[package - main-amd64-default][biology/abyss] Failed for abyss-2.3.5_1 in build
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Date: Sat, 11 Feb 2023 00:58:09 UTC
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: yuri@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy18/data/main-amd64-default/p58633340e9ed_s5636590214/logs/abyss-2.3.5_1.log
Build URL: https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=p58633340e9ed_s5636590214
Log:
=>> Building biology/abyss
build started at Sat Feb 11 00:55:34 UTC 2023
port directory: /usr/ports/biology/abyss
package name: abyss-2.3.5_1
building for: FreeBSD main-amd64-default-job-09 14.0-CURRENT FreeBSD 14.0-CURRENT 1400079 amd64
maintained by: yuri@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400073
Jail OSVERSION: 1400079
Job Id: 09
!!! Jail is newer than host. (Jail: 1400079, Host: 1400073) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
---Begin Environment---
SHELL=/bin/sh
OSVERSION=1400079
UNAME_v=FreeBSD 14.0-CURRENT 1400079
UNAME_r=14.0-CURRENT
BLOCKSIZE=K
MAIL=/var/mail/root
MM_CHARSET=UTF-8
LANG=C.UTF-8
STATUS=1
HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
LOCALBASE=/usr/local
USER=root
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.2.8-23-ga7f8d188
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OLDPWD=/usr/local/poudriere/data/.m/main-amd64-default/ref/.p
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
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---
===> The following configuration options are available for abyss-2.3.5_1:
DOCS=on: Build and/or install documentation
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--without-sparsehash --prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/abyss/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/abyss/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/abyss/work/.cache HOME=/wrkdirs/usr/ports/biology/abyss/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/abyss/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/abyss/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh DEFAULT_AUTOCONF=2.71 CMAKE_PREFIX_PATH="/usr/local" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288
--End CONFIGURE_ENV--
--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/abyss/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/abyss/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/abyss/work/.cache HOME=/wrkdirs/usr/ports/biology/abyss/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/abyss/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/abyss/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DEFAULT_AUTOCONF=2.71 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " 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=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/abyss" EXAMPLESDIR="share/examples/abyss" DATADIR="share/abyss" WWWDIR="www/abyss" ETCDIR="etc/abyss"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/abyss DOCSDIR=/usr/local/share/doc/abyss EXAMPLESDIR=/usr/local/share/examples/abyss WWWDIR=/usr/local/www/abyss ETCDIR=/usr/local/etc/abyss
--End SUB_LIST--
---Begin make.conf---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
#### /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 ####
_CCVERSION_921dbbb2=FreeBSD clang version 15.0.7 (https://github.com/llvm/llvm-project.git llvmorg-15.0.7-0-g8dfdcc7b7bf6) Target: x86_64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin
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CC_OUTPUT_921dbbb2_58173849=yes
CC_OUTPUT_921dbbb2_9bdba57c=yes
CC_OUTPUT_921dbbb2_6a4fe7f5=yes
CC_OUTPUT_921dbbb2_6bcac02b=yes
CC_OUTPUT_921dbbb2_67d20829=yes
CC_OUTPUT_921dbbb2_bfa62e83=yes
CC_OUTPUT_921dbbb2_f0b4d593=yes
CC_OUTPUT_921dbbb2_308abb44=yes
CC_OUTPUT_921dbbb2_f00456e5=yes
CC_OUTPUT_921dbbb2_65ad290d=yes
CC_OUTPUT_921dbbb2_f2776b26=yes
CC_OUTPUT_921dbbb2_53255a77=yes
CC_OUTPUT_921dbbb2_911cfe02=yes
CC_OUTPUT_921dbbb2_b2657cc3=yes
CC_OUTPUT_921dbbb2_380987f7=yes
CC_OUTPUT_921dbbb2_160933ec=yes
CC_OUTPUT_921dbbb2_fb62803b=yes
CC_OUTPUT_921dbbb2_af59ad06=yes
CC_OUTPUT_921dbbb2_a15f3fcf=yes
_OBJC_CCVERSION_921dbbb2=FreeBSD clang version 15.0.7 (https://github.com/llvm/llvm-project.git llvmorg-15.0.7-0-g8dfdcc7b7bf6) Target: x86_64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin
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ARCH=amd64
OPSYS=FreeBSD
_OSRELEASE=14.0-CURRENT
OSREL=14.0
OSVERSION=1400079
PYTHONBASE=/usr/local
HAVE_COMPAT_IA32_KERN=YES
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) 33554432
stack size (kbytes, -s) 524288
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 >============================
===> License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> abyss-2.3.5_1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.19.1.pkg
[main-amd64-default-job-09] Installing pkg-1.19.1...
