[package - main-armv7-default][biology/phyml] Failed for phyml-3.3.20200621,1 in stage
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Date: Fri, 30 Jul 2021 07:36:51 UTC
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: ports@FreeBSD.org
Log URL: http://beefy12.nyi.freebsd.org/data/main-armv7-default/pe8cfea34d340_s7685f8344d/logs/phyml-3.3.20200621,1.log
Build URL: http://beefy12.nyi.freebsd.org/build.html?mastername=main-armv7-default&build=pe8cfea34d340_s7685f8344d
Log:
=>> Building biology/phyml
build started at Fri Jul 30 07:34:43 UTC 2021
port directory: /usr/ports/biology/phyml
package name: phyml-3.3.20200621,1
building for: FreeBSD main-armv7-default-job-05 14.0-CURRENT FreeBSD 14.0-CURRENT 1400026 arm
maintained by: ports@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-8-gaf08dbda
Host OSVERSION: 1400003
Jail OSVERSION: 1400026
Job Id: 05
!!! Jail is newer than host. (Jail: 1400026, Host: 1400003) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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PORT_FLAGS=
PKGENV=
FLAVOR=
DEPENDS_ARGS=
MAKE_ARGS=
---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
===> The following configuration options are available for phyml-3.3.20200621,1:
DOCS=on: Build and/or install documentation
EXAMPLES=on: Build and/or install examples
====> MPI (Message Passing Interface) support: you can only select none or one of them
MPICH=off: Parallel processing support via MPICH 3
OPENMPI=off: Parallel processing support via Open MPI
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
ports@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--disable-beagle --disable-native --disable-mpi --prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/biology/phyml/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/phyml/work HOME=/wrkdirs/usr/ports/biology/phyml/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/phyml/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288
--End CONFIGURE_ENV--
--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/phyml/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/phyml/work HOME=/wrkdirs/usr/ports/biology/phyml/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/phyml/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444"
--End MAKE_ENV--
--PLIST_SUB--
PORTDOCS="" PORTEXAMPLES="" OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/phyml" EXAMPLESDIR="share/examples/phyml" DATADIR="share/phyml" WWWDIR="www/phyml" ETCDIR="etc/phyml"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/phyml DOCSDIR=/usr/local/share/doc/phyml EXAMPLESDIR=/usr/local/share/examples/phyml WWWDIR=/usr/local/www/phyml ETCDIR=/usr/local/etc/phyml
--End SUB_LIST--
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ARCH=${MACHINE_ARCH}
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--End resource limits--
=======================<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://docs.freebsd.org/en/articles/contributing/#ports-contributing
<snip>
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether /nxb-bin/usr/bin/cc accepts -g... yes
checking for /nxb-bin/usr/bin/cc option to accept ISO C89... none needed
checking whether /nxb-bin/usr/bin/cc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of /nxb-bin/usr/bin/cc... gcc3
checking dependency style of /nxb-bin/usr/bin/cc... (cached) gcc3
checking for log in -lm... yes
checking how to run the C preprocessor... /nxb-bin/usr/bin/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
===========================================================================
=======================<phase: build >============================
===> Building for phyml-3.3.20200621,1
/nxb-bin/usr/bin/make all-recursive
Making all in src
/nxb-bin/usr/bin/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
mv -f .deps/main.Tpo .deps/main.Po
/nxb-bin/usr/bin/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
utilities.c:8865:26: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare]
while((c != '(') && (c != EOF));
~ ^ ~~~
utilities.c:8867:7: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
if(c==EOF)
~^ ~~~
utilities.c:8879:11: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
if(c==EOF) break;
~^ ~~~
utilities.c:8886:11: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
if(c==EOF || c==';') break;
~^ ~~~
utilities.c:9167:12: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
if(c == EOF) break;
~ ^ ~~~
5 warnings generated.
