-------------------------------------------------------------------------------
-- Phase: Environment
-------------------------------------------------------------------------------

NO_DEPENDS=1
UNAME_r=5.9
UNAME_m=x86_64
UNAME_p=x86_64
UNAME_v=unknown
UNAME_s=DragonFly
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin
SSL_NO_VERIFY_PEER=1
LANG=C
HOME=/root
USER=root
TERM=dumb

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: showconfig
-------------------------------------------------------------------------------


SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: CONFIGURE_ENV
-------------------------------------------------------------------------------

PKG_CONFIG=pkgconf PYTHON="/usr/local/bin/python3.7" XDG_DATA_HOME=/construction/biology/pbbam  XDG_CONFIG_HOME=/construction/biology/pbbam  HOME=/construction/biology/pbbam TMPDIR="/tmp" PATH=/construction/biology/pbbam/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 CMAKE_PREFIX_PATH="/usr/local" LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: CONFIGURE_ARGS
-------------------------------------------------------------------------------

--prefix /usr/local  --mandir man  --infodir share/info --buildtype release  --strip  _build

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: MAKE_ENV
-------------------------------------------------------------------------------

XDG_DATA_HOME=/construction/biology/pbbam  XDG_CONFIG_HOME=/construction/biology/pbbam  HOME=/construction/biology/pbbam TMPDIR="/tmp" PATH=/construction/biology/pbbam/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 DESTDIR=/construction/biology/pbbam/stage LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 PREFIX=/usr/local  LOCALBASE=/usr/local  NOPROFILE=1  CC="cc" CFLAGS="-pipe -O2 -isystem /usr/local/include -fno-strict-aliasing "  CPP="cpp" CPPFLAGS="-isystem /usr/local/include"  LDFLAGS=" " LIBS="-L/usr/local/lib"  CXX="c++" CXXFLAGS=" -pipe -O2 -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"

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: MAKE_ARGS
-------------------------------------------------------------------------------

-v

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: PLIST_SUB
-------------------------------------------------------------------------------

PYTHON_INCLUDEDIR=include/python3.7m PYTHON_LIBDIR=lib/python3.7 PYTHON_PLATFORM=dragonfly5 PYTHON_SITELIBDIR=lib/python3.7/site-packages PYTHON_SUFFIX=37 PYTHON_EXT_SUFFIX= PYTHON_VER=3.7 PYTHON_VERSION=python3.7 PYTHON2="@comment " PYTHON3="" OSREL=5.9 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/pbbam"  EXAMPLESDIR="share/examples/pbbam"  DATADIR="share/pbbam"  WWWDIR="www/pbbam"  ETCDIR="etc/pbbam"

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: SUB_LIST
-------------------------------------------------------------------------------

PREFIX=/usr/local LOCALBASE=/usr/local  DATADIR=/usr/local/share/pbbam DOCSDIR=/usr/local/share/doc/pbbam EXAMPLESDIR=/usr/local/share/examples/pbbam  WWWDIR=/usr/local/www/pbbam ETCDIR=/usr/local/etc/pbbam

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: /etc/make.conf
-------------------------------------------------------------------------------

DPORTS_BUILDER=yes
DISABLE_LICENSES=yes
DEFAULT_VERSIONS=ssl=openssl
FORCE_PACKAGE=yes
DEVELOPER=yes
USE_PACKAGE_DEPENDS_ONLY=yes
PORTSDIR=/xports
PORT_DBDIR=/options
PKG_DBDIR=/var/db/pkg
PKG_CACHEDIR=/var/cache/pkg
PKG_SUFX=.txz
DEVELOPER=1
UID=0
ARCH=x86_64
OPSYS=DragonFly
DFLYVERSION=500909
OSVERSION=9999999
OSREL=5.9
_OSRELEASE=5.9-SYNTH
DISTDIR=/distfiles
WRKDIRPREFIX=/construction
BATCH=yes
PACKAGE_BUILDING=yes
PKG_CREATE_VERBOSE=yes
MAKE_JOBS_NUMBER=10

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: setup
-------------------------------------------------------------------------------

Installing /packages/All/indexinfo-0.3.1.txz
Installing /packages/All/libffi-3.3_1.txz
Installing /packages/All/expat-2.2.10.txz
Installing /packages/All/ncurses-6.2.20210213.txz
Installing /packages/All/readline-8.1.0.txz
Installing /packages/All/gettext-runtime-0.21.txz
Installing /packages/All/openssl-1.1.1k,1.txz
Installing /packages/All/python37-3.7.9_1.txz
=====
Message from python37-3.7.9_1:

