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:     j...@freebsd.org
Last committer: j...@freebsd.org
Ident:          $FreeBSD: head/biology/unanimity/Makefile 478089 2018-08-25 
22:54:54Z jwb $
Log URL:        
http://beefy16.nyi.freebsd.org/data/head-armv7-default/p479812_s338689/logs/unanimity-3.1.0.log
Build URL:      
http://beefy16.nyi.freebsd.org/build.html?mastername=head-armv7-default&build=p479812_s338689
Log:

=>> Building biology/unanimity
build started at Wed Sep 19 01:53:01 UTC 2018
port directory: /usr/ports/biology/unanimity
package name: unanimity-3.1.0
building for: FreeBSD head-armv7-default-job-06 12.0-ALPHA6 FreeBSD 12.0-ALPHA6 
1200084 arm
maintained by: j...@freebsd.org
Makefile ident:      $FreeBSD: head/biology/unanimity/Makefile 478089 
2018-08-25 22:54:54Z jwb $
Poudriere version: 3.2.7-6-g819c79a1
Host OSVERSION: 1200069
Jail OSVERSION: 1200084
Job Id: 06




!!! Jail is newer than host. (Jail: 1200084, Host: 1200069) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



---Begin Environment---
SHELL=/bin/csh
UNAME_p=armv7
UNAME_m=arm
ABI_FILE=/usr/lib/crt1.o
OSVERSION=1200084
UNAME_v=FreeBSD 12.0-ALPHA6 1200084
UNAME_r=12.0-ALPHA6
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
LOCALBASE=/usr/local
QEMU_EMULATING=1
USER=root
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.2.7-6-g819c79a1
MASTERMNT=/usr/local/poudriere/data/.m/head-armv7-default/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
PWD=/usr/local/poudriere/data/.m/head-armv7-default/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=head-armv7-default
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/head-armv7-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---
---End OPTIONS List---

--MAINTAINER--
j...@freebsd.org
--End MAINTAINER--

--CONFIGURE_ARGS--

--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
PKG_CONFIG=pkgconf PYTHON="/usr/local/bin/python2.7" 
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/unanimity/work  
XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/unanimity/work  
HOME=/wrkdirs/usr/ports/biology/unanimity/work TMPDIR="/tmp" 
PATH=/wrkdirs/usr/ports/biology/unanimity/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/unanimity/work  
XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/unanimity/work  
HOME=/wrkdirs/usr/ports/biology/unanimity/work TMPDIR="/tmp" 
PATH=/wrkdirs/usr/ports/biology/unanimity/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 
DESTDIR=/wrkdirs/usr/ports/biology/unanimity/work/stage PREFIX=/usr/local  
LOCALBASE=/usr/local  CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe  
-fno-strict-aliasing"  CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS=""  LDFLAGS="" 
LIBS=""  CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -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--
CMAKE_BUILD_TYPE="release" PYTHON_INCLUDEDIR=include/python2.7  
PYTHON_LIBDIR=lib/python2.7  PYTHON_PLATFORM=freebsd12  PYTHON_PYOEXTENSION=pyo 
 PYTHON_SITELIBDIR=lib/python2.7/site-packages  PYTHON_SUFFIX=27  
PYTHON_VER=2.7  PYTHON_VERSION=python2.7 PYTHON2="" PYTHON3="@comment " 
OSREL=12.0 PREFIX=%D LOCALBASE=/usr/local  RESETPREFIX=/usr/local LIB32DIR=lib 
DOCSDIR="share/doc/unanimity"  EXAMPLESDIR="share/examples/unanimity"  
DATADIR="share/unanimity"  WWWDIR="www/unanimity"  ETCDIR="etc/unanimity"
--End PLIST_SUB--

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

---Begin make.conf---
.sinclude "/etc/make.nxb.conf"
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
MACHINE=arm
MACHINE_ARCH=armv7
ARCH=${MACHINE_ARCH}
#### /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