mv -f .deps/utilities.Tpo .deps/utilities.Po
/nxb-bin/usr/bin/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
mv -f .deps/optimiz.Tpo .deps/optimiz.Po
/nxb-bin/usr/bin/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
mv -f .deps/lk.Tpo .deps/lk.Po
/nxb-bin/usr/bin/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
mv -f .deps/bionj.Tpo .deps/bionj.Po
/nxb-bin/usr/bin/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
mv -f .deps/models.Tpo .deps/models.Po
/nxb-bin/usr/bin/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
mv -f .deps/free.Tpo .deps/free.Po
/nxb-bin/usr/bin/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
mv -f .deps/help.Tpo .deps/help.Po
/nxb-bin/usr/bin/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
mv -f .deps/simu.Tpo .deps/simu.Po
/nxb-bin/usr/bin/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
mv -f .deps/eigen.Tpo .deps/eigen.Po
/nxb-bin/usr/bin/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
mv -f .deps/pars.Tpo .deps/pars.Po
/nxb-bin/usr/bin/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
mv -f .deps/alrt.Tpo .deps/alrt.Po
/nxb-bin/usr/bin/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
mv -f .deps/interface.Tpo .deps/interface.Po
/nxb-bin/usr/bin/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
mv -f .deps/cl.Tpo .deps/cl.Po
/nxb-bin/usr/bin/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
mv -f .deps/spr.Tpo .deps/spr.Po
/nxb-bin/usr/bin/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
mv -f .deps/draw.Tpo .deps/draw.Po
/nxb-bin/usr/bin/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
mv -f .deps/stats.Tpo .deps/stats.Po
/nxb-bin/usr/bin/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
mv -f .deps/rates.Tpo .deps/rates.Po
/nxb-bin/usr/bin/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
mv -f .deps/mcmc.Tpo .deps/mcmc.Po
/nxb-bin/usr/bin/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
mv -f .deps/times.Tpo .deps/times.Po
/nxb-bin/usr/bin/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
mv -f .deps/tiporder.Tpo .deps/tiporder.Po
/nxb-bin/usr/bin/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
io.c:1167:12: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
if(c == EOF) return 0;
~ ^ ~~~
io.c:1177:16: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
if(c == EOF) return 0;
~ ^ ~~~
io.c:1182:12: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
if(c == EOF) return 0;
~ ^ ~~~
io.c:1193:12: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
if(c == EOF) return 0;
~ ^ ~~~
io.c:1214:16: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
if(c == EOF) return 0;
~ ^ ~~~
io.c:1542:17: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
else if(c == EOF)
~ ^ ~~~
io.c:1571:8: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
if(c == EOF) return 0;
~ ^ ~~~
io.c:1633:26: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare]
while((c != '(') && (c != EOF));
~ ^ ~~~
io.c:1636:7: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
if(c==EOF) return NULL;
~^ ~~~
io.c:1648:16: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
if(c == EOF || c == ';') break;
~ ^ ~~~
io.c:1664:11: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
if(c==EOF || c==';') break;
~^ ~~~
11 warnings generated.
mv -f .deps/io.Tpo .deps/io.Po
/nxb-bin/usr/bin/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
mv -f .deps/make.Tpo .deps/make.Po
/nxb-bin/usr/bin/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
mv -f .deps/nexus.Tpo .deps/nexus.Po
/nxb-bin/usr/bin/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
mv -f .deps/init.Tpo .deps/init.Po
/nxb-bin/usr/bin/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
mv -f .deps/xml.Tpo .deps/xml.Po
/nxb-bin/usr/bin/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
mv -f .deps/date.Tpo .deps/date.Po
/nxb-bin/usr/bin/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
/nxb-bin/usr/bin/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
mv -f .deps/avx.Tpo .deps/avx.Po
/nxb-bin/usr/bin/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
mv -f .deps/tbe.Tpo .deps/tbe.Po
/nxb-bin/usr/bin/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
mv -f .deps/ancestral.Tpo .deps/ancestral.Po
/nxb-bin/usr/bin/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
mv -f .deps/mixt.Tpo .deps/mixt.Po
/nxb-bin/usr/bin/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 io.o make.o nexus.o init.o xml.o date.o sse.o avx.o tbe.o ancestral.o mixt.o -lm -lm
.: Building [phyml]. Version 3.3.20200621 :.
Done.
===========================================================================
=======================<phase: run-depends >============================
===========================================================================
=======================<phase: stage >============================
===> Staging for phyml-3.3.20200621,1
===> Generating temporary packing list
Making install in src
.: Building [phyml]. Version 3.3.20200621 :.
Done.
/bin/mkdir -p '/wrkdirs/usr/ports/biology/phyml/work/stage/usr/local/bin'
install -s -m 555 phyml '/wrkdirs/usr/ports/biology/phyml/work/stage/usr/local/bin'
(cd /wrkdirs/usr/ports/biology/phyml/work/phyml-3.3.20200621/doc && install -m 0644 *.pdf /wrkdirs/usr/ports/biology/phyml/work/stage/usr/local/share/doc/phyml)
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/phyml