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Date:      Mon, 31 Aug 2020 03:54:49 GMT
From:      pkg-fallout@FreeBSD.org
To:        pkg-fallout@FreeBSD.org
Subject:   [package - head-armv6-default][biology/grappa] Failed for grappa-2.0 in build
Message-ID:  <202008310354.07V3snx1016123@beefy8.nyi.freebsd.org>

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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
Last committer: rm@FreeBSD.org
Ident:          $FreeBSD: head/biology/grappa/Makefile 397864 2015-09-25 18:55:08Z rm $
Log URL:        http://beefy8.nyi.freebsd.org/data/head-armv6-default/p546860_s364942/logs/grappa-2.0.log
Build URL:      http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p546860_s364942
Log:

=>> Building biology/grappa
build started at Mon Aug 31 03:54:25 UTC 2020
port directory: /usr/ports/biology/grappa
package name: grappa-2.0
building for: FreeBSD head-armv6-default-job-16 13.0-CURRENT FreeBSD 13.0-CURRENT 1300113 arm
maintained by: ports@FreeBSD.org
Makefile ident:      $FreeBSD: head/biology/grappa/Makefile 397864 2015-09-25 18:55:08Z rm $
Poudriere version: 3.2.8-5-gc81843e5
Host OSVERSION: 1300100
Jail OSVERSION: 1300113
Job Id: 16




!!! Jail is newer than host. (Jail: 1300113, Host: 1300100) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



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---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
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FLAVOR=
DEPENDS_ARGS=
MAKE_ARGS=
---End Poudriere Port Flags/Env---

---Begin OPTIONS List---
---End OPTIONS List---

--MAINTAINER--
ports@FreeBSD.org
--End MAINTAINER--

--CONFIGURE_ARGS--

--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/grappa/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/grappa/work  HOME=/wrkdirs/usr/ports/biology/grappa/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/grappa/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/grappa/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/grappa/work  HOME=/wrkdirs/usr/ports/biology/grappa/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/grappa/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--
OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local  RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/grappa"  EXAMPLESDIR="share/examples/grappa"  DATADIR="share/grappa"  WWWDIR="www/grappa"  ETCDIR="etc/grappa"
--End PLIST_SUB--

--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local  DATADIR=/usr/local/share/grappa DOCSDIR=/usr/local/share/doc/grappa EXAMPLESDIR=/usr/local/share/examples/grappa  WWWDIR=/usr/local/www/grappa ETCDIR=/usr/local/etc/grappa
--End SUB_LIST--

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#### /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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kqueues                         (-k)  unlimited
umtx shared locks               (-o)  unlimited
--End resource limits--
=======================<phase: check-sanity   >============================
===>   NOTICE:

The grappa 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 GPLv2 accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   grappa-2.0 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.14.7.txz
[head-armv6-default-job-16] Installing pkg-1.14.7...
[head-armv6-default-job-16] Extracting pkg-1.14.7: .......... done
===>   grappa-2.0 depends on file: /usr/local/sbin/pkg - found
<snip>
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for grappa-2.0
===>  Applying FreeBSD patches for grappa-2.0 from /usr/ports/biology/grappa/files
===========================================================================
=======================<phase: build-depends  >============================
===>   grappa-2.0 depends on package: gmake>=4.3 - not found
===>   Installing existing package /packages/All/gmake-4.3_2.txz
[head-armv6-default-job-16] Installing gmake-4.3_2...
[head-armv6-default-job-16] `-- Installing gettext-runtime-0.21...
[head-armv6-default-job-16] |   `-- Installing indexinfo-0.3.1...
[head-armv6-default-job-16] |   `-- Extracting indexinfo-0.3.1: .... done
[head-armv6-default-job-16] `-- Extracting gettext-runtime-0.21: .......... done
[head-armv6-default-job-16] Extracting gmake-4.3_2: .......... done
===>   grappa-2.0 depends on package: gmake>=4.3 - found
===>   Returning to build of grappa-2.0
===========================================================================
=======================<phase: lib-depends    >============================
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for grappa-2.0
===========================================================================
=======================<phase: build          >============================
===>  Building for grappa-2.0
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/grappa/work/GRAPPA20'
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c convert.c -o convert.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c labeltree.c -o labeltree.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c main.c -o main.o
main.c:2679:18: warning: overflow converting case value to switch condition type (-1 to 255) [-Wswitch]
            case EOF:
                 ^
/usr/include/stdio.h:210:13: note: expanded from macro 'EOF'
#define EOF     (-1)
                ^
1 warning generated.
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c binencode.c -o binencode.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c gen_tree.c -o gen_tree.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c inittree.c -o inittree.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c circ_order.c -o circ_order.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c lk_main.c -o lk_main.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c bbtsp.c -o bbtsp.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c condense.c -o condense.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c const_tree.c -o const_tree.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c greedy_median.c -o greedy_median.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c invdist.c -o invdist.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c uf.c -o uf.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c neighborj.c -o neighborj.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c condense3.c -o condense3.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c getopt3.c -o getopt3.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c randomBSD.c -o randomBSD.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c cheaptsp.c -o cheaptsp.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c specialtsp.c -o specialtsp.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c specialinit.c -o specialinit.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c read_input.c -o read_input.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c circular_ordering.c -o circular_ordering.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c correction.c -o correction.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c inversion_median.c -o inversion_median.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c inversion_median_alberto.c -o inversion_median_alberto.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c priority_stack.c -o priority_stack.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c hashtable.c -o hashtable.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c med_util.c -o med_util.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c simpleio.c -o simpleio.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c vertex_factory.c -o vertex_factory.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c growTree.c -o growTree.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c bitvector.c -o bitvector.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c lists.c -o lists.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c sorting_reversal_median.c -o sorting_reversal_median.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c mythread_rwlock.c -o mythread_rwlock.o
/nxb-bin/usr/bin/cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT  -c all_sorting_reversals.c -o all_sorting_reversals.o
/nxb-bin/usr/bin/cc  -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DFreeBSD   -DINIT   -o grappa  convert.o labeltree.o main.o binencode.o gen_tree.o inittree.o circ_order.o lk_main.o bbtsp.o condense.o const_tree.o greedy_median.o invdist.o uf.o neighborj.o condense3.o getopt3.o randomBSD.o cheaptsp.o specialtsp.o specialinit.o read_input.o circular_ordering.o correction.o inversion_median.o inversion_median_alberto.o priority_stack.o hashtable.o med_util.o simpleio.o vertex_factory.o growTree.o bitvector.o lists.o sorting_reversal_median.o mythread_rwlock.o all_sorting_reversals.o   -lm -pthread 
ld: error: duplicate symbol: MAXEDG
>>> defined at labeltree.c
>>>            labeltree.o:(MAXEDG)
>>> defined at main.c
>>>            main.o:(.bss+0x18)

