[package - main-arm64-default][biology/phyml] Failed for phyml-3.3.20220408_1,1 in build
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Date: Sun, 16 Jun 2024 13:29:33 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: https://pkg-status.freebsd.org/ampere2/data/main-arm64-default/p6208b5403c95_sa16cb8709de/logs/phyml-3.3.20220408_1,1.log
Build URL: https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-arm64-default&build=p6208b5403c95_sa16cb8709de
Log:
=>> Building biology/phyml
build started at Sun Jun 16 13:29:11 UTC 2024
port directory: /usr/ports/biology/phyml
package name: phyml-3.3.20220408_1,1
building for: FreeBSD main-arm64-default-job-08 15.0-CURRENT FreeBSD 15.0-CURRENT 1500019 arm64
maintained by: ports@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 1441 May 13 2023 /usr/ports/biology/phyml/Makefile
Ports top last git commit: 6208b5403c9
Ports top unclean checkout: no
Port dir last git commit: 8e2ec289a2d
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.1-30-g79e3edcd
Host OSVERSION: 1500018
Jail OSVERSION: 1500019
Job Id: 08
!!! Jail is newer than host. (Jail: 1500019, Host: 1500018) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
---Begin Environment---
SHELL=/bin/sh
OSVERSION=1500019
UNAME_v=FreeBSD 15.0-CURRENT 1500019
UNAME_r=15.0-CURRENT
BLOCKSIZE=K
MAIL=/var/mail/root
MM_CHARSET=UTF-8
LANG=C.UTF-8
STATUS=1
HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
MAKE_OBJDIR_CHECK_WRITABLE=0
LOCALBASE=/usr/local
USER=root
POUDRIERE_NAME=poudriere-git
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.4.1-30-g79e3edcd
MASTERMNT=/usr/local/poudriere/data/.m/main-arm64-default/ref
LC_COLLATE=C
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
OUTPUT_REDIRECTED_STDERR=4
OUTPUT_REDIRECTED=1
PWD=/usr/local/poudriere/data/.m/main-arm64-default/08/.p
OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS
MASTERNAME=main-arm64-default
SCRIPTPREFIX=/usr/local/share/poudriere
SCRIPTNAME=bulk.sh
OLDPWD=/usr/local/poudriere/data/.m/main-arm64-default/ref/.p/pool
POUDRIERE_PKGNAME=poudriere-git-3.4.1-30-g79e3edcd
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
POUDRIEREPATH=/usr/local/bin/poudriere
---End Environment---
---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=
FLAVOR=
MAKE_ARGS=
---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
===> The following configuration options are available for phyml-3.3.20220408_1,1:
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 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/phyml/work/.cache 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 PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/phyml/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh DEFAULT_AUTOCONF=2.72 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 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/phyml/work/.cache 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 PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/phyml/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DEFAULT_AUTOCONF=2.72 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " 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=15.0 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--