[main-amd64-default-job-09] Extracting pkg-1.19.1: .......... done
===> abyss-2.3.5_1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of abyss-2.3.5_1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by abyss-2.3.5_1 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by abyss-2.3.5_1 for building
=> SHA256 Checksum OK for bcgsc-abyss-2.3.5_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by abyss-2.3.5_1 for building
===> Extracting for abyss-2.3.5_1
=> SHA256 Checksum OK for bcgsc-abyss-2.3.5_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for abyss-2.3.5_1
===> Applying FreeBSD patches for abyss-2.3.5_1 from /usr/ports/biology/abyss/files
===========================================================================
=======================<phase: build-depends >============================
===> abyss-2.3.5_1 depends on file: /usr/local/include/boost/version.hpp - not found
<snip>
rm -f libdatalayer.a
ar cru libdatalayer.a libdatalayer_a-FastaReader.o libdatalayer_a-FastaWriter.o
ranlib libdatalayer.a
c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-fac abyss_fac-fac.o libdatalayer.a ../Common/libcommon.a -ldl -lm
mv -f .deps/abyss_tofastq-abyss-tofastq.Tpo .deps/abyss_tofastq-abyss-tofastq.Po
c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-tofastq abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -ldl -lm
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/DataLayer'
Making all in DataBase
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/DataBase'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_db_csv-DB.o -MD -MP -MF .deps/abyss_db_csv-DB.Tpo -c -o abyss_db_csv-DB.o `test -f 'DB.cc' || echo './'`DB.cc
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_db_csv-db-csv.o -MD -MP -MF .deps/abyss_db_csv-db-csv.Tpo -c -o abyss_db_csv-db-csv.o `test -f 'db-csv.cc' || echo './'`db-csv.cc
mv -f .deps/abyss_db_csv-db-csv.Tpo .deps/abyss_db_csv-db-csv.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libdb_a-DB.o -MD -MP -MF .deps/libdb_a-DB.Tpo -c -o libdb_a-DB.o `test -f 'DB.cc' || echo './'`DB.cc
mv -f .deps/abyss_db_csv-DB.Tpo .deps/abyss_db_csv-DB.Po
c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-db-csv abyss_db_csv-DB.o abyss_db_csv-db-csv.o -lsqlite3 -ldl -lm
mv -f .deps/libdb_a-DB.Tpo .deps/libdb_a-DB.Po
rm -f libdb.a
ar cru libdb.a libdb_a-DB.o ../Common/libcommon.a
ranlib libdb.a
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/DataBase'
Making all in FMIndex
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/FMIndex'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_count-count.o -MD -MP -MF .deps/abyss_count-count.Tpo -c -o abyss_count-count.o `test -f 'count.cc' || echo './'`count.cc
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libfmindex_a-bit_array.o -MD -MP -MF .deps/libfmindex_a-bit_array.Tpo -c -o libfmindex_a-bit_array.o `test -f 'bit_array.cc' || echo './'`bit_array.cc
mv -f .deps/libfmindex_a-bit_array.Tpo .deps/libfmindex_a-bit_array.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_dawg-abyss-dawg.o -MD -MP -MF .deps/abyss_dawg-abyss-dawg.Tpo -c -o abyss_dawg-abyss-dawg.o `test -f 'abyss-dawg.cc' || echo './'`abyss-dawg.cc
mv -f .deps/abyss_count-count.Tpo .deps/abyss_count-count.Po
rm -f libfmindex.a
ar cru libfmindex.a libfmindex_a-bit_array.o
ranlib libfmindex.a
c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-count abyss_count-count.o libfmindex.a ../Common/libcommon.a -ldl -lm
mv -f .deps/abyss_dawg-abyss-dawg.Tpo .deps/abyss_dawg-abyss-dawg.Po
c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-dawg abyss_dawg-abyss-dawg.o libfmindex.a ../Common/libcommon.a -ldl -lm
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/FMIndex'
Making all in Assembly
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/Assembly'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libassembly_a-AssemblyAlgorithms.o -MD -MP -MF .deps/libassembly_a-AssemblyAlgorithms.Tpo -c -o libassembly_a-AssemblyAlgorithms.o `test -f 'AssemblyAlgorithms.cc' || echo './'`AssemblyAlgorithms.cc
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libassembly_a-Options.o -MD -MP -MF .deps/libassembly_a-Options.Tpo -c -o libassembly_a-Options.o `test -f 'Options.cc' || echo './'`Options.cc