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

py37-gdbm       databases/py-gdbm@py37
py37-sqlite3    databases/py-sqlite3@py37
py37-tkinter    x11-toolkits/py-tkinter@py37
Installing /packages/All/ninja-1.10.2,2.txz
Installing /packages/All/py37-setuptools-44.0.0.txz
Installing /packages/All/meson-0.57.1.txz
Installing /packages/All/pkgconf-1.7.3,1.txz
Installing /packages/All/libdeflate-1.7.txz
Installing /packages/All/libnghttp2-1.43.0.txz
Installing /packages/All/ca_root_nss-3.61.txz
=====
Message from ca_root_nss-3.61:

--
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.


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
Installing /packages/All/curl-7.75.0.txz
Installing /packages/All/htslib-1.11.0.txz
Installing /packages/All/icu-68.2,1.txz
Installing /packages/All/boost-libs-1.72.0_3.txz
=====
Message from boost-libs-1.72.0_3:

--
You have built the Boost library with thread support.

Don't forget to add -pthread to your linker options when
linking your code.

SUCCEEDED 00:00:12

-------------------------------------------------------------------------------
-- Phase: check-sanity
-------------------------------------------------------------------------------

===>   NOTICE:

The pbbam port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:

https://bugs.freebsd.org/bugzilla

More information about port maintainership is available at:

https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port


SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: pkg-depends
-------------------------------------------------------------------------------

===>   pbbam-0.18.0_5 depends on file: /usr/local/sbin/pkg - found

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: fetch-depends
-------------------------------------------------------------------------------


SUCCEEDED 00:00:01

-------------------------------------------------------------------------------
-- Phase: fetch
-------------------------------------------------------------------------------

===>   NOTICE:

The pbbam port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:

https://bugs.freebsd.org/bugzilla

More information about port maintainership is available at:

https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port

===>   pbbam-0.18.0_5 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by pbbam-0.18.0_5 for building

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: checksum
-------------------------------------------------------------------------------

===>   NOTICE:

The pbbam port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:

https://bugs.freebsd.org/bugzilla

More information about port maintainership is available at:

https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port

===>   pbbam-0.18.0_5 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by pbbam-0.18.0_5 for building
=> SHA256 Checksum OK for PacificBiosciences-pbbam-0.18.0_GH0.tar.gz.

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: extract-depends
-------------------------------------------------------------------------------


SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: extract
-------------------------------------------------------------------------------

===>   NOTICE:

The pbbam port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:

https://bugs.freebsd.org/bugzilla

More information about port maintainership is available at:

https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port

===>   pbbam-0.18.0_5 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by pbbam-0.18.0_5 for building
===>  Extracting for pbbam-0.18.0_5
=> SHA256 Checksum OK for PacificBiosciences-pbbam-0.18.0_GH0.tar.gz.

Extracted Memory Use:  16.07M
SUCCEEDED 00:00:01

-------------------------------------------------------------------------------
-- Phase: patch-depends
-------------------------------------------------------------------------------


SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: patch
-------------------------------------------------------------------------------

===>  Patching for pbbam-0.18.0_5
===>  Applying ports patches for pbbam-0.18.0_5 from /xports/biology/pbbam/files

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: build-depends
-------------------------------------------------------------------------------

===>   pbbam-0.18.0_5 depends on executable: meson - found
===>   pbbam-0.18.0_5 depends on executable: ninja - found
===>   pbbam-0.18.0_5 depends on package: pkgconf>=1.3.0_1 - found
===>   pbbam-0.18.0_5 depends on file: /usr/local/bin/python3.7 - found

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: lib-depends
-------------------------------------------------------------------------------

===>   pbbam-0.18.0_5 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so)
===>   pbbam-0.18.0_5 depends on shared library: libboost_regex.so - found (/usr/local/lib/libboost_regex.so)

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: configure
-------------------------------------------------------------------------------

