------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/pkgconf-1.6.3,1.txz pkg: Cannot runscript POST-INSTALL:Bad file descriptor Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/m4-1.4.18_1,1.txz pkg: Cannot runscript POST-INSTALL:Bad file descriptor Installing /packages/All/autoconf-wrapper-20131203.txz Installing /packages/All/perl5-5.30.1.txz pkg: Cannot runscript POST-INSTALL:Bad file descriptor ===== Message from perl5-5.30.1: -- The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. Installing /packages/All/autoconf-2.69_3.txz pkg: Cannot runscript POST-INSTALL:Bad file descriptor Installing /packages/All/automake-1.16.1_2.txz pkg: Cannot runscript POST-INSTALL:Bad file descriptor Installing /packages/All/libtool-2.4.6_1.txz pkg: Cannot runscript POST-INSTALL:Bad file descriptor SUCCEEDED 00:00:04 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- ===> NOTICE: The phyml port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> phyml-3.3.20190909_1,1 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> NOTICE: The phyml port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> phyml-3.3.20190909_1,1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by phyml-3.3.20190909_1,1 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> NOTICE: The phyml port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> phyml-3.3.20190909_1,1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by phyml-3.3.20190909_1,1 for building => SHA256 Checksum OK for stephaneguindon-phyml-v3.3.20190909_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> NOTICE: The phyml port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> phyml-3.3.20190909_1,1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by phyml-3.3.20190909_1,1 for building ===> Extracting for phyml-3.3.20190909_1,1 => SHA256 Checksum OK for stephaneguindon-phyml-v3.3.20190909_GH0.tar.gz. Extracted Memory Use: 5.61M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for phyml-3.3.20190909_1,1 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> phyml-3.3.20190909_1,1 depends on package: pkgconf>=1.3.0_1 - found ===> phyml-3.3.20190909_1,1 depends on package: autoconf>=2.69 - found ===> phyml-3.3.20190909_1,1 depends on package: automake>=1.16.1 - found ===> phyml-3.3.20190909_1,1 depends on executable: libtoolize - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> phyml-3.3.20190909_1,1 depends on package: pkgconf>=1.3.0_1 - found ===> phyml-3.3.20190909_1,1 depends on package: autoconf>=2.69 - found ===> phyml-3.3.20190909_1,1 depends on package: automake>=1.16.1 - found ===> phyml-3.3.20190909_1,1 depends on executable: libtoolize - found ===> Configuring for phyml-3.3.20190909_1,1 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' configure: WARNING: unrecognized options: --disable-beagle configure: loading site script /xports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking build system type... x86_64-portbld-dragonfly5.9 checking host system type... x86_64-portbld-dragonfly5.9 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 cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking whether cc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of cc... gcc3 checking dependency style of cc... (cached) gcc3 checking for log in -lm... yes checking how to run the C preprocessor... cpp checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for float.h... (cached) 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... (cached) yes checking for pdflatex... no checking for latex... no configure: WARNING: Documentation will not be built! checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for vprintf... (cached) yes checking for _doprnt... no checking for floor... yes checking for pow... yes checking for rint... yes checking for sqrt... yes checking for strchr... (cached) yes checking for strstr... (cached) 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 configure: WARNING: unrecognized options: --disable-beagle SUCCEEDED 00:00:09 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for phyml-3.3.20190909_1,1 --- all --- /usr/bin/make all-recursive --- all-recursive --- Making all in src --- intro --- --- main.o --- --- utilities.o --- --- optimiz.o --- --- lk.o --- --- bionj.o --- --- models.o --- --- free.o --- --- help.o --- --- simu.o --- --- main.