ld: error: duplicate symbol: MAXM
>>> defined at labeltree.c
>>>            labeltree.o:(MAXM)
>>> defined at main.c
>>>            main.o:(.bss+0x14)

ld: error: duplicate symbol: MAXNOD
>>> defined at labeltree.c
>>>            labeltree.o:(MAXNOD)
>>> defined at main.c
>>>            main.o:(.bss+0x10)

ld: error: duplicate symbol: Num_Genes
>>> defined at labeltree.c
>>>            labeltree.o:(Num_Genes)
>>> defined at main.c
>>>            main.o:(.bss+0xC)

ld: error: duplicate symbol: UB
>>> defined at labeltree.c
>>>            labeltree.o:(UB)
>>> defined at main.c
>>>            main.o:(.bss+0xA8)

ld: error: duplicate symbol: at_root
>>> defined at labeltree.c
>>>            labeltree.o:(at_root)
>>> defined at main.c
>>>            main.o:(.bss+0x80)

ld: error: duplicate symbol: bcyceq
>>> defined at labeltree.c
>>>            labeltree.o:(bcyceq)
>>> defined at main.c
>>>            main.o:(.bss+0x74)

ld: error: duplicate symbol: bcycvar
>>> defined at labeltree.c
>>>            labeltree.o:(bcycvar)
>>> defined at main.c
>>>            main.o:(.bss+0x64)

ld: error: duplicate symbol: bdegree
>>> defined at labeltree.c
>>>            labeltree.o:(bdegree)
>>> defined at main.c
>>>            main.o:(.bss+0x6C)

ld: error: duplicate symbol: bedge
>>> defined at labeltree.c
>>>            labeltree.o:(bedge)
>>> defined at main.c
>>>            main.o:(.bss+0x58)

ld: error: duplicate symbol: best_now
>>> defined at labeltree.c
>>>            labeltree.o:(best_now)
>>> defined at main.c
>>>            main.o:(.bss+0xAC)

ld: error: duplicate symbol: bestsol
>>> defined at labeltree.c
>>>            labeltree.o:(bestsol)
>>> defined at main.c
>>>            main.o:(.bss+0x90)

ld: error: duplicate symbol: bestub
>>> defined at labeltree.c
>>>            labeltree.o:(bestub)
>>> defined at main.c
>>>            main.o:(.bss+0x88)

ld: error: duplicate symbol: bsec
>>> defined at labeltree.c
>>>            labeltree.o:(bsec)
>>> defined at main.c
>>>            main.o:(.bss+0x7C)

ld: error: duplicate symbol: cycvar
>>> defined at labeltree.c
>>>            labeltree.o:(cycvar)
>>> defined at main.c
>>>            main.o:(.bss+0xA4)

ld: error: duplicate symbol: e_ind
>>> defined at labeltree.c
>>>            labeltree.o:(e_ind)
>>> defined at main.c
>>>            main.o:(.bss+0x2C)

ld: error: duplicate symbol: ec
>>> defined at labeltree.c
>>>            labeltree.o:(ec)
>>> defined at main.c
>>>            main.o:(.bss+0x28)

ld: error: duplicate symbol: fid
>>> defined at labeltree.c
>>>            labeltree.o:(fid)
>>> defined at main.c
>>>            main.o:(.bss+0x98)

ld: error: duplicate symbol: fout
>>> defined at labeltree.c
>>>            labeltree.o:(fout)
>>> defined at main.c
>>>            main.o:(.bss+0x9C)

ld: error: duplicate symbol: gen
>>> defined at labeltree.c
>>>            labeltree.o:(gen)
>>> defined at main.c
>>>            main.o:(.bss+0xF4)

ld: error: too many errors emitted, stopping now (use -error-limit=0 to see all errors)
cc: error: linker command failed with exit code 1 (use -v to see invocation)
gmake[1]: *** [Makefile:129: grappa] Error 1
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/grappa/work/GRAPPA20'
*** Error code 1

Stop.
make: stopped in /usr/ports/biology/grappa



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