[package - head-i386-default][biology/phylip] Failed for phylip-3.697, 1 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Tue Aug 25 14:12:17 UTC 2020
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 at FreeBSD.org
Last committer: zeising at FreeBSD.org
Ident: $FreeBSD: head/biology/phylip/Makefile 516742 2019-11-04 21:08:20Z zeising $
Log URL: http://beefy17.nyi.freebsd.org/data/head-i386-default/p546132_s364744/logs/phylip-3.697,1.log
Build URL: http://beefy17.nyi.freebsd.org/build.html?mastername=head-i386-default&build=p546132_s364744
Log:
=>> Building biology/phylip
build started at Tue Aug 25 14:11:55 UTC 2020
port directory: /usr/ports/biology/phylip
package name: phylip-3.697,1
building for: FreeBSD head-i386-default-job-01 13.0-CURRENT FreeBSD 13.0-CURRENT 1300111 i386
maintained by: ports at FreeBSD.org
Makefile ident: $FreeBSD: head/biology/phylip/Makefile 516742 2019-11-04 21:08:20Z zeising $
Poudriere version: 3.2.8-5-gc81843e5
Host OSVERSION: 1300100
Jail OSVERSION: 1300111
Job Id: 01
!!! Jail is newer than host. (Jail: 1300111, Host: 1300100) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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PORT_FLAGS=
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FLAVOR=
DEPENDS_ARGS=
MAKE_ARGS=
---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
===> The following configuration options are available for phylip-3.697,1:
DOCS=on: Build and/or install documentation
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
ports at FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/phylip/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/phylip/work HOME=/wrkdirs/usr/ports/biology/phylip/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/phylip/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh
--End CONFIGURE_ENV--
--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/phylip/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/phylip/work HOME=/wrkdirs/usr/ports/biology/phylip/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/phylip/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="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="" OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/phylip" EXAMPLESDIR="share/examples/phylip" DATADIR="share/phylip" WWWDIR="www/phylip" ETCDIR="etc/phylip"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/phylip DOCSDIR=/usr/local/share/doc/phylip EXAMPLESDIR=/usr/local/share/examples/phylip WWWDIR=/usr/local/www/phylip ETCDIR=/usr/local/etc/phylip
--End SUB_LIST--
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USE_PACKAGE_DEPENDS=yes
BATCH=yes
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DISTDIR=/distfiles
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MACHINE=i386
MACHINE_ARCH=i386
ARCH=${MACHINE_ARCH}
#### /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
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MAKE_JOBS_NUMBER=2
#### /usr/ports/Mk/Scripts/ports_env.sh ####
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ARCH=i386
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_OSRELEASE=13.0-CURRENT
OSREL=13.0
OSVERSION=1300111
PYTHONBASE=/usr/local
CONFIGURE_MAX_CMD_LEN=524288
HAVE_PORTS_ENV=1
#### Misc Poudriere ####
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) 524288
stack size (kbytes, -s) 65536
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) 1024
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 >============================
===> NOTICE:
The phylip 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
===> License BSD2CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> phylip-3.697,1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.14.7.txz
[head-i386-default-job-01] Installing pkg-1.14.7...
[head-i386-default-job-01] Extracting pkg-1.14.7: .......... done
===> phylip-3.697,1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of phylip-3.697,1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> NOTICE:
The phylip 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
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by phylip-3.697,1 for building
<snip>
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
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by phylip-3.697,1 for building
=> SHA256 Checksum OK for phylip-3.697.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> NOTICE:
The phylip 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
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by phylip-3.697,1 for building
===> Extracting for phylip-3.697,1
=> SHA256 Checksum OK for phylip-3.697.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for phylip-3.697,1
===========================================================================
=======================<phase: build-depends >============================
===> phylip-3.697,1 depends on executable: bash - not found
===> Installing existing package /packages/All/bash-5.0.18_3.txz
[head-i386-default-job-01] Installing bash-5.0.18_3...
[head-i386-default-job-01] `-- Installing gettext-runtime-0.21...
