[package - head-powerpc64-default][biology/grappa] Failed for grappa-2.0 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Thu Sep 3 08:02:35 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: rm at FreeBSD.org
Ident: $FreeBSD: head/biology/grappa/Makefile 397864 2015-09-25 18:55:08Z rm $
Log URL: http://pylon.nyi.freebsd.org/data/head-powerpc64-default/p545799_s364495/logs/grappa-2.0.log
Build URL: http://pylon.nyi.freebsd.org/build.html?mastername=head-powerpc64-default&build=p545799_s364495
Log:
=>> Building biology/grappa
build started at Thu Sep 3 08:01:51 UTC 2020
port directory: /usr/ports/biology/grappa
package name: grappa-2.0
building for: FreeBSD head-powerpc64-default-job-01 13.0-CURRENT FreeBSD 13.0-CURRENT 1300111 powerpc
maintained by: ports at 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: 1300084
Jail OSVERSION: 1300111
Job Id: 01
!!! Jail is newer than host. (Jail: 1300111, Host: 1300084) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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UNAME_v=FreeBSD 13.0-CURRENT 1300111
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MAIL=/var/mail/root
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P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
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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---
---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/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="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--
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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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BATCH=yes
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# 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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CC_OUTPUT_921dbbb2_308abb44=yes
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CC_OUTPUT_921dbbb2_b2657cc3=yes
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CC_OUTPUT_921dbbb2_fb62803b=yes
_OBJC_CCVERSION_921dbbb2=FreeBSD clang version 11.0.0 (git at github.com:llvm/llvm-project.git llvmorg-11.0.0-rc1-47-gff47911ddfc) Target: powerpc64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin
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GID=0
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cpu time (seconds, -t) unlimited
file size (512-blocks, -f) unlimited
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max memory size (kbytes, -m) unlimited
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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 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-powerpc64-default-job-01] Installing pkg-1.14.7...
[head-powerpc64-default-job-01] Extracting pkg-1.14.7: .......... done
===> grappa-2.0 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of grappa-2.0
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> 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
===> Fetching all distfiles required by grappa-2.0 for building
===========================================================================
=======================<phase: checksum >============================
===> 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:
<snip>
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
all_sorting_reversals.c:1345:16: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast]
next = ( int ) list_get ( &adj_list[v], 0 ) == prev ?
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
all_sorting_reversals.c:1346:13: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast]
( int ) list_get ( &adj_list[v], 1 ) :
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
all_sorting_reversals.c:1347:13: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast]
( int ) list_get ( &adj_list[v], 0 );
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
all_sorting_reversals.c:1687:17: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast]
label = ( int ) list_get ( V, i );
^~~~~~~~~~~~~~~~~~~~~~~~~
all_sorting_reversals.c:1791:49: warning: cast to 'void *' from smaller integer type 'int' [-Wint-to-void-pointer-cast]
push ( &mem->comp_grey_edges[comp], ( void * ) mem->upi_cpy[i] );
^~~~~~~~~~~~~~~~~~~~~~~~~~
all_sorting_reversals.c:1860:36: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast]
( int ) list_get ( &c1->cyclelist, i )];
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
all_sorting_reversals.c:1863:36: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast]
( int ) list_get ( &c2->cyclelist, j )];
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
all_sorting_reversals.c:1868:33: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast]
a = ( int ) list_get ( edges1, k );
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
all_sorting_reversals.c:1869:33: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast]
b = ( int ) list_get ( edges2, k2 );
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
all_sorting_reversals.c:1892:28: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast]
edges = &cyclelist[( int ) list_get ( &cc->cyclelist, j )];
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
all_sorting_reversals.c:1897:21: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast]
a = ( int ) list_get ( edges, k );
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
all_sorting_reversals.c:1898:21: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast]
b = ( int ) list_get ( edges, k2 );
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
all_sorting_reversals.c:1940:12: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast]
( int ) list_get ( &conn_comp[h1].double_superhurdle_partners,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
all_sorting_reversals.c:1943:18: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast]
&& ( int ) list_get ( &conn_comp[h1].
