deps/mg.Tpo -c -o mg.o mg.c mv -f .deps/mg.Tpo .deps/mg.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT tiporder.o -MD -MP -MF .deps/tiporder.Tpo -c -o tiporder.o tiporder.c mv -f .deps/tiporder.Tpo .deps/tiporder.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT io.o -MD -MP -MF .deps/io.Tpo -c -o io.o io.c io.c: In function ‘Print_Fp_Out’: io.c:2315:47: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 6 [-Wformat-truncation=] 2315 | if (precision > 0) snprintf (format, 8, "%%.%df", precision); | ^~ io.c:2315:43: note: directive argument in the range [1, 2147483647] 2315 | if (precision > 0) snprintf (format, 8, "%%.%df", precision); | ^~~~~~~~ io.c:2315:22: note: ‘snprintf’ output between 5 and 14 bytes into a destination of size 8 2315 | if (precision > 0) snprintf (format, 8, "%%.%df", precision); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/io.Tpo .deps/io.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT make.o -MD -MP -MF .deps/make.Tpo -c -o make.o make.c mv -f .deps/make.Tpo .deps/make.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT mixt.o -MD -MP -MF .deps/mixt.Tpo -c -o mixt.o mixt.c mv -f .deps/mixt.Tpo .deps/mixt.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT init.o -MD -MP -MF .deps/init.Tpo -c -o init.o init.c mv -f .deps/init.Tpo .deps/init.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT nexus.o -MD -MP -MF .deps/nexus.Tpo -c -o nexus.o nexus.c mv -f .deps/nexus.Tpo .deps/nexus.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT date.o -MD -MP -MF .deps/date.Tpo -c -o date.o date.c mv -f .deps/date.Tpo .deps/date.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT tbe.o -MD -MP -MF .deps/tbe.Tpo -c -o tbe.o tbe.c mv -f .deps/tbe.Tpo .deps/tbe.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT sse.o -MD -MP -MF .deps/sse.Tpo -c -o sse.o sse.c mv -f .deps/sse.Tpo .deps/sse.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT avx.o -MD -MP -MF .deps/avx.Tpo -c -o avx.o avx.c mv -f .deps/avx.Tpo .deps/avx.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT ancestral.o -MD -MP -MF .deps/ancestral.Tpo -c -o ancestral.o ancestral.c mv -f .deps/ancestral.Tpo .deps/ancestral.Po gcc -I. -I.. -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT xml.o -MD -MP -MF .deps/xml.Tpo -c -o xml.o xml.c mv -f .deps/xml.Tpo .deps/xml.Po gcc -O2 -march=i586 -mtune=i686 -mfma -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -o phytime main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o times.o draw.o rates.o mcmc.o stats.o mg.o tiporder.o io.o make.o mixt.o init.o nexus.o date.o tbe.o sse.o avx.o ancestral.o xml.o -lm -lm Done. make[2]: Leaving directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621/src' make[2]: Entering directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621' make[2]: Leaving directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621' make[1]: Leaving directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621' Making install in src make[1]: Entering directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621/src' .: Building [phytime]. Version 3.3.20200621 :. Done. make[2]: Entering directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621/src' /usr/bin/mkdir -p '/usr/src/slapt-src/academic/PhyML/package-PhyML/usr/bin' /usr/bin/ginstall -c phytime '/usr/src/slapt-src/academic/PhyML/package-PhyML/usr/bin' make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621/src' make[1]: Leaving directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621/src' make[1]: Entering directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621' make[2]: Entering directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621' make[1]: Leaving directory '/usr/src/slapt-src/academic/PhyML/phyml-3.3.20200621' Slackware package maker, version 3.14159265. Searching for symbolic links: No symbolic links were found, so we won't make an installation script. You can make your own later in ./install/doinst.sh and rebuild the package if you like. This next step is optional - you can set the directories in your package to some sane permissions. If any of the directories in your package have special permissions, then DO NOT reset them here! Would you like to reset all directory permissions to 755 (drwxr-xr-x) and directory ownerships to root.root ([y]es, [n]o)? n Creating Slackware package: /usr/src/slapt-src/academic/PhyML/PhyML-3.3.20200621-i586-1salix15.0.txz ./ install/ install/slack-desc usr/ usr/bin/ usr/bin/phyml usr/bin/phyml-mpi usr/bin/phyrex usr/bin/phytime usr/doc/ usr/doc/PhyML-3.3.20200621/ usr/doc/PhyML-3.3.20200621/COPYING usr/doc/PhyML-3.3.20200621/PhyML.SlackBuild usr/doc/PhyML-3.3.20200621/README.md usr/doc/PhyML-3.3.20200621/References usr/doc/PhyML-3.3.20200621/fig/ usr/doc/PhyML-3.3.20200621/fig/phyrexlog.pdf usr/doc/PhyML-3.3.20200621/fig/phytimetrace.pdf usr/doc/PhyML-3.3.20200621/phyml-manual.pdf usr/doc/PhyML-3.3.20200621/phyml-manual.tex usr/doc/PhyML-3.3.20200621/ref.bib usr/share/ usr/share/PhyML/ usr/share/PhyML/examples/ usr/share/PhyML/examples/lg4x/ usr/share/PhyML/examples/lg4x/X1.mat usr/share/PhyML/examples/lg4x/X2.mat usr/share/PhyML/examples/lg4x/X3.mat usr/share/PhyML/examples/lg4x/X4.mat usr/share/PhyML/examples/lg4x/lg4x.xml usr/share/PhyML/examples/nexus_example.nxs usr/share/PhyML/examples/nucleic usr/share/PhyML/examples/phyrex/ usr/share/PhyML/examples/phyrex/flu.xml usr/share/PhyML/examples/phyrex/h1n1.nxs usr/share/PhyML/examples/phyrex/usa_coord.txt usr/share/PhyML/examples/phytime/ usr/share/PhyML/examples/phytime/dating_example.xml usr/share/PhyML/examples/phytime/seq.txt usr/share/PhyML/examples/proteic Slackware package /usr/src/slapt-src/academic/PhyML/PhyML-3.3.20200621-i586-1salix15.0.txz created. Installing package PhyML-3.3.20200621-i586-1salix15.0... | PhyML (Phylogenetic estimation using Maximum Likelihood) | | PhyML is a software that estimates maximum likelihood phylogenies | from alignments of nucleotide or amino acid sequences. It provides a | wide range of options that were designed to facilitate standard | phylogenetic analyses. | | Home: http://code.google.com/p/phyml/ | References: /usr/doc/PhyML-3.3.20170530/References | | | |