# stable/10 includes src.conf too late but make.conf is in sys.mk
.if ${.CURDIR:M/poudriere/jails/10*/usr/src/usr.bin/xlint*}
# Disable build of llib now that head no longer has lint(1)
LINT=   true
.endif
#### /usr/ports/Mk/Scripts/ports_env.sh ####
_CCVERSION_9d218390=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) 
(based on LLVM 6.0.1) Target: armv7-unknown-freebsd12.0-gnueabihf Thread model: 
posix InstalledDir: /nxb-bin/usr/bin
_ALTCCVERSION_9d218390=none
_CXXINTERNAL_9c45a5b1=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 
335540) (based on LLVM 6.0.1) Target: armv7-unknown-freebsd12.0-gnueabihf 
Thread model: posix InstalledDir: /nxb-bin/usr/bin "/nxb-bin/usr/bin/ld" 
"--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" 
"--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" 
"/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" 
"--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" 
"--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o"
CC_OUTPUT_9d218390_58173849=yes
CC_OUTPUT_9d218390_9bdba57c=yes
CC_OUTPUT_9d218390_6a4fe7f5=yes
CC_OUTPUT_9d218390_6bcac02b=yes
CC_OUTPUT_9d218390_67d20829=yes
CC_OUTPUT_9d218390_bfa62e83=yes
CC_OUTPUT_9d218390_f0b4d593=yes
CC_OUTPUT_9d218390_308abb44=yes
CC_OUTPUT_9d218390_f00456e5=yes
CC_OUTPUT_9d218390_65ad290d=yes
CC_OUTPUT_9d218390_f2776b26=yes
CC_OUTPUT_9d218390_b2657cc3=yes
CC_OUTPUT_9d218390_380987f7=yes
CC_OUTPUT_9d218390_160933ec=yes
CC_OUTPUT_9d218390_fb62803b=yes
_OBJC_CCVERSION_9d218390=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 
335540) (based on LLVM 6.0.1) Target: armv7-unknown-freebsd12.0-gnueabihf 
Thread model: posix InstalledDir: /nxb-bin/usr/bin
_OBJC_ALTCCVERSION_9d218390=none
ARCH=armv7
OPSYS=FreeBSD
_OSRELEASE=12.0-ALPHA6
OSREL=12.0
OSVERSION=1200084
PYTHONBASE=/usr/local
CONFIGURE_MAX_CMD_LEN=262144
HAVE_PORTS_ENV=1
#### Misc Poudriere ####
GID=0
UID=0
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
---Begin make.nxb.conf---
CC=/nxb-bin/usr/bin/cc
CPP=/nxb-bin/usr/bin/cpp
CXX=/nxb-bin/usr/bin/c++
AS=/nxb-bin/usr/bin/as
NM=/nxb-bin/usr/bin/nm
LD=/nxb-bin/usr/bin/ld
OBJCOPY=/nxb-bin/usr/bin/objcopy
SIZE=/nxb-bin/usr/bin/size
STRIPBIN=/nxb-bin/usr/bin/strip
SED=/nxb-bin/usr/bin/sed
RANLIB=/nxb-bin/usr/bin/ranlib
YACC=/nxb-bin/usr/bin/yacc
MAKE=/nxb-bin/usr/bin/make
STRINGS=/nxb-bin/usr/bin/strings
AWK=/nxb-bin/usr/bin/awk
FLEX=/nxb-bin/usr/bin/flex
---End make.nxb.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 BSD3CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   unanimity-3.1.0 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.10.5_3.txz
[head-armv7-default-job-06] Installing pkg-1.10.5_3...
[head-armv7-default-job-06] Extracting pkg-1.10.5_3: .......... done
===>   unanimity-3.1.0 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of unanimity-3.1.0
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License BSD3CLAUSE accepted by the user
<snip>

*********************************** NOTE **********************************

This package installs symlinks to support root certificates discovery by
default for software that uses OpenSSL.

This enables SSL Certificate Verification by client software without manual
intervention.

If you prefer to do this manually, replace the following symlinks with
either an empty file or your site-local certificate bundle.

  * /etc/ssl/cert.pem
  * /usr/local/etc/ssl/cert.pem
  * /usr/local/openssl/cert.pem