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
all_sorting_reversals.c:2219:24: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast]
comp = ( int ) pop_stack ( &tmpl );
^~~~~~~~~~~~~~~~~~~~~~~~~~~
all_sorting_reversals.c:2222:40: warning: cast to 'void *' from smaller integer type 'int' [-Wint-to-void-pointer-cast]
push ( &separated_ocs, ( void * ) comp );
^~~~~~~~~~~~~~~
all_sorting_reversals.c:2223:45: warning: cast to 'void *' from smaller integer type 'int' [-Wint-to-void-pointer-cast]
push ( &separating_hurdles, ( void * ) currenth );
^~~~~~~~~~~~~~~~~~~
all_sorting_reversals.c:2248:25: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast]
int c = ( int ) pop_stack ( &tmpl );
^~~~~~~~~~~~~~~~~~~~~~~~~~~
all_sorting_reversals.c:2324:27: warning: cast to 'void *' from smaller integer type 'int' [-Wint-to-void-pointer-cast]
push ( &tmpl, ( void * ) comp );
^~~~~~~~~~~~~~~
all_sorting_reversals.c:2347:18: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast]
oc = ( int ) list_get ( &separated_ocs, i );
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
all_sorting_reversals.c:2349:17: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast]
h = ( int ) list_get ( &separating_hurdles, i );
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
all_sorting_reversals.c:2357:34: warning: cast to 'void *' from smaller integer type 'int' [-Wint-to-void-pointer-cast]
push ( &( *ocs )[j], ( void * ) oc );
^~~~~~~~~~~~~
90 warnings generated.
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+0x24)
ld: error: duplicate symbol: MAXM
>>> defined at labeltree.c
>>> labeltree.o:(MAXM)
>>> defined at main.c
>>> main.o:(.bss+0x20)
ld: error: duplicate symbol: MAXNOD
>>> defined at labeltree.c
>>> labeltree.o:(MAXNOD)
>>> defined at main.c
>>> main.o:(.bss+0x1C)
ld: error: duplicate symbol: Num_Genes
>>> defined at labeltree.c
>>> labeltree.o:(Num_Genes)
>>> defined at main.c
>>> main.o:(.bss+0x18)
ld: error: duplicate symbol: UB
>>> defined at labeltree.c
>>> labeltree.o:(UB)
>>> defined at main.c
>>> main.o:(.bss+0xF8)
ld: error: duplicate symbol: at_root
>>> defined at labeltree.c
>>> labeltree.o:(at_root)
>>> defined at main.c
>>> main.o:(.bss+0xBC)
ld: error: duplicate symbol: bcyceq
>>> defined at labeltree.c
>>> labeltree.o:(bcyceq)
>>> defined at main.c
>>> main.o:(.bss+0xB0)
ld: error: duplicate symbol: bcycvar
>>> defined at labeltree.c
>>> labeltree.o:(bcycvar)
>>> defined at main.c
>>> main.o:(.bss+0xA0)
ld: error: duplicate symbol: bdegree
>>> defined at labeltree.c
>>> labeltree.o:(bdegree)
>>> defined at main.c
>>> main.o:(.bss+0xA8)
ld: error: duplicate symbol: bedge
>>> defined at labeltree.c
>>> labeltree.o:(bedge)
>>> defined at main.c
>>> main.o:(.bss+0x94)
ld: error: duplicate symbol: best_now
>>> defined at labeltree.c
>>> labeltree.o:(best_now)
>>> defined at main.c
>>> main.o:(.bss+0xFC)
ld: error: duplicate symbol: bestsol
>>> defined at labeltree.c
>>> labeltree.o:(bestsol)
>>> defined at main.c
>>> main.o:(.bss+0xC8)
ld: error: duplicate symbol: bestub
>>> defined at labeltree.c
>>> labeltree.o:(bestub)
>>> defined at main.c
>>> main.o:(.bss+0xC0)
ld: error: duplicate symbol: bsec
>>> defined at labeltree.c
>>> labeltree.o:(bsec)
>>> defined at main.c
>>> main.o:(.bss+0xB8)
ld: error: duplicate symbol: cycvar
>>> defined at labeltree.c
>>> labeltree.o:(cycvar)
>>> defined at main.c
>>> main.o:(.bss+0xF0)
ld: error: duplicate symbol: e_ind
>>> defined at labeltree.c
>>> labeltree.o:(e_ind)
>>> defined at main.c
>>> main.o:(.bss+0x40)
ld: error: duplicate symbol: ec
>>> defined at labeltree.c
>>> labeltree.o:(ec)
>>> defined at main.c
>>> main.o:(.bss+0x38)
ld: error: duplicate symbol: fid
>>> defined at labeltree.c
>>> labeltree.o:(fid)
>>> defined at main.c
>>> main.o:(.bss+0xD8)
ld: error: duplicate symbol: fout
>>> defined at labeltree.c
>>> labeltree.o:(fout)
>>> defined at main.c
>>> main.o:(.bss+0xE0)
ld: error: duplicate symbol: gen
>>> defined at labeltree.c
>>> labeltree.o:(gen)
>>> defined at main.c
>>> main.o:(.bss+0x170)
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'
===> 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/grappa
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