[package - head-armv6-default][biology/grappa] Failed for grappa-2.0 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Mon Aug 31 03:54:49 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://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 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: 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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=======================<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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