mv -f .deps/libassembly_a-Options.Tpo .deps/libassembly_a-Options.Po
mv -f .deps/libassembly_a-AssemblyAlgorithms.Tpo .deps/libassembly_a-AssemblyAlgorithms.Po
rm -f libassembly.a
ar cru libassembly.a libassembly_a-AssemblyAlgorithms.o libassembly_a-Options.o ../Common/libcommon.a
ranlib libassembly.a
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/Assembly'
Making all in dialign
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/dialign'
depbase=`echo museq.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT museq.o -MD -MP -MF $depbase.Tpo -c -o museq.o museq.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo alig.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT alig.o -MD -MP -MF $depbase.Tpo -c -o alig.o alig.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo assemble.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT assemble.o -MD -MP -MF $depbase.Tpo -c -o assemble.o assemble.c &&\
mv -f $depbase.Tpo $depbase.Po
assemble.c:37:32: warning: inline function 'find_eqc' is not defined [-Wundefined-inline]
extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos);
^
assemble.c:115:9: note: used here
tap = find_eqc(ap, s1, sp1);
^
assemble.c:13:20: warning: inline function 'calc_weight' is not defined [-Wundefined-inline]
extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
^
assemble.c:459:4: note: used here
calc_weight(dg, smatrix, pdist);
^
assemble.c:40:20: warning: inline function 'align_diag' is not defined [-Wundefined-inline]
extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
^
assemble.c:532:24: note: used here
alignedSomething = align_diag(algn, smatrix, dg) || alignedSomething;
^
depbase=`echo diag.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT diag.o -MD -MP -MF $depbase.Tpo -c -o diag.o diag.c &&\
mv -f $depbase.Tpo $depbase.Po
diag.c:739:9: warning: equality comparison result unused [-Wunused-comparison]
sdg == NULL;
~~~~^~~~~~~
diag.c:739:9: note: use '=' to turn this equality comparison into an assignment
sdg == NULL;
^~
=
3 warnings generated.
depbase=`echo io.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT io.o -MD -MP -MF $depbase.Tpo -c -o io.o io.c &&\
mv -f $depbase.Tpo $depbase.Po
1 warning generated.
depbase=`echo orf.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT orf.o -MD -MP -MF $depbase.Tpo -c -o orf.o orf.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo parameters.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT parameters.o -MD -MP -MF $depbase.Tpo -c -o parameters.o parameters.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo prob.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT prob.o -MD -MP -MF $depbase.Tpo -c -o prob.o prob.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo translate.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT translate.o -MD -MP -MF $depbase.Tpo -c -o translate.o translate.c &&\
mv -f $depbase.Tpo $depbase.Po
rm -f libdialign.a
ar cru libdialign.a alig.o assemble.o diag.o io.o orf.o parameters.o prob.o translate.o
ranlib libdialign.a
cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -L/usr/local/lib -o dialign museq.o libdialign.a -ldl -lm
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/dialign'
Making all in Align
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/Align'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_align-align.o -MD -MP -MF .deps/abyss_align-align.Tpo -c -o abyss_align-align.o `test -f 'align.cc' || echo './'`align.cc
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libalign_a-alignGlobal.o -MD -MP -MF .deps/libalign_a-alignGlobal.Tpo -c -o libalign_a-alignGlobal.o `test -f 'alignGlobal.cc' || echo './'`alignGlobal.cc
mv -f .deps/libalign_a-alignGlobal.Tpo .deps/libalign_a-alignGlobal.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libalign_a-dialign.o -MD -MP -MF .deps/libalign_a-dialign.Tpo -c -o libalign_a-dialign.o `test -f 'dialign.cpp' || echo './'`dialign.cpp
mv -f .deps/abyss_align-align.Tpo .deps/abyss_align-align.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libalign_a-dna_diag_prob.o -MD -MP -MF .deps/libalign_a-dna_diag_prob.Tpo -c -o libalign_a-dna_diag_prob.o `test -f 'dna_diag_prob.cc' || echo './'`dna_diag_prob.cc
