[package - 131arm64-default][biology/phyml] Failed for phyml-3.3.20220408,1 in build
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Date: Tue, 28 Feb 2023 21:33:10 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/ampere3/data/131arm64-default/d0f8db852755/logs/phyml-3.3.20220408,1.log
Build URL: https://pkg-status.freebsd.org/ampere3/build.html?mastername=131arm64-default&build=d0f8db852755
Log:
=>> Building biology/phyml
build started at Tue Feb 28 21:32:48 UTC 2023
port directory: /usr/ports/biology/phyml
package name: phyml-3.3.20220408,1
building for: FreeBSD 131arm64-default-job-09 13.1-RELEASE-p7 FreeBSD 13.1-RELEASE-p7 arm64
maintained by: ports@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400073
Jail OSVERSION: 1301000
Job Id: 09
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SHELL=/bin/csh
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UNAME_r=13.1-RELEASE-p7
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POUDRIEREPATH=/usr/local/bin/poudriere
---End Environment---
---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=
FLAVOR=
DEPENDS_ARGS=
MAKE_ARGS=
---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
===> The following configuration options are available for phyml-3.3.20220408,1:
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=2.71 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=2.71 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 " 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=13.1 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---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
#### /usr/local/etc/poudriere.d/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 2 jobs
MAKE_JOBS_NUMBER=2
#### /usr/ports/Mk/Scripts/ports_env.sh ####
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#### Misc Poudriere ####
GID=0
UID=0
---End make.conf---
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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
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socket buffer size (bytes, -b) unlimited
pseudo-terminals (-p) unlimited
kqueues (-k) unlimited
umtx shared locks (-o) unlimited
--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
===> License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> phyml-3.3.20220408,1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.19.1_1.pkg
[131arm64-default-job-09] Installing pkg-1.19.1_1...
[131arm64-default-job-09] Extracting pkg-1.19.1_1: .......... done
===> phyml-3.3.20220408,1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of phyml-3.3.20220408,1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<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://docs.freebsd.org/en/articles/contributing/#ports-contributing
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by phyml-3.3.20220408,1 for building
===========================================================================
=======================<phase: checksum >============================
===> NOTICE:
The phyml port currently does not have a maintainer. As a result, it is
<snip>
=======================<phase: configure >============================
===> Configuring for phyml-3.3.20220408,1
configure.ac:21: warning: The macro `AC_HEADER_STDC' is obsolete.
configure.ac:21: You should run autoupdate.
./lib/autoconf/headers.m4:704: 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.m4:1766: 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-freebsd13.1
checking host system type... aarch64-portbld-freebsd13.1
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 >============================
===> Building for phyml-3.3.20220408,1
--- all ---
/usr/bin/make all-recursive
--- all-recursive ---
Making all in src
--- intro ---
--- main.o ---
--- intro ---
.: Building [phyml]. Version 3.3.20220408 :.
--- 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
--- 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
--- main.o ---
cc: warning: argument unused during compilation: '-msse3' [-Wunused-command-line-argument]
--- utilities.o ---
cc: warning: argument unused during compilation: '-msse3' [-Wunused-command-line-argument]
utilities.c:3212:18: error: no member named '_tPij1' in 'struct __Tree'
boot_tree->_tPij1 = tree->_tPij1;
~~~~~~~~~ ^
utilities.c:3212:47: error: no member named '_tPij1' in 'struct __Tree'
boot_tree->_tPij1 = tree->_tPij1;
~~~~ ^
utilities.c:3213:18: error: no member named '_tPij2' in 'struct __Tree'
boot_tree->_tPij2 = tree->_tPij2;
~~~~~~~~~ ^
utilities.c:3213:47: error: no member named '_tPij2' in 'struct __Tree'
boot_tree->_tPij2 = tree->_tPij2;
~~~~ ^
utilities.c:3214:18: error: no member named '_pmat1plk1' in 'struct __Tree'
boot_tree->_pmat1plk1 = tree->_pmat1plk1;
~~~~~~~~~ ^
utilities.c:3214:47: error: no member named '_pmat1plk1' in 'struct __Tree'
boot_tree->_pmat1plk1 = tree->_pmat1plk1;
~~~~ ^
utilities.c:3215:18: error: no member named '_pmat2plk2' in 'struct __Tree'
boot_tree->_pmat2plk2 = tree->_pmat2plk2;
~~~~~~~~~ ^
utilities.c:3215:47: error: no member named '_pmat2plk2' in 'struct __Tree'
boot_tree->_pmat2plk2 = tree->_pmat2plk2;
~~~~ ^
utilities.c:3216:18: error: no member named '_plk0' in 'struct __Tree'
boot_tree->_plk0 = tree->_plk0;
~~~~~~~~~ ^
utilities.c:3216:47: error: no member named '_plk0' in 'struct __Tree'
boot_tree->_plk0 = tree->_plk0;
~~~~ ^
utilities.c:3219:18: error: no member named '_l_ev' in 'struct __Tree'; did you mean 'l_ev'?
boot_tree->_l_ev = tree->_l_ev;
^~~~~
l_ev
./utilities.h:779:42: note: 'l_ev' declared here
phydbl *p_lk_left_pi,*l_ev;
^
utilities.c:3219:47: error: no member named '_l_ev' in 'struct __Tree'; did you mean 'l_ev'?
boot_tree->_l_ev = tree->_l_ev;
^~~~~
l_ev
./utilities.h:779:42: note: 'l_ev' declared here
phydbl *p_lk_left_pi,*l_ev;
^
utilities.c:3220:18: error: no member named '_r_ev' in 'struct __Tree'
boot_tree->_r_ev = tree->_r_ev;
~~~~~~~~~ ^
utilities.c:3220:47: error: no member named '_r_ev' in 'struct __Tree'
boot_tree->_r_ev = tree->_r_ev;
~~~~ ^
utilities.c:3221:18: error: no member named '_prod_left' in 'struct __Tree'
boot_tree->_prod_left = tree->_prod_left;
~~~~~~~~~ ^
utilities.c:3221:47: error: no member named '_prod_left' in 'struct __Tree'
boot_tree->_prod_left = tree->_prod_left;
~~~~ ^
utilities.c:3222:18: error: no member named '_prod_rght' in 'struct __Tree'
boot_tree->_prod_rght = tree->_prod_rght;
~~~~~~~~~ ^
utilities.c:3222:47: error: no member named '_prod_rght' in 'struct __Tree'
boot_tree->_prod_rght = tree->_prod_rght;
~~~~ ^
--- main.o ---
mv -f .deps/main.Tpo .deps/main.Po
--- 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
cc: warning: argument unused during compilation: '-msse3' [-Wunused-command-line-argument]
--- utilities.o ---
utilities.c:6546:22: warning: variable 'sd' set but not used [-Wunused-but-set-variable]
phydbl *delta,mean,sd,obs_stat,threshold;
^
utilities.c:8913:26: 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:8915:7: 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:8927:11: 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:8934:11: 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:9215:12: 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;
~ ^ ~~~
6 warnings and 18 errors generated.
*** [utilities.o] Error code 1
make[3]: stopped in /wrkdirs/usr/ports/biology/phyml/work/phyml-3.3.20220408/src
--- optimiz.o ---
mv -f .deps/optimiz.Tpo .deps/optimiz.Po
1 error
make[3]: stopped in /wrkdirs/usr/ports/biology/phyml/work/phyml-3.3.20220408/src
make[2]: stopped in /wrkdirs/usr/ports/biology/phyml/work/phyml-3.3.20220408
make[1]: 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