===>   pbbam-0.18.0_5 depends on executable: meson - found
===>   pbbam-0.18.0_5 depends on executable: ninja - found
===>   pbbam-0.18.0_5 depends on package: pkgconf>=1.3.0_1 - found
===>   pbbam-0.18.0_5 depends on file: /usr/local/bin/python3.7 - found
===>   pbbam-0.18.0_5 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so)
===>   pbbam-0.18.0_5 depends on shared library: libboost_regex.so - found (/usr/local/lib/libboost_regex.so)
===>  Configuring for pbbam-0.18.0_5
The Meson build system
Version: 0.57.1
Source dir: /construction/biology/pbbam/pbbam-0.18.0
Build dir: /construction/biology/pbbam/pbbam-0.18.0/_build
Build type: native build
Project name: PacBioBAM
Project version: 0.18.0
C++ compiler for the host machine: c++ (gcc 8.3.0 "c++ 8.3 [DragonFly] Release/2019-02-22")
C++ linker for the host machine: c++ ld.gold 2.34
Host machine cpu family: x86_64
Host machine cpu: x86_64
Compiler for C++ supports arguments -Wduplicated-cond: YES 
Compiler for C++ supports arguments -Wduplicated-branches: YES 
Compiler for C++ supports arguments -Wlogical-op: YES 
Compiler for C++ supports arguments -Wrestrict: YES 
Compiler for C++ supports arguments -Wnull-dereference: YES 
Compiler for C++ supports arguments -Wuseless-cast: YES 
Compiler for C++ supports arguments -Wdouble-promotion: YES 
Compiler for C++ supports arguments -Wshadow: YES 
Compiler for C++ supports arguments -Wformat=1: YES 
Run-time dependency threads found: YES
Found pkg-config: /usr/local/bin/pkgconf (1.7.3)
Run-time dependency Boost found: YES 1.72.0 (/usr/local)
Run-time dependency zlib found: YES 1.2.11
Run-time dependency htslib found: YES 1.11
Program python3.7 found: YES (/usr/local/bin/python3.7)
Configuring Bam2SamVersion.h using configuration
Configuring PbIndexVersion.h using configuration
Configuring PbIndexDumpVersion.h using configuration
Configuring PbMergeVersion.h using configuration
Configuring PbBamifyVersion.h using configuration
Build targets in project: 6

Found ninja-1.10.2 at /usr/local/bin/ninja

SUCCEEDED 00:00:06

-------------------------------------------------------------------------------
-- Phase: build
-------------------------------------------------------------------------------