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.c --- utilities.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT utilities.o -MD -MP -MF .deps/utilities.Tpo -c -o utilities.o utilities.c --- optimiz.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT optimiz.o -MD -MP -MF .deps/optimiz.Tpo -c -o optimiz.o optimiz.c --- lk.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT lk.o -MD -MP -MF .deps/lk.Tpo -c -o lk.o lk.c --- bionj.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT bionj.o -MD -MP -MF .deps/bionj.Tpo -c -o bionj.o bionj.c --- models.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT models.o -MD -MP -MF .deps/models.Tpo -c -o models.o models.c --- free.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT free.o -MD -MP -MF .deps/free.Tpo -c -o free.o free.c --- help.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT help.o -MD -MP -MF .deps/help.Tpo -c -o help.o help.c --- simu.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT simu.o -MD -MP -MF .deps/simu.Tpo -c -o simu.o simu.c --- intro --- .: Building [phyml]. Version 3.3.20190909 :. --- eigen.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT eigen.o -MD -MP -MF .deps/eigen.Tpo -c -o eigen.o eigen.c --- main.o --- mv -f .deps/main.Tpo .deps/main.Po --- pars.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT pars.o -MD -MP -MF .deps/pars.Tpo -c -o pars.o pars.c --- help.o --- mv -f .deps/help.Tpo .deps/help.Po --- alrt.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT alrt.o -MD -MP -MF .deps/alrt.Tpo -c -o alrt.o alrt.c --- simu.o --- mv -f .deps/simu.Tpo .deps/simu.Po --- interface.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT interface.o -MD -MP -MF .deps/interface.Tpo -c -o interface.o interface.c --- alrt.o --- mv -f .deps/alrt.Tpo .deps/alrt.Po --- cl.o --- --- bionj.o --- mv -f .deps/bionj.Tpo .deps/bionj.Po --- cl.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT cl.o -MD -MP -MF .deps/cl.Tpo -c -o cl.o cl.c --- spr.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT spr.o -MD -MP -MF .deps/spr.Tpo -c -o spr.o spr.c --- free.o --- mv -f .deps/free.Tpo .deps/free.Po --- draw.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT draw.o -MD -MP -MF .deps/draw.Tpo -c -o draw.o draw.c --- pars.o --- mv -f .deps/pars.Tpo .deps/pars.Po --- stats.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT stats.o -MD -MP -MF .deps/stats.Tpo -c -o stats.o stats.c --- interface.o --- mv -f .deps/interface.Tpo .deps/interface.Po --- rates.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT rates.o -MD -MP -MF .deps/rates.Tpo -c -o rates.o rates.c --- draw.o --- mv -f .deps/draw.Tpo .deps/draw.Po --- mcmc.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT mcmc.o -MD -MP -MF .deps/mcmc.Tpo -c -o mcmc.o mcmc.c --- cl.o --- mv -f .deps/cl.Tpo .deps/cl.Po --- times.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT times.o -MD -MP -MF .deps/times.Tpo -c -o times.o times.c --- spr.o --- mv -f .deps/spr.Tpo .deps/spr.Po --- tiporder.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT tiporder.o -MD -MP -MF .deps/tiporder.Tpo -c -o tiporder.o tiporder.c --- models.o --- mv -f .deps/models.Tpo .deps/models.Po --- m4.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT m4.o -MD -MP -MF .deps/m4.Tpo -c -o m4.o m4.c --- eigen.o --- mv -f .deps/eigen.Tpo .deps/eigen.Po --- io.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT io.o -MD -MP -MF .deps/io.Tpo -c -o io.o io.c --- lk.o --- mv -f .deps/lk.Tpo .deps/lk.Po --- make.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT make.o -MD -MP -MF .deps/make.Tpo -c -o make.o make.c --- times.o --- mv -f .deps/times.Tpo .deps/times.Po --- nexus.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT nexus.o -MD -MP -MF .deps/nexus.Tpo -c -o nexus.o nexus.c --- tiporder.o --- mv -f .deps/tiporder.Tpo .deps/tiporder.Po --- init.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT init.o -MD -MP -MF .deps/init.Tpo -c -o init.o init.c --- make.o --- mv -f .deps/make.Tpo .deps/make.Po --- xml.