[package - head-i386-default][biology/bwa] Failed for bwa-0.7.17 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Thu Aug 27 20:30:25 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: jwb at FreeBSD.org
Last committer: jwb at FreeBSD.org
Ident: $FreeBSD: head/biology/bwa/Makefile 460452 2018-01-31 01:07:07Z jwb $
Log URL: http://beefy17.nyi.freebsd.org/data/head-i386-default/p546309_s364850/logs/bwa-0.7.17.log
Build URL: http://beefy17.nyi.freebsd.org/build.html?mastername=head-i386-default&build=p546309_s364850
Log:
=>> Building biology/bwa
build started at Thu Aug 27 20:30:15 UTC 2020
port directory: /usr/ports/biology/bwa
package name: bwa-0.7.17
building for: FreeBSD head-i386-default-job-02 13.0-CURRENT FreeBSD 13.0-CURRENT 1300113 i386
maintained by: jwb at FreeBSD.org
Makefile ident: $FreeBSD: head/biology/bwa/Makefile 460452 2018-01-31 01:07:07Z jwb $
Poudriere version: 3.2.8-5-gc81843e5
Host OSVERSION: 1300100
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Job Id: 02
!!! 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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jwb at FreeBSD.org
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=======================<phase: check-sanity >============================
===> License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> bwa-0.7.17 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.14.7.txz
[head-i386-default-job-02] Installing pkg-1.14.7...
[head-i386-default-job-02] Extracting pkg-1.14.7: .......... done
===> bwa-0.7.17 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of bwa-0.7.17
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by bwa-0.7.17 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by bwa-0.7.17 for building
=> SHA256 Checksum OK for lh3-bwa-v0.7.17_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by bwa-0.7.17 for building
===> Extracting for bwa-0.7.17
=> SHA256 Checksum OK for lh3-bwa-v0.7.17_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for bwa-0.7.17
===> Applying FreeBSD patches for bwa-0.7.17 from /usr/ports/biology/bwa/files
===========================================================================
=======================<phase: build-depends >============================
===> bwa-0.7.17 depends on package: gmake>=4.3 - not found
===> Installing existing package /packages/All/gmake-4.3_2.txz
[head-i386-default-job-02] Installing gmake-4.3_2...
[head-i386-default-job-02] `-- Installing gettext-runtime-0.21...
[head-i386-default-job-02] | `-- Installing indexinfo-0.3.1...
[head-i386-default-job-02] | `-- Extracting indexinfo-0.3.1: .... done
[head-i386-default-job-02] `-- Extracting gettext-runtime-0.21: .......... done
[head-i386-default-job-02] Extracting gmake-4.3_2: .......... done
===> bwa-0.7.17 depends on package: gmake>=4.3 - found
===> Returning to build of bwa-0.7.17
===========================================================================
=======================<phase: lib-depends >============================
===========================================================================
=======================<phase: configure >============================
===> Configuring for bwa-0.7.17
===========================================================================
=======================<phase: build >============================
===> Building for bwa-0.7.17
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/bwa/work/bwa-0.7.17'
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kthread.c -o kthread.o
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kstring.c -o kstring.o
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt.c -o bwt.o
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bntseq.c -o bntseq.o
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwa.c -o bwa.o
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem.c -o bwamem.o
bwamem.c:1075:72: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
err_printf("* %ld chains remain after removing duplicated chains\n", regs.n);
~~~ ^~~~~~
%zu
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_pair.c -o bwamem_pair.o
bwamem_pair.c:65:131: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n);
~~~ ^~~~~~~~~~
%zu
bwamem_pair.c:65:143: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n);
~~~ ^~~~~~~~~~
%zu
bwamem_pair.c:65:155: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n);
~~~ ^~~~~~~~~~
%zu
bwamem_pair.c:65:167: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n);
~~~ ^~~~~~~~~~
%zu
4 warnings generated.
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_extra.c -o bwamem_extra.o
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS malloc_wrap.c -o malloc_wrap.o
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS QSufSort.c -o QSufSort.o
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_gen.c -o bwt_gen.o
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS rope.c -o rope.o
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS rle.c -o rle.o
1 warning generated.
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS is.c -o is.o
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtindex.c -o bwtindex.o
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.c -o bwashm.o
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwase.c -o bwase.o
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwaseqio.c -o bwaseqio.o
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtgap.c -o bwtgap.o
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtaln.c -o bwtaln.o
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bamlite.c -o bamlite.o
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwape.c -o bwape.o
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kopen.c -o kopen.o
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS pemerge.c -o pemerge.o
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS maxk.c -o maxk.o
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_core.c -o bwtsw2_core.o
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_main.c -o bwtsw2_main.o
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_aux.c -o bwtsw2_aux.o
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_lite.c -o bwt_lite.o
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_chain.c -o bwtsw2_chain.o
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS fastmap.c -o fastmap.o
fastmap.c:413:42: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
err_printf("SQ\t%s\t%ld", seq->name.s, seq->seq.l);
~~~ ^~~~~~~~~~
%zu
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_pair.c -o bwtsw2_pair.o
1 warning generated.
cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS main.c -o main.o
ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o
cc -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o bwape.o kopen.o pemerge.o maxk.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread
ld: error: duplicate symbol: rle_auxtab
>>> defined at bwtindex.c
>>> bwtindex.o:(rle_auxtab) in archive ./libbwa.a
>>> defined at rope.c
>>> rope.o:(.rodata+0x0) in archive ./libbwa.a
ld: error: duplicate symbol: rle_auxtab
>>> defined at bwtindex.c
>>> bwtindex.o:(rle_auxtab) in archive ./libbwa.a
>>> defined at rle.c
>>> rle.o:(.rodata+0x0) in archive ./libbwa.a
cc: error: linker command failed with exit code 1 (use -v to see invocation)
gmake[1]: *** [Makefile:30: bwa] Error 1
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/bwa/work/bwa-0.7.17'
===> 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/bwa
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