You are receiving this mail as a port that you maintain
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Please investigate the failure and submit a PR to fix
build.

Maintainer:     j...@freebsd.org
Last committer: lini...@freebsd.org
Ident:          $FreeBSD: branches/2018Q3/biology/unanimity/Makefile 473010 
2018-06-22 00:03:08Z linimon $
Log URL:        
http://beefy15.nyi.freebsd.org/data/111armv6-quarterly/476830/logs/unanimity-g20180307.log
Build URL:      
http://beefy15.nyi.freebsd.org/build.html?mastername=111armv6-quarterly&build=476830
Log:

=>> Building biology/unanimity
build started at Sat Aug 11 14:13:42 UTC 2018
port directory: /usr/ports/biology/unanimity
package name: unanimity-g20180307
building for: FreeBSD 111armv6-quarterly-job-09 11.1-RELEASE-p12 FreeBSD 
11.1-RELEASE-p12 1101001 arm
maintained by: j...@freebsd.org
Makefile ident:      $FreeBSD: branches/2018Q3/biology/unanimity/Makefile 
473010 2018-06-22 00:03:08Z linimon $
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=======================<phase: check-sanity   >============================
===>  License BSD3CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   unanimity-g20180307 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.10.5_1.txz
[111armv6-quarterly-job-09] Installing pkg-1.10.5_1...
[111armv6-quarterly-job-09] Extracting pkg-1.10.5_1: .......... done
===>   unanimity-g20180307 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of unanimity-g20180307
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by unanimity-g20180307 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by unanimity-g20180307 for building
=> SHA256 Checksum OK for 
PacificBiosciences-unanimity-g20180307-6f11a13e1472b8c00337ba8c5e94bf83bdab31d6_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
<snip>
linking your code.
Message from ca_root_nss-3.38:

********************************* WARNING *********************************

FreeBSD does not, and can not warrant that the certification authorities
whose certificates are included in this package have in any way been
audited for trustworthiness or RFC 3647 compliance.

Assessment and verification of trust is the complete responsibility of the
system administrator.

*********************************** 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-g20180307 depends on package: pbbam==g20180416 - found
===>   Returning to build of unanimity-g20180307
===>   unanimity-g20180307 depends on package: pbcopper==g20180413 - not found
===>   Installing existing package /packages/All/pbcopper-g20180413.txz
[111armv6-quarterly-job-09] Installing pbcopper-g20180413...
[111armv6-quarterly-job-09] Extracting pbcopper-g20180413: .......... done
===>   unanimity-g20180307 depends on package: pbcopper==g20180413 - found
===>   Returning to build of unanimity-g20180307
===>   unanimity-g20180307 depends on file: /usr/local/bin/cmake - not found
===>   Installing existing package /packages/All/cmake-3.11.4_1.txz
[111armv6-quarterly-job-09] Installing cmake-3.11.4_1...
[111armv6-quarterly-job-09] `-- Installing expat-2.2.5...
[111armv6-quarterly-job-09] `-- Extracting expat-2.2.5: .......... done
[111armv6-quarterly-job-09] `-- Installing jsoncpp-1.8.1_3...
[111armv6-quarterly-job-09] `-- Extracting jsoncpp-1.8.1_3: .......... done
[111armv6-quarterly-job-09] `-- Installing libarchive-3.3.2,1...
[111armv6-quarterly-job-09] |   `-- Installing liblz4-1.8.2,1...
[111armv6-quarterly-job-09] |   `-- Extracting liblz4-1.8.2,1: .......... done
[111armv6-quarterly-job-09] |   `-- Installing lzo2-2.10_1...
[111armv6-quarterly-job-09] |   `-- Extracting lzo2-2.10_1: .......... done
[111armv6-quarterly-job-09] `-- Extracting libarchive-3.3.2,1: .......... done
[111armv6-quarterly-job-09] `-- Installing libuv-1.21.0...
[111armv6-quarterly-job-09] `-- Extracting libuv-1.21.0: .......... done
[111armv6-quarterly-job-09] `-- Installing rhash-1.3.5...
[111armv6-quarterly-job-09] `-- Extracting rhash-1.3.5: .......... done
[111armv6-quarterly-job-09] Extracting cmake-3.11.4_1: .......... done
===>   unanimity-g20180307 depends on file: /usr/local/bin/cmake - found
===>   Returning to build of unanimity-g20180307
===>   unanimity-g20180307 depends on executable: ninja - not found
===>   Installing existing package /packages/All/ninja-1.8.2,2.txz
[111armv6-quarterly-job-09] Installing ninja-1.8.2,2...
[111armv6-quarterly-job-09] `-- Installing python27-2.7.15...
[111armv6-quarterly-job-09] |   `-- Installing gettext-runtime-0.19.8.1_1...
[111armv6-quarterly-job-09] |   | `-- Installing indexinfo-0.3.1...
[111armv6-quarterly-job-09] |   | `-- Extracting indexinfo-0.3.1: .... done
[111armv6-quarterly-job-09] |   `-- Extracting gettext-runtime-0.19.8.1_1: 
.......... done
[111armv6-quarterly-job-09] |   `-- Installing libffi-3.2.1_2...
[111armv6-quarterly-job-09] |   `-- Extracting libffi-3.2.1_2: .......... done
[111armv6-quarterly-job-09] |   `-- Installing readline-7.0.3_1...
[111armv6-quarterly-job-09] |   `-- Extracting readline-7.0.3_1: .......... done
[111armv6-quarterly-job-09] `-- Extracting python27-2.7.15: .......... done
[111armv6-quarterly-job-09] 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-g20180307 depends on executable: ninja - found
===>   Returning to build of unanimity-g20180307
===>   unanimity-g20180307 depends on package: pkgconf>=1.3.0_1 - not found
===>   Installing existing package /packages/All/pkgconf-1.4.2,1.txz
[111armv6-quarterly-job-09] Installing pkgconf-1.4.2,1...
[111armv6-quarterly-job-09] Extracting pkgconf-1.4.2,1: .......... done
===>   unanimity-g20180307 depends on package: pkgconf>=1.3.0_1 - found
===>   Returning to build of unanimity-g20180307
===>   unanimity-g20180307 depends on file: /usr/local/bin/python2.7 - found
===========================================================================
=======================<phase: lib-depends    >============================
===>   unanimity-g20180307 depends on shared library: libhts.so - found 
(/usr/local/lib/libhts.so)
===>   unanimity-g20180307 depends on shared library: libboost_regex.so - found 
(/usr/local/lib/libboost_regex.so)
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for unanimity-g20180307
===>  Performing in-source build
/bin/mkdir -p 
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-- Detecting CXX compile features
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-- Check for working C compiler: /nxb-bin/usr/bin/cc -- works
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-- Detecting C compile features
-- Detecting C compile features - done
-- Boost version: 1.67.0
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-- Looking for pthread.h - found
-- Found Threads: TRUE  
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--   Found zlib, version 1.2.10
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-- Build files have been written to: 
/wrkdirs/usr/ports/biology/unanimity/work/unanimity-6f11a13e1472b8c00337ba8c5e94bf83bdab31d6
===========================================================================
=======================<phase: build          >============================
===>  Building for unanimity-g20180307
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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.
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-O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter 
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 -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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