***************************************************************************
===>   unanimity-3.1.0 depends on package: pbbam>=g20180416 - found
===>   Returning to build of unanimity-3.1.0
===>   unanimity-3.1.0 depends on package: pbcopper>=g20180413 - not found
===>   Installing existing package /packages/All/pbcopper-g20180413_1.txz
[head-armv7-default-job-06] Installing pbcopper-g20180413_1...
[head-armv7-default-job-06] Extracting pbcopper-g20180413_1: .......... done
===>   unanimity-3.1.0 depends on package: pbcopper>=g20180413 - found
===>   Returning to build of unanimity-3.1.0
===>   unanimity-3.1.0 depends on file: /usr/local/bin/cmake - not found
===>   Installing existing package /packages/All/cmake-3.12.1.txz
[head-armv7-default-job-06] Installing cmake-3.12.1...
[head-armv7-default-job-06] `-- Installing expat-2.2.6_1...
[head-armv7-default-job-06] `-- Extracting expat-2.2.6_1: .......... done
[head-armv7-default-job-06] `-- Installing jsoncpp-1.8.1_4...
[head-armv7-default-job-06] `-- Extracting jsoncpp-1.8.1_4: .......... done
[head-armv7-default-job-06] `-- Installing libarchive-3.3.2,1...
[head-armv7-default-job-06] |   `-- Installing liblz4-1.8.2,1...
[head-armv7-default-job-06] |   `-- Extracting liblz4-1.8.2,1: .......... done
[head-armv7-default-job-06] |   `-- Installing lzo2-2.10_1...
[head-armv7-default-job-06] |   `-- Extracting lzo2-2.10_1: .......... done
[head-armv7-default-job-06] `-- Extracting libarchive-3.3.2,1: .......... done
[head-armv7-default-job-06] `-- Installing libuv-1.23.0...
[head-armv7-default-job-06] `-- Extracting libuv-1.23.0: .......... done
[head-armv7-default-job-06] `-- Installing rhash-1.3.5...
[head-armv7-default-job-06] `-- Extracting rhash-1.3.5: .......... done
[head-armv7-default-job-06] Extracting cmake-3.12.1: .......... done
===>   unanimity-3.1.0 depends on file: /usr/local/bin/cmake - found
===>   Returning to build of unanimity-3.1.0
===>   unanimity-3.1.0 depends on executable: ninja - not found
===>   Installing existing package /packages/All/ninja-1.8.2,2.txz
[head-armv7-default-job-06] Installing ninja-1.8.2,2...
[head-armv7-default-job-06] `-- Installing python27-2.7.15...
[head-armv7-default-job-06] |   `-- Installing gettext-runtime-0.19.8.1_1...
[head-armv7-default-job-06] |   | `-- Installing indexinfo-0.3.1...
[head-armv7-default-job-06] |   | `-- Extracting indexinfo-0.3.1: .... done
[head-armv7-default-job-06] |   `-- Extracting gettext-runtime-0.19.8.1_1: 
.......... done
[head-armv7-default-job-06] |   `-- Installing libffi-3.2.1_2...
[head-armv7-default-job-06] |   `-- Extracting libffi-3.2.1_2: .......... done
[head-armv7-default-job-06] |   `-- Installing readline-7.0.3_1...
[head-armv7-default-job-06] |   `-- Extracting readline-7.0.3_1: .......... done
[head-armv7-default-job-06] `-- Extracting python27-2.7.15: .......... done
[head-armv7-default-job-06] Extracting ninja-1.8.2,2: ....... done
Message from python27-2.7.15:

===========================================================================

Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:

bsddb           databases/py-bsddb
gdbm            databases/py-gdbm
sqlite3         databases/py-sqlite3
tkinter         x11-toolkits/py-tkinter

===========================================================================
===>   unanimity-3.1.0 depends on executable: ninja - found
===>   Returning to build of unanimity-3.1.0
===>   unanimity-3.1.0 depends on package: pkgconf>=1.3.0_1 - not found
===>   Installing existing package /packages/All/pkgconf-1.4.2,1.txz
[head-armv7-default-job-06] Installing pkgconf-1.4.2,1...
[head-armv7-default-job-06] Extracting pkgconf-1.4.2,1: .......... done
===>   unanimity-3.1.0 depends on package: pkgconf>=1.3.0_1 - found
===>   Returning to build of unanimity-3.1.0
===>   unanimity-3.1.0 depends on file: /usr/local/bin/python2.7 - found
===========================================================================
=======================<phase: lib-depends    >============================
===>   unanimity-3.1.0 depends on shared library: libhts.so - found 
(/usr/local/lib/libhts.so)
===>   unanimity-3.1.0 depends on shared library: libboost_regex.so - found 
(/usr/local/lib/libboost_regex.so)
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for unanimity-3.1.0
===>  Performing in-source build
/bin/mkdir -p /wrkdirs/usr/ports/biology/unanimity/work/unanimity-3.1.0
-- The CXX compiler identification is Clang 6.0.1
-- The C compiler identification is Clang 6.0.1
-- Check for working CXX compiler: /nxb-bin/usr/bin/c++
-- Check for working CXX compiler: /nxb-bin/usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for working C compiler: /nxb-bin/usr/bin/cc
-- Check for working C compiler: /nxb-bin/usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Boost version: 1.68.0
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Found Threads: TRUE  
-- Found PkgConfig: pkgconf (found version "1.4.2") 
-- Checking for module 'zlib'
--   Found zlib, version 1.2.10
-- Performing Test HAS_NO_UNUSED_LOCAL_TYPEDEFS
-- Performing Test HAS_NO_UNUSED_LOCAL_TYPEDEFS - Success
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    BOOST_PYTHON_SUFFIX
    CMAKE_COLOR_MAKEFILE
    CMAKE_C_FLAGS_DEBUG
    CMAKE_MODULE_LINKER_FLAGS
    CMAKE_SHARED_LINKER_FLAGS
    CMAKE_VERBOSE_MAKEFILE
    Python_ADDITIONAL_VERSIONS