===>  Building for pbbam-0.18.0_5
[1/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/Cigar.cpp.o -MF src/libpbbam.so.0.18.0.p/Cigar.cpp.o.d -o src/libpbbam.so.0.18.0.p/Cigar.cpp.o -c ../src/Cigar.cpp
[2/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/ChemistryTable.cpp.o -MF src/libpbbam.so.0.18.0.p/ChemistryTable.cpp.o.d -o src/libpbbam.so.0.18.0.p/ChemistryTable.cpp.o -c ../src/ChemistryTable.cpp
[3/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/BamRecordTags.cpp.o -MF src/libpbbam.so.0.18.0.p/BamRecordTags.cpp.o.d -o src/libpbbam.so.0.18.0.p/BamRecordTags.cpp.o -c ../src/BamRecordTags.cpp
[4/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/BamRecordBuilder.cpp.o -MF src/libpbbam.so.0.18.0.p/BamRecordBuilder.cpp.o.d -o src/libpbbam.so.0.18.0.p/BamRecordBuilder.cpp.o -c ../src/BamRecordBuilder.cpp
[5/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/BamWriter.cpp.o -MF src/libpbbam.so.0.18.0.p/BamWriter.cpp.o.d -o src/libpbbam.so.0.18.0.p/BamWriter.cpp.o -c ../src/BamWriter.cpp
[6/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/Accuracy.cpp.o -MF src/libpbbam.so.0.18.0.p/Accuracy.cpp.o.d -o src/libpbbam.so.0.18.0.p/Accuracy.cpp.o -c ../src/Accuracy.cpp
[7/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/BamReader.cpp.o -MF src/libpbbam.so.0.18.0.p/BamReader.cpp.o.d -o src/libpbbam.so.0.18.0.p/BamReader.cpp.o -c ../src/BamReader.cpp
[8/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/BamRecordImpl.cpp.o -MF src/libpbbam.so.0.18.0.p/BamRecordImpl.cpp.o.d -o src/libpbbam.so.0.18.0.p/BamRecordImpl.cpp.o -c ../src/BamRecordImpl.cpp
../src/BamRecordImpl.cpp: In member function 'PacBio::BAM::BamRecordImpl& PacBio::BAM::BamRecordImpl::operator=(const PacBio::BAM::BamRecordImpl&)':
../src/BamRecordImpl.cpp:93:18: warning: ignoring return value of 'bam1_t* bam_copy1(bam1_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result]
         bam_copy1(d_.get(), other.d_.get());
         ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
../src/BamRecordImpl.cpp: In static member function 'static PacBio::BAM::BamRecordImpl PacBio::BAM::BamRecordImpl::FromRawData(const std::shared_ptr<bam1_t>&)':
../src/BamRecordImpl.cpp:233:14: warning: ignoring return value of 'bam1_t* bam_copy1(bam1_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result]
     bam_copy1(result.d_.get(), rawData.get());
     ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[9/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/Frames.cpp.o -MF src/libpbbam.so.0.18.0.p/Frames.cpp.o.d -o src/libpbbam.so.0.18.0.p/Frames.cpp.o -c ../src/Frames.cpp
[10/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/FileProducer.cpp.o -MF src/libpbbam.so.0.18.0.p/FileProducer.cpp.o.d -o src/libpbbam.so.0.18.0.p/FileProducer.cpp.o -c ../src/FileProducer.cpp
[11/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/FofnReader.cpp.o -MF src/libpbbam.so.0.18.0.p/FofnReader.cpp.o.d -o src/libpbbam.so.0.18.0.p/FofnReader.cpp.o -c ../src/FofnReader.cpp
[12/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/FastqReader.cpp.o -MF src/libpbbam.so.0.18.0.p/FastqReader.cpp.o.d -o src/libpbbam.so.0.18.0.p/FastqReader.cpp.o -c ../src/FastqReader.cpp
[13/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/BamHeader.cpp.o -MF src/libpbbam.so.0.18.0.p/BamHeader.cpp.o.d -o src/libpbbam.so.0.18.0.p/BamHeader.cpp.o -c ../src/BamHeader.cpp
[14/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/BamFile.cpp.o -MF src/libpbbam.so.0.18.0.p/BamFile.cpp.o.d -o src/libpbbam.so.0.18.0.p/BamFile.cpp.o -c ../src/BamFile.cpp
[15/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/BamTagCodec.cpp.o -MF src/libpbbam.so.0.18.0.p/BamTagCodec.cpp.o.d -o src/libpbbam.so.0.18.0.p/BamTagCodec.cpp.o -c ../src/BamTagCodec.cpp
[16/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/FastaReader.cpp.o -MF src/libpbbam.so.0.18.0.p/FastaReader.cpp.o.d -o src/libpbbam.so.0.18.0.p/FastaReader.cpp.o -c ../src/FastaReader.cpp