---Begin make.conf---
# XXX: We really need this but cannot use it while 'make checksum' does not
# try the next mirror on checksum failure. It currently retries the same
# failed mirror and then fails rather then trying another. It *does*
# try the next if the size is mismatched though.
#MASTER_SITE_FREEBSD=yes
# Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs
MAKE_JOBS_NUMBER=3
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
#### ####
# XXX: We really need this but cannot use it while 'make checksum' does not
# try the next mirror on checksum failure. It currently retries the same
# failed mirror and then fails rather then trying another. It *does*
# try the next if the size is mismatched though.
#MASTER_SITE_FREEBSD=yes
# Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs
MAKE_JOBS_NUMBER=3
#### Misc Poudriere ####
.include "/etc/make.conf.ports_env"
GID=0
UID=0
---End make.conf---
--Resource limits--
cpu time (seconds, -t) unlimited
file size (512-blocks, -f) unlimited
data seg size (kbytes, -d) 1048576
stack size (kbytes, -s) 1048576
core file size (512-blocks, -c) unlimited
max memory size (kbytes, -m) unlimited
locked memory (kbytes, -l) unlimited
max user processes (-u) 89999
open files (-n) 8192
virtual mem size (kbytes, -v) unlimited
swap limit (kbytes, -w) unlimited
socket buffer size (bytes, -b) unlimited
pseudo-terminals (-p) unlimited
kqueues (-k) unlimited
umtx shared locks (-o) unlimited
--End resource limits--
=======================<phase: check-sanity >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> 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
===> License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> phyml-3.3.20220408_1,1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.21.3.pkg
[main-arm64-default-job-08] Installing pkg-1.21.3...
[main-arm64-default-job-08] Extracting pkg-1.21.3: .......... done
===> phyml-3.3.20220408_1,1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of phyml-3.3.20220408_1,1
===========================================================================
=======================<phase: fetch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: fetch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> 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
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by phyml-3.3.20220408_1,1 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> NOTICE:
<snip>
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by phyml-3.3.20220408_1,1 for building
=> SHA256 Checksum OK for stephaneguindon-phyml-v3.3.20220408_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: extract >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> 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
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by phyml-3.3.20220408_1,1 for building
===> Extracting for phyml-3.3.20220408_1,1
=> SHA256 Checksum OK for stephaneguindon-phyml-v3.3.20220408_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: patch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Patching for phyml-3.3.20220408_1,1
===> Applying FreeBSD patches for phyml-3.3.20220408_1,1 from /usr/ports/biology/phyml/files
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> phyml-3.3.20220408_1,1 depends on package: pkgconf>=1.3.0_1 - not found
===> Installing existing package /packages/All/pkgconf-2.2.0,1.pkg
[main-arm64-default-job-08] Installing pkgconf-2.2.0,1...
[main-arm64-default-job-08] Extracting pkgconf-2.2.0,1: .......... done
===> phyml-3.3.20220408_1,1 depends on package: pkgconf>=1.3.0_1 - found
===> Returning to build of phyml-3.3.20220408_1,1
===> phyml-3.3.20220408_1,1 depends on package: autoconf>=2.72 - not found
===> Installing existing package /packages/All/autoconf-2.72.pkg
[main-arm64-default-job-08] Installing autoconf-2.72...
[main-arm64-default-job-08] `-- Installing autoconf-switch-20220527...
[main-arm64-default-job-08] `-- Extracting autoconf-switch-20220527: .......... done
[main-arm64-default-job-08] `-- Installing indexinfo-0.3.1...
[main-arm64-default-job-08] `-- Extracting indexinfo-0.3.1: .... done
[main-arm64-default-job-08] `-- Installing m4-1.4.19_1,1...
[main-arm64-default-job-08] | `-- Installing gettext-runtime-0.22.5...
[main-arm64-default-job-08] | `-- Extracting gettext-runtime-0.22.5: .......... done
[main-arm64-default-job-08] `-- Extracting m4-1.4.19_1,1: .......... done
[main-arm64-default-job-08] `-- Installing perl5-5.36.3_1...
[main-arm64-default-job-08] `-- Extracting perl5-5.36.3_1: .......... done
[main-arm64-default-job-08] Extracting autoconf-2.72: .......... done
===> phyml-3.3.20220408_1,1 depends on package: autoconf>=2.72 - found
===> Returning to build of phyml-3.3.20220408_1,1
===> phyml-3.3.20220408_1,1 depends on package: automake>=1.16.5 - not found
===> Installing existing package /packages/All/automake-1.16.5_1.pkg
[main-arm64-default-job-08] Installing automake-1.16.5_1...
[main-arm64-default-job-08] Extracting automake-1.16.5_1: .......... done
===> phyml-3.3.20220408_1,1 depends on package: automake>=1.16.5 - found
===> Returning to build of phyml-3.3.20220408_1,1
===> phyml-3.3.20220408_1,1 depends on executable: libtoolize - not found
===> Installing existing package /packages/All/libtool-2.4.7_2.pkg
[main-arm64-default-job-08] Installing libtool-2.4.7_2...