-- Build files have been written to: 
/wrkdirs/usr/ports/biology/unanimity/work/unanimity-3.1.0
===========================================================================
=======================<phase: build          >============================
===>  Building for unanimity-3.1.0
[1/82] /nxb-bin/usr/bin/c++   -I/usr/local/include/PacBio -Iinclude -Igenerated 
-I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse 
-I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe 
-fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable 
-Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing   -std=c++14 -MD -MT 
src/CMakeFiles/ccs.dir/main/ccs.cpp.o -MF 
src/CMakeFiles/ccs.dir/main/ccs.cpp.o.d -o 
src/CMakeFiles/ccs.dir/main/ccs.cpp.o -c src/main/ccs.cpp
[2/82] /nxb-bin/usr/bin/c++   -I/usr/local/include/PacBio -Iinclude -Igenerated 
-I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse 
-I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe 
-fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable 
-Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing   -std=c++14 -MD -MT 
src/CMakeFiles/gcpp.dir/main/gcpp.cpp.o -MF 
src/CMakeFiles/gcpp.dir/main/gcpp.cpp.o.d -o 
src/CMakeFiles/gcpp.dir/main/gcpp.cpp.o -c src/main/gcpp.cpp
[3/82] /nxb-bin/usr/bin/c++   -I/usr/local/include/PacBio -Iinclude -Igenerated 
-I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse 
-I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe 
-fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable 
-Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing   -std=c++14 -MD -MT 
src/CMakeFiles/unanimity.dir/__/third-party/cpp-optparse/OptionParser.cpp.o -MF 
src/CMakeFiles/unanimity.dir/__/third-party/cpp-optparse/OptionParser.cpp.o.d 
-o src/CMakeFiles/unanimity.dir/__/third-party/cpp-optparse/OptionParser.cpp.o 
-c third-party/cpp-optparse/OptionParser.cpp
[4/82] /nxb-bin/usr/bin/c++   -I/usr/local/include/PacBio -Iinclude -Igenerated 
-I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse 
-I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe 
-fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable 
-Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing   -std=c++14 -MD -MT 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Consensus.cpp.o -MF 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Consensus.cpp.o.d -o 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Consensus.cpp.o -c 
src/genomicconsensus/experimental/Consensus.cpp
[5/82] /nxb-bin/usr/bin/c++   -I/usr/local/include/PacBio -Iinclude -Igenerated 
-I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse 
-I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe 
-fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable 
-Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing   -std=c++14 -MD -MT 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/ConsensusModelFactory.cpp.o
 -MF 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/ConsensusModelFactory.cpp.o.d
 -o 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/ConsensusModelFactory.cpp.o
 -c src/genomicconsensus/experimental/ConsensusModelFactory.cpp
[6/82] /nxb-bin/usr/bin/c++   -I/usr/local/include/PacBio -Iinclude -Igenerated 
-I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse 
-I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe 
-fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable 
-Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing   -std=c++14 -MD -MT 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Filters.cpp.o -MF 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Filters.cpp.o.d -o 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Filters.cpp.o -c 
src/genomicconsensus/experimental/Filters.cpp
[7/82] /nxb-bin/usr/bin/c++   -I/usr/local/include/PacBio -Iinclude -Igenerated 
-I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse 
-I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe 
-fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable 
-Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing   -std=c++14 -MD -MT 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/GenomicConsensus.cpp.o
 -MF 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/GenomicConsensus.cpp.o.d
 -o 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/GenomicConsensus.cpp.o
 -c src/genomicconsensus/experimental/GenomicConsensus.cpp
[8/82] /nxb-bin/usr/bin/c++   -I/usr/local/include/PacBio -Iinclude -Igenerated 
-I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse 
-I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe 
-fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable 
-Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing   -std=c++14 -MD -MT 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/IPoaModel.cpp.o -MF 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/IPoaModel.cpp.o.d -o 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/IPoaModel.cpp.o -c 
src/genomicconsensus/experimental/IPoaModel.cpp
[9/82] /nxb-bin/usr/bin/c++   -I/usr/local/include/PacBio -Iinclude -Igenerated 
-I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse 
-I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe 
-fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable 
-Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing   -std=c++14 -MD -MT 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Input.cpp.o -MF 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Input.cpp.o.d -o 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Input.cpp.o -c 
src/genomicconsensus/experimental/Input.cpp
src/genomicconsensus/experimental/Input.cpp:72:21: warning: lambda capture 
'window' is not used [-Wunused-lambda-capture]
                  [&window, &partialHitLength](const BamRecord& lhs, const 
BamRecord& rhs) {
                    ^
1 warning generated.
[10/82] /nxb-bin/usr/bin/c++   -I/usr/local/include/PacBio -Iinclude 
-Igenerated -I/usr/local/include -I/usr/local/include/htslib 
-Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc 
-O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter 
-Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing  
 -std=c++14 -MD -MT 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Intervals.cpp.o -MF 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Intervals.cpp.o.d -o 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Intervals.cpp.o -c 
src/genomicconsensus/experimental/Intervals.cpp
[11/82] /nxb-bin/usr/bin/c++   -I/usr/local/include/PacBio -Iinclude 
-Igenerated -I/usr/local/include -I/usr/local/include/htslib 
-Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc 
-O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter 
-Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing  
 -std=c++14 -MD -MT 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Output.cpp.o -MF 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Output.cpp.o.d -o 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Output.cpp.o -c 
src/genomicconsensus/experimental/Output.cpp
[12/82] /nxb-bin/usr/bin/c++   -I/usr/local/include/PacBio -Iinclude 
-Igenerated -I/usr/local/include -I/usr/local/include/htslib 
-Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc 
-O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter 
-Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing  
 -std=c++14 -MD -MT 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Settings.cpp.o -MF 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Settings.cpp.o.d -o 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Settings.cpp.o -c 
src/genomicconsensus/experimental/Settings.cpp
[13/82] /nxb-bin/usr/bin/c++   -I/usr/local/include/PacBio -Iinclude 
-Igenerated -I/usr/local/include -I/usr/local/include/htslib 
-Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc 
-O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter 
-Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing  
 -std=c++14 -MD -MT 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Sorting.cpp.o -MF 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Sorting.cpp.o.d -o 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Sorting.cpp.o -c 
src/genomicconsensus/experimental/Sorting.cpp
src/genomicconsensus/experimental/Sorting.cpp:40:32: warning: lambda capture 
'window' is not used [-Wunused-lambda-capture]
                             [&window, lengthInWindow](const BamRecord& lhs, 
const BamRecord& rhs) {
                               ^
src/genomicconsensus/experimental/Sorting.cpp:49:32: warning: lambda capture 
'window' is not used [-Wunused-lambda-capture]
                             [&window, lengthInWindow](const 
PacBio::BAM::BamRecord& lhs,
                               ^
2 warnings generated.
[14/82] /nxb-bin/usr/bin/c++   -I/usr/local/include/PacBio -Iinclude 
-Igenerated -I/usr/local/include -I/usr/local/include/htslib 
-Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc 
-O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter 
-Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing  
 -std=c++14 -MD -MT 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Workflow.cpp.o -MF 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Workflow.cpp.o.d -o 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Workflow.cpp.o -c 
src/genomicconsensus/experimental/Workflow.cpp
[15/82] /nxb-bin/usr/bin/c++   -I/usr/local/include/PacBio -Iinclude 
-Igenerated -I/usr/local/include -I/usr/local/include/htslib 
-Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc 
-O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter 
-Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing  
 -std=c++14 -MD -MT 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/arrow/ArrowModel.cpp.o
 -MF 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/arrow/ArrowModel.cpp.o.d
 -o 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/arrow/ArrowModel.cpp.o
 -c src/genomicconsensus/experimental/arrow/ArrowModel.cpp
[16/82] /nxb-bin/usr/bin/c++   -I/usr/local/include/PacBio -Iinclude 
-Igenerated -I/usr/local/include -I/usr/local/include/htslib 
-Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc 
-O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter 
-Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing  
 -std=c++14 -MD -MT 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/FastaWriter.cpp.o 
-MF 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/FastaWriter.cpp.o.d
 -o 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/FastaWriter.cpp.o 
-c src/genomicconsensus/experimental/io/FastaWriter.cpp
[17/82] /nxb-bin/usr/bin/c++   -I/usr/local/include/PacBio -Iinclude 
-Igenerated -I/usr/local/include -I/usr/local/include/htslib 
-Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc 
-O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter 
-Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing  
 -std=c++14 -MD -MT 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/FastqWriter.cpp.o 
-MF 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/FastqWriter.cpp.o.d
 -o 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/FastqWriter.cpp.o 
-c src/genomicconsensus/experimental/io/FastqWriter.cpp
[18/82] /nxb-bin/usr/bin/c++   -I/usr/local/include/PacBio -Iinclude 
-Igenerated -I/usr/local/include -I/usr/local/include/htslib 
-Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc 
-O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter 
-Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing  
 -std=c++14 -MD -MT 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/GffWriter.cpp.o 
-MF 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/GffWriter.cpp.o.d 
-o 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/GffWriter.cpp.o 
-c src/genomicconsensus/experimental/io/GffWriter.cpp
[19/82] /nxb-bin/usr/bin/c++   -I/usr/local/include/PacBio -Iinclude 
-Igenerated -I/usr/local/include -I/usr/local/include/htslib 
-Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc 
-O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter 
-Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing  
 -std=c++14 -MD -MT 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/VcfWriter.cpp.o 
-MF 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/VcfWriter.cpp.o.d 
-o 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/VcfWriter.cpp.o 
-c src/genomicconsensus/experimental/io/VcfWriter.cpp
[20/82] /nxb-bin/usr/bin/c++   -I/usr/local/include/PacBio -Iinclude 
-Igenerated -I/usr/local/include -I/usr/local/include/htslib 
-Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc 
-O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter 
-Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing  
 -std=c++14 -MD -MT 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/plurality/PluralityModel.cpp.o
 -MF 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/plurality/PluralityModel.cpp.o.d
 -o 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/plurality/PluralityModel.cpp.o
 -c src/genomicconsensus/experimental/plurality/PluralityModel.cpp
In file included from 
src/genomicconsensus/experimental/plurality/PluralityModel.cpp:9:
include/pacbio/genomicconsensus/experimental/plurality/Plurality.h:129:31: 
warning: field 'bases' is uninitialized when used here [-Wuninitialized]
            : bases{std::move(bases)}, frequency{frequency_}
                              ^
1 warning generated.
[21/82] /nxb-bin/usr/bin/c++   -I/usr/local/include/PacBio -Iinclude 
-Igenerated -I/usr/local/include -I/usr/local/include/htslib 
-Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc 
-O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter 
-Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing  
 -std=c++14 -MD -MT 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/poa/PoaModel.cpp.o 
-MF 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/poa/PoaModel.cpp.o.d 
-o 
src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/poa/PoaModel.cpp.o 
-c src/genomicconsensus/experimental/poa/PoaModel.cpp
[22/82] /nxb-bin/usr/bin/c++   -I/usr/local/include/PacBio -Iinclude 
-Igenerated -I/usr/local/include -I/usr/local/include/htslib 
-Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc 