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT xml.o -MD -MP -MF .deps/xml.Tpo -c -o xml.o xml.c --- nexus.o --- mv -f .deps/nexus.Tpo .deps/nexus.Po --- date.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT date.o -MD -MP -MF .deps/date.Tpo -c -o date.o date.c --- io.o --- io.c: In function 'Print_Fp_Out': io.c:2629:47: warning: '%d' directive output may be truncated writing between 1 and 10 bytes into a region of size 6 [-Wformat-truncation=] if (precision > 0) snprintf (format, 8, "%%.%df", precision); ^~ io.c:2629:43: note: directive argument in the range [1, 2147483647] if (precision > 0) snprintf (format, 8, "%%.%df", precision); ^~~~~~~~ io.c:2629:22: note: 'snprintf' output between 5 and 14 bytes into a destination of size 8 if (precision > 0) snprintf (format, 8, "%%.%df", precision); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ --- m4.o --- mv -f .deps/m4.Tpo .deps/m4.Po --- sse.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT sse.o -MD -MP -MF .deps/sse.Tpo -c -o sse.o sse.c mv -f .deps/sse.Tpo .deps/sse.Po --- avx.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT avx.o -MD -MP -MF .deps/avx.Tpo -c -o avx.o avx.c --- date.o --- mv -f .deps/date.Tpo .deps/date.Po --- tbe.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT tbe.o -MD -MP -MF .deps/tbe.Tpo -c -o tbe.o tbe.c --- utilities.o --- utilities.c: In function 'Assign_State_With_Ambiguity': utilities.c:3045:29: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] sprintf(format,"%%%dd",stepsize); ^~ utilities.c:3045:26: note: directive argument in the range [0, 2147483647] sprintf(format,"%%%dd",stepsize); ^~~~~~~ utilities.c:3045:11: note: 'sprintf' output between 4 and 13 bytes into a destination of size 6 sprintf(format,"%%%dd",stepsize); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ --- avx.o --- mv -f .deps/avx.Tpo .deps/avx.Po --- ancestral.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT ancestral.o -MD -MP -MF .deps/ancestral.Tpo -c -o ancestral.o ancestral.c --- tbe.o --- mv -f .deps/tbe.Tpo .deps/tbe.Po --- mixt.o --- cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -MT mixt.o -MD -MP -MF .deps/mixt.Tpo -c -o mixt.o mixt.c --- mcmc.o --- mv -f .deps/mcmc.Tpo .deps/mcmc.Po --- io.o --- mv -f .deps/io.Tpo .deps/io.Po --- ancestral.o --- mv -f .deps/ancestral.Tpo .deps/ancestral.Po --- utilities.o --- utilities.c: In function 'Are_Compatible': utilities.c:4877:29: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] sprintf(format,"%%%dd",stepsize); ^~ utilities.c:4877:26: note: directive argument in the range [0, 2147483647] sprintf(format,"%%%dd",stepsize); ^~~~~~~ utilities.c:4877:11: note: 'sprintf' output between 4 and 13 bytes into a destination of size 6 sprintf(format,"%%%dd",stepsize); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ --- rates.o --- mv -f .deps/rates.Tpo .deps/rates.Po --- optimiz.o --- mv -f .deps/optimiz.Tpo .deps/optimiz.Po --- mixt.o --- mv -f .deps/mixt.Tpo .deps/mixt.Po --- init.o --- mv -f .deps/init.Tpo .deps/init.Po --- xml.o --- mv -f .deps/xml.Tpo .deps/xml.Po --- stats.o --- mv -f .deps/stats.Tpo .deps/stats.Po --- utilities.o --- mv -f .deps/utilities.Tpo .deps/utilities.Po --- phyml --- cc -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -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 m4.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 --- all-am --- Done. SUCCEEDED 00:00:17 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for phyml-3.3.20190909_1,1 ===> Generating temporary packing list Making install in src .: Building [phyml]. Version 3.3.20190909 :. Done. /bin/mkdir -p '/construction/biology/phyml/stage/usr/local/bin' install -s -m 555 phyml '/construction/biology/phyml/stage/usr/local/bin' (cd /construction/biology/phyml/phyml-3.3.20190909/doc && install -m 0644 *.pdf /construction/biology/phyml/stage/usr/local/share/doc/phyml) ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks Warning: Possible REINPLACE_CMD issues sed failed: file content unchanged from backup: configure.ac SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for phyml-3.3.20190909_1,1 file sizes/checksums [15]: 0% file sizes/checksums [15]: 100% packing files [15]: 0% packing files [15]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:02 TOTAL TIME 00:00:34