[head-i386-default-job-01] | `-- Installing indexinfo-0.3.1...
[head-i386-default-job-01] | `-- Extracting indexinfo-0.3.1: .... done
[head-i386-default-job-01] `-- Extracting gettext-runtime-0.21: .......... done
[head-i386-default-job-01] `-- Installing readline-8.0.4...
[head-i386-default-job-01] `-- Extracting readline-8.0.4: .......... done
[head-i386-default-job-01] Extracting bash-5.0.18_3: .......... done
===> phylip-3.697,1 depends on executable: bash - found
===> Returning to build of phylip-3.697,1
===> phylip-3.697,1 depends on package: gmake>=4.3 - not found
===> Installing existing package /packages/All/gmake-4.3_2.txz
[head-i386-default-job-01] Installing gmake-4.3_2...
[head-i386-default-job-01] Extracting gmake-4.3_2: .......... done
===> phylip-3.697,1 depends on package: gmake>=4.3 - found
===> Returning to build of phylip-3.697,1
===> phylip-3.697,1 depends on file: /usr/local/libdata/pkgconfig/x11.pc - not found
===> Installing existing package /packages/All/libX11-1.6.11_1,1.txz
[head-i386-default-job-01] Installing libX11-1.6.11_1,1...
[head-i386-default-job-01] `-- Installing libxcb-1.13.1...
[head-i386-default-job-01] | `-- Installing libXau-1.0.9...
[head-i386-default-job-01] | `-- Extracting libXau-1.0.9: .......... done
[head-i386-default-job-01] | `-- Installing libXdmcp-1.1.3...
[head-i386-default-job-01] | | `-- Installing xorgproto-2020.1...
[head-i386-default-job-01] | | `-- Extracting xorgproto-2020.1: .......... done
[head-i386-default-job-01] | `-- Extracting libXdmcp-1.1.3: ......... done
[head-i386-default-job-01] | `-- Installing libpthread-stubs-0.4...
[head-i386-default-job-01] | `-- Extracting libpthread-stubs-0.4: .... done
[head-i386-default-job-01] | `-- Installing libxml2-2.9.10...
[head-i386-default-job-01] | `-- Extracting libxml2-2.9.10: .......... done
[head-i386-default-job-01] `-- Extracting libxcb-1.13.1: .......... done
[head-i386-default-job-01] Extracting libX11-1.6.11_1,1: .......... done
===> phylip-3.697,1 depends on file: /usr/local/libdata/pkgconfig/x11.pc - found
===> Returning to build of phylip-3.697,1
===> phylip-3.697,1 depends on file: /usr/local/libdata/pkgconfig/xaw7.pc - not found
===> Installing existing package /packages/All/libXaw-1.0.13_3,2.txz
[head-i386-default-job-01] Installing libXaw-1.0.13_3,2...
[head-i386-default-job-01] `-- Installing libXext-1.3.4,1...
[head-i386-default-job-01] `-- Extracting libXext-1.3.4,1: .......... done
[head-i386-default-job-01] `-- Installing libXmu-1.1.3,1...
[head-i386-default-job-01] | `-- Installing libXt-1.2.0,1...
[head-i386-default-job-01] | | `-- Installing libICE-1.0.10,1...
[head-i386-default-job-01] | | `-- Extracting libICE-1.0.10,1: .......... done
[head-i386-default-job-01] | | `-- Installing libSM-1.2.3,1...
[head-i386-default-job-01] | | `-- Extracting libSM-1.2.3,1: .......... done
[head-i386-default-job-01] | `-- Extracting libXt-1.2.0,1: .......... done
[head-i386-default-job-01] `-- Extracting libXmu-1.1.3,1: .......... done
[head-i386-default-job-01] `-- Installing libXpm-3.5.13...