[17/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/BarcodeQuery.cpp.o -MF src/libpbbam.so.0.18.0.p/BarcodeQuery.cpp.o.d -o src/libpbbam.so.0.18.0.p/BarcodeQuery.cpp.o -c ../src/BarcodeQuery.cpp
[18/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/DataSetXsd.cpp.o -MF src/libpbbam.so.0.18.0.p/DataSetXsd.cpp.o.d -o src/libpbbam.so.0.18.0.p/DataSetXsd.cpp.o -c ../src/DataSetXsd.cpp
[19/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/AlignmentPrinter.cpp.o -MF src/libpbbam.so.0.18.0.p/AlignmentPrinter.cpp.o.d -o src/libpbbam.so.0.18.0.p/AlignmentPrinter.cpp.o -c ../src/AlignmentPrinter.cpp
[20/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/BaiIndexedBamReader.cpp.o -MF src/libpbbam.so.0.18.0.p/BaiIndexedBamReader.cpp.o.d -o src/libpbbam.so.0.18.0.p/BaiIndexedBamReader.cpp.o -c ../src/BaiIndexedBamReader.cpp
[21/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/Config.cpp.o -MF src/libpbbam.so.0.18.0.p/Config.cpp.o.d -o src/libpbbam.so.0.18.0.p/Config.cpp.o -c ../src/Config.cpp
[22/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/DataSetElement.cpp.o -MF src/libpbbam.so.0.18.0.p/DataSetElement.cpp.o.d -o src/libpbbam.so.0.18.0.p/DataSetElement.cpp.o -c ../src/DataSetElement.cpp
[23/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/CigarOperation.cpp.o -MF src/libpbbam.so.0.18.0.p/CigarOperation.cpp.o.d -o src/libpbbam.so.0.18.0.p/CigarOperation.cpp.o -c ../src/CigarOperation.cpp
[24/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/FileUtils.cpp.o -MF src/libpbbam.so.0.18.0.p/FileUtils.cpp.o.d -o src/libpbbam.so.0.18.0.p/FileUtils.cpp.o -c ../src/FileUtils.cpp
[25/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/FastaSequenceQuery.cpp.o -MF src/libpbbam.so.0.18.0.p/FastaSequenceQuery.cpp.o.d -o src/libpbbam.so.0.18.0.p/FastaSequenceQuery.cpp.o -c ../src/FastaSequenceQuery.cpp
[26/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/BamRecord.cpp.o -MF src/libpbbam.so.0.18.0.p/BamRecord.cpp.o.d -o src/libpbbam.so.0.18.0.p/BamRecord.cpp.o -c ../src/BamRecord.cpp
[27/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/DataSet.cpp.o -MF src/libpbbam.so.0.18.0.p/DataSet.cpp.o.d -o src/libpbbam.so.0.18.0.p/DataSet.cpp.o -c ../src/DataSet.cpp
[28/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/EntireFileQuery.cpp.o -MF src/libpbbam.so.0.18.0.p/EntireFileQuery.cpp.o.d -o src/libpbbam.so.0.18.0.p/EntireFileQuery.cpp.o -c ../src/EntireFileQuery.cpp
[29/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/DataSetBaseTypes.cpp.o -MF src/libpbbam.so.0.18.0.p/DataSetBaseTypes.cpp.o.d -o src/libpbbam.so.0.18.0.p/DataSetBaseTypes.cpp.o -c ../src/DataSetBaseTypes.cpp
[30/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/DataSetTypes.cpp.o -MF src/libpbbam.so.0.18.0.p/DataSetTypes.cpp.o.d -o src/libpbbam.so.0.18.0.p/DataSetTypes.cpp.o -c ../src/DataSetTypes.cpp
[31/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/DataSetIO.cpp.o -MF src/libpbbam.so.0.18.0.p/DataSetIO.cpp.o.d -o src/libpbbam.so.0.18.0.p/DataSetIO.cpp.o -c ../src/DataSetIO.cpp
[32/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/Compare.cpp.o -MF src/libpbbam.so.0.18.0.p/Compare.cpp.o.d -o src/libpbbam.so.0.18.0.p/Compare.cpp.o -c ../src/Compare.cpp
[33/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/ProgramInfo.cpp.o -MF src/libpbbam.so.0.18.0.p/ProgramInfo.cpp.o.d -o src/libpbbam.so.0.18.0.p/ProgramInfo.cpp.o -c ../src/ProgramInfo.cpp
[34/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/QNameQuery.cpp.o -MF src/libpbbam.so.0.18.0.p/QNameQuery.cpp.o.d -o src/libpbbam.so.0.18.0.p/QNameQuery.cpp.o -c ../src/QNameQuery.cpp
[35/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/MD5.cpp.o -MF src/libpbbam.so.0.18.0.p/MD5.cpp.o.d -o src/libpbbam.so.0.18.0.p/MD5.cpp.o -c ../src/MD5.cpp
[36/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/PbiRawData.cpp.o -MF src/libpbbam.so.0.18.0.p/PbiRawData.cpp.o.d -o src/libpbbam.so.0.18.0.p/PbiRawData.cpp.o -c ../src/PbiRawData.cpp