-O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter 
-Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing  
 -std=c++14 -MD -MT src/CMakeFiles/unanimity.dir/ChemistryMapping.cpp.o -MF 
src/CMakeFiles/unanimity.dir/ChemistryMapping.cpp.o.d -o 
src/CMakeFiles/unanimity.dir/ChemistryMapping.cpp.o -c src/ChemistryMapping.cpp
[23/82] /nxb-bin/usr/bin/c++   -I/usr/local/include/PacBio -Iinclude 
-Igenerated -I/usr/local/include -I/usr/local/include/htslib 
-Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc 
-O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter 
-Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing  
 -std=c++14 -MD -MT src/CMakeFiles/unanimity.dir/ChemistryTriple.cpp.o -MF 
src/CMakeFiles/unanimity.dir/ChemistryTriple.cpp.o.d -o 
src/CMakeFiles/unanimity.dir/ChemistryTriple.cpp.o -c src/ChemistryTriple.cpp
[24/82] /nxb-bin/usr/bin/c++   -I/usr/local/include/PacBio -Iinclude 
-Igenerated -I/usr/local/include -I/usr/local/include/htslib 
-Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc 
-O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter 
-Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing  
 -std=c++14 -MD -MT src/CMakeFiles/unanimity.dir/Interval.cpp.o -MF 
src/CMakeFiles/unanimity.dir/Interval.cpp.o.d -o 
src/CMakeFiles/unanimity.dir/Interval.cpp.o -c src/Interval.cpp
[25/82] /nxb-bin/usr/bin/c++   -I/usr/local/include/PacBio -Iinclude 
-Igenerated -I/usr/local/include -I/usr/local/include/htslib 
-Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc 
-O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter 
-Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing  
 -std=c++14 -MD -MT src/CMakeFiles/unanimity.dir/ReadId.cpp.o -MF 
src/CMakeFiles/unanimity.dir/ReadId.cpp.o.d -o 
src/CMakeFiles/unanimity.dir/ReadId.cpp.o -c src/ReadId.cpp
[26/82] /nxb-bin/usr/bin/c++   -I/usr/local/include/PacBio -Iinclude 
-Igenerated -I/usr/local/include -I/usr/local/include/htslib 
-Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc 
-O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter 
-Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing  
 -std=c++14 -MD -MT src/CMakeFiles/unanimity.dir/SparsePoa.cpp.o -MF 
src/CMakeFiles/unanimity.dir/SparsePoa.cpp.o.d -o 
src/CMakeFiles/unanimity.dir/SparsePoa.cpp.o -c src/SparsePoa.cpp
FAILED: src/CMakeFiles/unanimity.dir/SparsePoa.cpp.o 
/nxb-bin/usr/bin/c++   -I/usr/local/include/PacBio -Iinclude -Igenerated 
-I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse 
-I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe 
-fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable 
-Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing   -std=c++14 -MD -MT 
src/CMakeFiles/unanimity.dir/SparsePoa.cpp.o -MF 
src/CMakeFiles/unanimity.dir/SparsePoa.cpp.o.d -o 
src/CMakeFiles/unanimity.dir/SparsePoa.cpp.o -c src/SparsePoa.cpp
In file included from src/SparsePoa.cpp:14:
In file included from include/pacbio/ccs/SparseAlignment.h:18:
In file included from include/pacbio/align/SparseAlignment.h:16:
In file included from include/pacbio/align/FindSeeds.h:11:
In file included from /usr/local/include/pbcopper/qgram/Index.h:76:
/usr/local/include/pbcopper/qgram/internal/Index-inl.h:120:37: error: 
non-constant-expression cannot be narrowed from type 'unsigned long long' to 
'size_t' (aka 'unsigned int') in initializer list [-Wc++11-narrowing]
    return IndexHits{&suffixArray_, iter, end, queryPos};
                                    ^~~~
/usr/local/include/pbcopper/qgram/internal/Index-inl.h:120:37: note: insert an 
explicit cast to silence this issue
    return IndexHits{&suffixArray_, iter, end, queryPos};
                                    ^~~~
                                    static_cast<size_t>( )
/usr/local/include/pbcopper/qgram/internal/Index-inl.h:120:43: error: 
non-constant-expression cannot be narrowed from type 'unsigned long long' to 
'size_t' (aka 'unsigned int') in initializer list [-Wc++11-narrowing]
    return IndexHits{&suffixArray_, iter, end, queryPos};
                                          ^~~
/usr/local/include/pbcopper/qgram/internal/Index-inl.h:120:43: note: insert an 
explicit cast to silence this issue
    return IndexHits{&suffixArray_, iter, end, queryPos};
                                          ^~~
                                          static_cast<size_t>( )
2 errors generated.
ninja: build stopped: subcommand failed.
*** Error code 1

Stop.
make: stopped in /usr/ports/biology/unanimity
_______________________________________________
freebsd-pkg-fallout@freebsd.org mailing list
https://lists.freebsd.org/mailman/listinfo/freebsd-pkg-fallout
To unsubscribe, send any mail to "freebsd-pkg-fallout-unsubscr...@freebsd.org"

Reply via email to