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Date:      Fri, 22 Feb 2019 03:47:55 GMT
From:      pkg-fallout@FreeBSD.org
To:        pkg-fallout@FreeBSD.org
Subject:   [package - 120armv7-quarterly][biology/unanimity] Failed for unanimity-3.1.0_2 in build
Message-ID:  <201902220347.x1M3lt7I069702@beefy13.nyi.freebsd.org>

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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@FreeBSD.org
Last committer: tcberner@FreeBSD.org
Ident:          $FreeBSD: branches/2019Q1/biology/unanimity/Makefile 488341 2018-12-25 20:25:39Z tcberner $
Log URL:        http://beefy13.nyi.freebsd.org/data/120armv7-quarterly/493483/logs/unanimity-3.1.0_2.log
Build URL:      http://beefy13.nyi.freebsd.org/build.html?mastername=120armv7-quarterly&build=493483
Log:

=>> Building biology/unanimity
build started at Fri Feb 22 03:46:03 UTC 2019
port directory: /usr/ports/biology/unanimity
package name: unanimity-3.1.0_2
building for: FreeBSD 120armv7-quarterly-job-07 12.0-RELEASE-p3 FreeBSD 12.0-RELEASE-p3 1200086 arm
maintained by: jwb@FreeBSD.org
Makefile ident:      $FreeBSD: branches/2019Q1/biology/unanimity/Makefile 488341 2018-12-25 20:25:39Z tcberner $
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=======================<phase: check-sanity   >============================
===>  License BSD3CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   unanimity-3.1.0_2 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.10.5_5.txz
[120armv7-quarterly-job-07] Installing pkg-1.10.5_5...
[120armv7-quarterly-job-07] Extracting pkg-1.10.5_5: .......... done
===>   unanimity-3.1.0_2 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of unanimity-3.1.0_2
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by unanimity-3.1.0_2 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by unanimity-3.1.0_2 for building
=> SHA256 Checksum OK for PacificBiosciences-unanimity-v3.1.0_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
<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_2 depends on package: pbbam>=g20180416 - found
===>   Returning to build of unanimity-3.1.0_2
===>   unanimity-3.1.0_2 depends on package: pbcopper>=g20180413 - not found
===>   Installing existing package /packages/All/pbcopper-g20180413_3.txz
[120armv7-quarterly-job-07] Installing pbcopper-g20180413_3...
[120armv7-quarterly-job-07] Extracting pbcopper-g20180413_3: .......... done
===>   unanimity-3.1.0_2 depends on package: pbcopper>=g20180413 - found
===>   Returning to build of unanimity-3.1.0_2
===>   unanimity-3.1.0_2 depends on file: /usr/local/bin/cmake - not found
===>   Installing existing package /packages/All/cmake-3.13.2.txz
[120armv7-quarterly-job-07] Installing cmake-3.13.2...
[120armv7-quarterly-job-07] `-- Installing expat-2.2.6_1...
[120armv7-quarterly-job-07] `-- Extracting expat-2.2.6_1: .......... done
[120armv7-quarterly-job-07] `-- Installing jsoncpp-1.8.1_5...
[120armv7-quarterly-job-07] `-- Extracting jsoncpp-1.8.1_5: .......... done
[120armv7-quarterly-job-07] `-- Installing libarchive-3.3.3,1...
[120armv7-quarterly-job-07] |   `-- Installing liblz4-1.8.3,1...
[120armv7-quarterly-job-07] |   `-- Extracting liblz4-1.8.3,1: .......... done
[120armv7-quarterly-job-07] |   `-- Installing lzo2-2.10_1...
[120armv7-quarterly-job-07] |   `-- Extracting lzo2-2.10_1: .......... done
[120armv7-quarterly-job-07] `-- Extracting libarchive-3.3.3,1: .......... done
[120armv7-quarterly-job-07] `-- Installing libuv-1.24.1...
[120armv7-quarterly-job-07] `-- Extracting libuv-1.24.1: .......... done
[120armv7-quarterly-job-07] `-- Installing rhash-1.3.5...
[120armv7-quarterly-job-07] `-- Extracting rhash-1.3.5: .......... done
[120armv7-quarterly-job-07] Extracting cmake-3.13.2: .......... done
===>   unanimity-3.1.0_2 depends on file: /usr/local/bin/cmake - found
===>   Returning to build of unanimity-3.1.0_2
===>   unanimity-3.1.0_2 depends on executable: ninja - not found
===>   Installing existing package /packages/All/ninja-1.8.2_1,2.txz
[120armv7-quarterly-job-07] Installing ninja-1.8.2_1,2...
[120armv7-quarterly-job-07] `-- Installing python27-2.7.15...
[120armv7-quarterly-job-07] |   `-- Installing gettext-runtime-0.19.8.1_2...
[120armv7-quarterly-job-07] |   | `-- Installing indexinfo-0.3.1...
[120armv7-quarterly-job-07] |   | `-- Extracting indexinfo-0.3.1: .... done
[120armv7-quarterly-job-07] |   `-- Extracting gettext-runtime-0.19.8.1_2: .......... done
[120armv7-quarterly-job-07] |   `-- Installing libffi-3.2.1_3...
[120armv7-quarterly-job-07] |   `-- Extracting libffi-3.2.1_3: .......... done
[120armv7-quarterly-job-07] |   `-- Installing readline-7.0.5...
[120armv7-quarterly-job-07] |   `-- Extracting readline-7.0.5: .......... done
[120armv7-quarterly-job-07] `-- Extracting python27-2.7.15: .......... done
[120armv7-quarterly-job-07] Extracting ninja-1.8.2_1,2: ......... 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_2 depends on executable: ninja - found
===>   Returning to build of unanimity-3.1.0_2
===>   unanimity-3.1.0_2 depends on package: pkgconf>=1.3.0_1 - not found
===>   Installing existing package /packages/All/pkgconf-1.5.4,1.txz
[120armv7-quarterly-job-07] Installing pkgconf-1.5.4,1...
[120armv7-quarterly-job-07] Extracting pkgconf-1.5.4,1: .......... done
===>   unanimity-3.1.0_2 depends on package: pkgconf>=1.3.0_1 - found
===>   Returning to build of unanimity-3.1.0_2
===>   unanimity-3.1.0_2 depends on file: /usr/local/bin/python2.7 - found
===========================================================================
=======================<phase: lib-depends    >============================
===>   unanimity-3.1.0_2 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so)
===>   unanimity-3.1.0_2 depends on shared library: libboost_regex.so - found (/usr/local/lib/libboost_regex.so)
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for unanimity-3.1.0_2
===>  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: 1.69.0
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Found Threads: TRUE  
-- Found PkgConfig: pkgconf (found version "1.5.4") 
-- 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_2
[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



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