[37/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/PbiFile.cpp.o -MF src/libpbbam.so.0.18.0.p/PbiFile.cpp.o.d -o src/libpbbam.so.0.18.0.p/PbiFile.cpp.o -c ../src/PbiFile.cpp
[38/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/PbiIndexIO.cpp.o -MF src/libpbbam.so.0.18.0.p/PbiIndexIO.cpp.o.d -o src/libpbbam.so.0.18.0.p/PbiIndexIO.cpp.o -c ../src/PbiIndexIO.cpp
[39/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/PbiIndexedBamReader.cpp.o -MF src/libpbbam.so.0.18.0.p/PbiIndexedBamReader.cpp.o.d -o src/libpbbam.so.0.18.0.p/PbiIndexedBamReader.cpp.o -c ../src/PbiIndexedBamReader.cpp
[40/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/PbiFilterQuery.cpp.o -MF src/libpbbam.so.0.18.0.p/PbiFilterQuery.cpp.o.d -o src/libpbbam.so.0.18.0.p/PbiFilterQuery.cpp.o -c ../src/PbiFilterQuery.cpp
[41/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/XmlWriter.cpp.o -MF src/libpbbam.so.0.18.0.p/XmlWriter.cpp.o.d -o src/libpbbam.so.0.18.0.p/XmlWriter.cpp.o -c ../src/XmlWriter.cpp
[42/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/MemoryUtils.cpp.o -MF src/libpbbam.so.0.18.0.p/MemoryUtils.cpp.o.d -o src/libpbbam.so.0.18.0.p/MemoryUtils.cpp.o -c ../src/MemoryUtils.cpp
../src/MemoryUtils.cpp: In static member function 'static std::shared_ptr<sam_hdr_t> PacBio::BAM::internal::BamHeaderMemory::MakeRawHeader(const PacBio::BAM::BamHeader&)':
../src/MemoryUtils.cpp:37:14: warning: 'sam_hdr_t::cigar_tab' is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations]
     rawData->cigar_tab = nullptr;
              ^~~~~~~~~
In file included from /usr/local/include/htslib/bgzf.h:36,
                 from ../src/MemoryUtils.h:9,
                 from ../src/MemoryUtils.cpp:5:
/usr/local/include/htslib/sam.h:75:29: note: declared here
     const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead");
                             ^~~~~~~~~~~~~~
../src/MemoryUtils.cpp:37:14: warning: 'sam_hdr_t::cigar_tab' is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations]
     rawData->cigar_tab = nullptr;
              ^~~~~~~~~
In file included from /usr/local/include/htslib/bgzf.h:36,
                 from ../src/MemoryUtils.h:9,
                 from ../src/MemoryUtils.cpp:5:
/usr/local/include/htslib/sam.h:75:29: note: declared here
     const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead");
                             ^~~~~~~~~~~~~~
../src/MemoryUtils.cpp:37:14: warning: 'sam_hdr_t::cigar_tab' is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations]
     rawData->cigar_tab = nullptr;
              ^~~~~~~~~
In file included from /usr/local/include/htslib/bgzf.h:36,
                 from ../src/MemoryUtils.h:9,
                 from ../src/MemoryUtils.cpp:5:
/usr/local/include/htslib/sam.h:75:29: note: declared here
     const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead");
                             ^~~~~~~~~~~~~~
[43/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/VirtualRegionTypeMap.cpp.o -MF src/libpbbam.so.0.18.0.p/VirtualRegionTypeMap.cpp.o.d -o src/libpbbam.so.0.18.0.p/VirtualRegionTypeMap.cpp.o -c ../src/VirtualRegionTypeMap.cpp
[44/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/PbiBuilder.cpp.o -MF src/libpbbam.so.0.18.0.p/PbiBuilder.cpp.o.d -o src/libpbbam.so.0.18.0.p/PbiBuilder.cpp.o -c ../src/PbiBuilder.cpp
[45/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/IndexedBamWriter.cpp.o -MF src/libpbbam.so.0.18.0.p/IndexedBamWriter.cpp.o.d -o src/libpbbam.so.0.18.0.p/IndexedBamWriter.cpp.o -c ../src/IndexedBamWriter.cpp
[46/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/IndexedFastaReader.cpp.o -MF src/libpbbam.so.0.18.0.p/IndexedFastaReader.cpp.o.d -o src/libpbbam.so.0.18.0.p/IndexedFastaReader.cpp.o -c ../src/IndexedFastaReader.cpp
[47/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/PbiFilterTypes.cpp.o -MF src/libpbbam.so.0.18.0.p/PbiFilterTypes.cpp.o.d -o src/libpbbam.so.0.18.0.p/PbiFilterTypes.cpp.o -c ../src/PbiFilterTypes.cpp