[main-arm64-default-job-08] Extracting libtool-2.4.7_2: .......... done
===> phyml-3.3.20220408_1,1 depends on executable: libtoolize - found
===> Returning to build of phyml-3.3.20220408_1,1
===========================================================================
=======================<phase: lib-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: configure >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Configuring for phyml-3.3.20220408_1,1
configure.ac:21: warning: The macro 'AC_HEADER_STDC' is obsolete.
configure.ac:21: You should run autoupdate.
./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from...
configure.ac:21: the top level
configure.ac:42: warning: The macro 'AC_FUNC_SETVBUF_REVERSED' is obsolete. Remove it and all references to SETVBUF_REVERSED.
./lib/autoconf/functions.m4:1785: AC_FUNC_SETVBUF_REVERSED is expanded from...
configure.ac:42: the top level
configure.ac:14: installing './compile'
configure.ac:12: installing './config.guess'
configure.ac:12: 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, --disable-mpi
configure: loading site script /usr/ports/Templates/config.site
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free 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... aarch64-portbld-freebsd15.0
checking host system type... aarch64-portbld-freebsd15.0
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 the compiler supports GNU C... yes
checking whether cc accepts -g... yes
checking for cc option to enable C11 features... 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 for log in -lm... yes
checking for stdio.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for inttypes.h... (cached) yes
checking for stdint.h... (cached) yes
checking for strings.h... (cached) yes
checking for sys/stat.h... (cached) yes
checking for sys/types.h... (cached) yes
checking for unistd.h... (cached) yes
checking for grep that handles long lines and -e... (cached) /usr/bin/grep
checking for egrep... (cached) /usr/bin/egrep
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 GNU libc compatible malloc... (cached) yes
checking for GNU libc compatible realloc... yes
checking for vprintf... (cached) yes
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, --disable-mpi
===========================================================================
=======================<phase: build >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Building for phyml-3.3.20220408_1,1
--- all ---
/usr/bin/make all-recursive
--- all-recursive ---
Making all in src
--- intro ---
--- main.o ---
--- utilities.o ---
--- main.o ---
cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -msse3 -Wall -Winline -finline -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.c
--- intro ---
.: Building [phyml]. Version 3.3.20220408 :.
--- utilities.o ---
cc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -msse3 -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 -msse3 -Wall -Winline -finline -MT optimiz.o -MD -MP -MF .deps/optimiz.Tpo -c -o optimiz.o optimiz.c
--- utilities.o ---
cc: error: unsupported option '-msse3' for target 'aarch64-unknown-freebsd15.0'
--- main.o ---
cc: error: unsupported option '-msse3' for target 'aarch64-unknown-freebsd15.0'
--- optimiz.o ---
cc: error: unsupported option '-msse3' for target 'aarch64-unknown-freebsd15.0'
*** [optimiz.o] Error code 1
make[2]: stopped in /wrkdirs/usr/ports/biology/phyml/work/phyml-3.3.20220408/src
--- utilities.o ---
*** [utilities.o] Error code 1
make[2]: stopped in /wrkdirs/usr/ports/biology/phyml/work/phyml-3.3.20220408/src
--- main.o ---
*** [main.o] Error code 1
make[2]: stopped in /wrkdirs/usr/ports/biology/phyml/work/phyml-3.3.20220408/src
make[2]: 3 errors
make[2]: stopped in /wrkdirs/usr/ports/biology/phyml/work/phyml-3.3.20220408/src
make[1]: stopped in /wrkdirs/usr/ports/biology/phyml/work/phyml-3.3.20220408
make: stopped in /wrkdirs/usr/ports/biology/phyml/work/phyml-3.3.20220408
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/phyml