mv -f .deps/libalign_a-dialign.Tpo .deps/libalign_a-dialign.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libalign_a-smith_waterman.o -MD -MP -MF .deps/libalign_a-smith_waterman.Tpo -c -o libalign_a-smith_waterman.o `test -f 'smith_waterman.cpp' || echo './'`smith_waterman.cpp
mv -f .deps/libalign_a-dna_diag_prob.Tpo .deps/libalign_a-dna_diag_prob.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_mergepairs-mergepairs.o -MD -MP -MF .deps/abyss_mergepairs-mergepairs.Tpo -c -o abyss_mergepairs-mergepairs.o `test -f 'mergepairs.cc' || echo './'`mergepairs.cc
mv -f .deps/libalign_a-smith_waterman.Tpo .deps/libalign_a-smith_waterman.Po
rm -f libalign.a
ar cru libalign.a libalign_a-alignGlobal.o libalign_a-dialign.o libalign_a-dna_diag_prob.o libalign_a-smith_waterman.o
ranlib libalign.a
c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-align abyss_align-align.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
mv -f .deps/abyss_mergepairs-mergepairs.Tpo .deps/abyss_mergepairs-mergepairs.Po
c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-mergepairs abyss_mergepairs-mergepairs.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/Align'
Making all in ABYSS
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/ABYSS'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ABYSS-abyss.o -MD -MP -MF .deps/ABYSS-abyss.Tpo -c -o ABYSS-abyss.o `test -f 'abyss.cc' || echo './'`abyss.cc
mv -f .deps/ABYSS-abyss.Tpo .deps/ABYSS-abyss.Po
c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o ABYSS ABYSS-abyss.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
ld: warning: ../DataBase/libdb.a: archive member 'libcommon.a' is neither ET_REL nor LLVM bitcode
ld: warning: ../Assembly/libassembly.a: archive member 'libcommon.a' is neither ET_REL nor LLVM bitcode
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/ABYSS'
Making all in Parallel
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/Parallel'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ABYSS_P-parallelAbyss.o -MD -MP -MF .deps/ABYSS_P-parallelAbyss.Tpo -c -o ABYSS_P-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ABYSS_P-CommLayer.o -MD -MP -MF .deps/ABYSS_P-CommLayer.Tpo -c -o ABYSS_P-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp
mv -f .deps/ABYSS_P-CommLayer.Tpo .deps/ABYSS_P-CommLayer.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ABYSS_P-NetworkSequenceCollection.o -MD -MP -MF .deps/ABYSS_P-NetworkSequenceCollection.Tpo -c -o ABYSS_P-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp
mv -f .deps/ABYSS_P-parallelAbyss.Tpo .deps/ABYSS_P-parallelAbyss.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ABYSS_P-MessageBuffer.o -MD -MP -MF .deps/ABYSS_P-MessageBuffer.Tpo -c -o ABYSS_P-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp
mv -f .deps/ABYSS_P-MessageBuffer.Tpo .deps/ABYSS_P-MessageBuffer.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ABYSS_P-Messages.o -MD -MP -MF .deps/ABYSS_P-Messages.Tpo -c -o ABYSS_P-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp
mv -f .deps/ABYSS_P-Messages.Tpo .deps/ABYSS_P-Messages.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_paired_dbg_mpi-parallelAbyss.o -MD -MP -MF .deps/abyss_paired_dbg_mpi-parallelAbyss.Tpo -c -o abyss_paired_dbg_mpi-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp
mv -f .deps/ABYSS_P-NetworkSequenceCollection.Tpo .deps/ABYSS_P-NetworkSequenceCollection.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_paired_dbg_mpi-CommLayer.o -MD -MP -MF .deps/abyss_paired_dbg_mpi-CommLayer.Tpo -c -o abyss_paired_dbg_mpi-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp
mv -f .deps/abyss_paired_dbg_mpi-CommLayer.Tpo .deps/abyss_paired_dbg_mpi-CommLayer.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_paired_dbg_mpi-NetworkSequenceCollection.o -MD -MP -MF .deps/abyss_paired_dbg_mpi-NetworkSequenceCollection.Tpo -c -o abyss_paired_dbg_mpi-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp
mv -f .deps/abyss_paired_dbg_mpi-parallelAbyss.Tpo .deps/abyss_paired_dbg_mpi-parallelAbyss.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_paired_dbg_mpi-MessageBuffer.o -MD -MP -MF .deps/abyss_paired_dbg_mpi-MessageBuffer.Tpo -c -o abyss_paired_dbg_mpi-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp
mv -f .deps/abyss_paired_dbg_mpi-MessageBuffer.Tpo .deps/abyss_paired_dbg_mpi-MessageBuffer.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_paired_dbg_mpi-Messages.o -MD -MP -MF .deps/abyss_paired_dbg_mpi-Messages.Tpo -c -o abyss_paired_dbg_mpi-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp
mv -f .deps/abyss_paired_dbg_mpi-Messages.Tpo .deps/abyss_paired_dbg_mpi-Messages.Po
c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o ABYSS-P ABYSS_P-parallelAbyss.o ABYSS_P-CommLayer.o ABYSS_P-NetworkSequenceCollection.o ABYSS_P-MessageBuffer.o ABYSS_P-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm
ld: warning: ../Assembly/libassembly.a: archive member 'libcommon.a' is neither ET_REL nor LLVM bitcode
ld: warning: ../DataBase/libdb.a: archive member 'libcommon.a' is neither ET_REL nor LLVM bitcode
mv -f .deps/abyss_paired_dbg_mpi-NetworkSequenceCollection.Tpo .deps/abyss_paired_dbg_mpi-NetworkSequenceCollection.Po
c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-paired-dbg-mpi abyss_paired_dbg_mpi-parallelAbyss.o abyss_paired_dbg_mpi-CommLayer.o abyss_paired_dbg_mpi-NetworkSequenceCollection.o abyss_paired_dbg_mpi-MessageBuffer.o abyss_paired_dbg_mpi-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm
ld: warning: ../Assembly/libassembly.a: archive member 'libcommon.a' is neither ET_REL nor LLVM bitcode
ld: warning: ../DataBase/libdb.a: archive member 'libcommon.a' is neither ET_REL nor LLVM bitcode
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/Parallel'
Making all in Bloom
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/Bloom'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../vendor -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_bloom-bloom.o -MD -MP -MF .deps/abyss_bloom-bloom.Tpo -c -o abyss_bloom-bloom.o `test -f 'bloom.cc' || echo './'`bloom.cc
mv -f .deps/abyss_bloom-bloom.Tpo .deps/abyss_bloom-bloom.Po
c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-bloom abyss_bloom-bloom.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/Bloom'
Making all in BloomDBG
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/BloomDBG'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../vendor -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_bloom_dbg-bloom-dbg.o -MD -MP -MF .deps/abyss_bloom_dbg-bloom-dbg.Tpo -c -o abyss_bloom_dbg-bloom-dbg.o `test -f 'bloom-dbg.cc' || echo './'`bloom-dbg.cc
mv -f .deps/abyss_bloom_dbg-bloom-dbg.Tpo .deps/abyss_bloom_dbg-bloom-dbg.Po
c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-bloom-dbg abyss_bloom_dbg-bloom-dbg.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/BloomDBG'
Making all in Konnector
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/Konnector'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT konnector-konnector.o -MD -MP -MF .deps/konnector-konnector.Tpo -c -o konnector-konnector.o `test -f 'konnector.cc' || echo './'`konnector.cc
mv -f .deps/konnector-konnector.Tpo .deps/konnector-konnector.Po
c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o konnector konnector-konnector.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/Konnector'
Making all in Consensus
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/Consensus'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT Consensus-Consensus.o -MD -MP -MF .deps/Consensus-Consensus.Tpo -c -o Consensus-Consensus.o `test -f 'Consensus.cpp' || echo './'`Consensus.cpp
Consensus.cpp:379:11: error: variable 'numIgnored' set but not used [-Werror,-Wunused-but-set-variable]
unsigned numIgnored = 0;
^
1 error generated.
gmake[3]: *** [Makefile:407: Consensus-Consensus.o] Error 1
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/Consensus'
gmake[2]: *** [Makefile:488: all-recursive] Error 1
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5'
gmake[1]: *** [Makefile:408: all] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5'
===> 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/abyss