[head-i386-default-job-01] `-- Extracting libXpm-3.5.13: .......... done
[head-i386-default-job-01] Extracting libXaw-1.0.13_3,2: .......... done
===> phylip-3.697,1 depends on file: /usr/local/libdata/pkgconfig/xaw7.pc - found
===> Returning to build of phylip-3.697,1
===> phylip-3.697,1 depends on file: /usr/local/libdata/pkgconfig/xt.pc - found
===========================================================================
=======================<phase: lib-depends >============================
===========================================================================
=======================<phase: configure >============================
===> Configuring for phylip-3.697,1
===========================================================================
=======================<phase: build >============================
===> Building for phylip-3.697,1
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/phylip/work/phylip-3.697/src'
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o clique.o clique.c
Building PHYLIP version 3.696
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o disc.o disc.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o phylip.o phylip.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o consense.o consense.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o cons.o cons.c
cons.c:257:33: warning: result of comparison of constant 10 with boolean expression is always true [-Wtautological-constant-out-of-range-compare]
if ( (c == gettc(intree)) != '\n')
~~~~~~~~~~~~~~~~~~~~ ^ ~~~~
1 warning generated.
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o contml.o contml.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o cont.o cont.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o contrast.o contrast.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o dnacomp.o dnacomp.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o seq.o seq.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o dnadist.o dnadist.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o dnainvar.o dnainvar.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o dnaml.o dnaml.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o dnamlk.o dnamlk.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o mlclock.o mlclock.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o printree.o printree.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o dnamove.o dnamove.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o moves.o moves.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o dnapars.o dnapars.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o dnapenny.o dnapenny.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o dolmove.o dolmove.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o dollo.o dollo.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o dollop.o dollop.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o dolpenny.o dolpenny.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o factor.o factor.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o fitch.o fitch.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o dist.o dist.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o gendist.o gendist.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o kitsch.o kitsch.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o mix.o mix.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o wagner.o wagner.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o move.o move.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o neighbor.o neighbor.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o pars.o pars.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o discrete.o discrete.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o penny.o penny.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o proml.o proml.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o promlk.o promlk.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o protdist.o protdist.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o protpars.o protpars.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o restdist.o restdist.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o restml.o restml.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o retree.o retree.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o seqboot.o seqboot.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX -c -o treedist.o treedist.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DX -I/usr/local/include -c drawgram.c
drawgram.c:2111:9: warning: implicit declaration of function 'makebox' is invalid in C99 [-Wimplicit-function-declaration]
makebox(fontname,&xoffset,&yoffset,&scale,spp);
^
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DX -I/usr/local/include -c draw.c
1 warning generated.
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DX -I/usr/local/include -c draw2.c
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DX -I/usr/local/include -shared -fPIC -c drawtree.c
cc: warning: argument unused during compilation: '-shared' [-Wunused-command-line-argument]
drawtree.c:3017:9: warning: implicit declaration of function 'makebox' is invalid in C99 [-Wimplicit-function-declaration]
makebox(fontname,&xoffset,&yoffset,&scale,spp);
^
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DUNX clique.o disc.o phylip.o -lm -o clique
ld: error: duplicate symbol: firstplotblock
>>> defined at clique.c
>>> clique.o:(firstplotblock)
>>> defined at disc.c
>>> disc.o:(.bss+0x1D)
ld: error: duplicate symbol: javarun
>>> defined at clique.c
>>> clique.o:(javarun)
>>> defined at disc.c
>>> disc.o:(.bss+0x1C)
ld: error: duplicate symbol: firstplotblock
>>> defined at clique.c
>>> clique.o:(firstplotblock)
>>> defined at phylip.c
>>> phylip.o:(.bss+0x24)
ld: error: duplicate symbol: javarun
>>> defined at clique.c
>>> clique.o:(javarun)
>>> defined at phylip.c
>>> phylip.o:(.bss+0x2)
cc: error: linker command failed with exit code 1 (use -v to see invocation)
gmake[1]: *** [Makefile.unx:273: clique] Error 1
gmake[1]: *** Waiting for unfinished jobs....
1 warning generated.
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/phylip/work/phylip-3.697/src'
===> 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/phylip
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