[48/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/ValidationException.cpp.o -MF src/libpbbam.so.0.18.0.p/ValidationException.cpp.o.d -o src/libpbbam.so.0.18.0.p/ValidationException.cpp.o -c ../src/ValidationException.cpp
[49/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/PbiFilter.cpp.o -MF src/libpbbam.so.0.18.0.p/PbiFilter.cpp.o.d -o src/libpbbam.so.0.18.0.p/PbiFilter.cpp.o -c ../src/PbiFilter.cpp
[50/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/GenomicInterval.cpp.o -MF src/libpbbam.so.0.18.0.p/GenomicInterval.cpp.o.d -o src/libpbbam.so.0.18.0.p/GenomicInterval.cpp.o -c ../src/GenomicInterval.cpp
[51/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/XmlReader.cpp.o -MF src/libpbbam.so.0.18.0.p/XmlReader.cpp.o.d -o src/libpbbam.so.0.18.0.p/XmlReader.cpp.o -c ../src/XmlReader.cpp
[52/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/Version.cpp.o -MF src/libpbbam.so.0.18.0.p/Version.cpp.o.d -o src/libpbbam.so.0.18.0.p/Version.cpp.o -c ../src/Version.cpp
[53/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/GenomicIntervalQuery.cpp.o -MF src/libpbbam.so.0.18.0.p/GenomicIntervalQuery.cpp.o.d -o src/libpbbam.so.0.18.0.p/GenomicIntervalQuery.cpp.o -c ../src/GenomicIntervalQuery.cpp
[54/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/ValidationErrors.cpp.o -MF src/libpbbam.so.0.18.0.p/ValidationErrors.cpp.o.d -o src/libpbbam.so.0.18.0.p/ValidationErrors.cpp.o -c ../src/ValidationErrors.cpp
[55/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/VirtualZmwBamRecord.cpp.o -MF src/libpbbam.so.0.18.0.p/VirtualZmwBamRecord.cpp.o.d -o src/libpbbam.so.0.18.0.p/VirtualZmwBamRecord.cpp.o -c ../src/VirtualZmwBamRecord.cpp
[56/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/QualityValue.cpp.o -MF src/libpbbam.so.0.18.0.p/QualityValue.cpp.o.d -o src/libpbbam.so.0.18.0.p/QualityValue.cpp.o -c ../src/QualityValue.cpp
[57/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/VirtualZmwCompositeReader.cpp.o -MF src/libpbbam.so.0.18.0.p/VirtualZmwCompositeReader.cpp.o.d -o src/libpbbam.so.0.18.0.p/VirtualZmwCompositeReader.cpp.o -c ../src/VirtualZmwCompositeReader.cpp
[58/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/VirtualZmwReader.cpp.o -MF src/libpbbam.so.0.18.0.p/VirtualZmwReader.cpp.o.d -o src/libpbbam.so.0.18.0.p/VirtualZmwReader.cpp.o -c ../src/VirtualZmwReader.cpp
[59/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/SequenceInfo.cpp.o -MF src/libpbbam.so.0.18.0.p/SequenceInfo.cpp.o.d -o src/libpbbam.so.0.18.0.p/SequenceInfo.cpp.o -c ../src/SequenceInfo.cpp
[60/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/vcf_VcfWriter.cpp.o -MF src/libpbbam.so.0.18.0.p/vcf_VcfWriter.cpp.o.d -o src/libpbbam.so.0.18.0.p/vcf_VcfWriter.cpp.o -c ../src/vcf/VcfWriter.cpp
[61/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/Validator.cpp.o -MF src/libpbbam.so.0.18.0.p/Validator.cpp.o.d -o src/libpbbam.so.0.18.0.p/Validator.cpp.o -c ../src/Validator.cpp
[62/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/SamWriter.cpp.o -MF src/libpbbam.so.0.18.0.p/SamWriter.cpp.o.d -o src/libpbbam.so.0.18.0.p/SamWriter.cpp.o -c ../src/SamWriter.cpp
[63/102] c++ -Itools/bam2sam.p -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/bam2sam.p/common_OptionParser.cpp.o -MF tools/bam2sam.p/common_OptionParser.cpp.o.d -o tools/bam2sam.p/common_OptionParser.cpp.o -c ../tools/common/OptionParser.cpp
[64/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/vcf_VcfHeader.cpp.o -MF src/libpbbam.so.0.18.0.p/vcf_VcfHeader.cpp.o.d -o src/libpbbam.so.0.18.0.p/vcf_VcfHeader.cpp.o -c ../src/vcf/VcfHeader.cpp
[65/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/vcf_VcfReader.cpp.o -MF src/libpbbam.so.0.18.0.p/vcf_VcfReader.cpp.o.d -o src/libpbbam.so.0.18.0.p/vcf_VcfReader.cpp.o -c ../src/vcf/VcfReader.cpp
[66/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/ZmwTypeMap.cpp.o -MF src/libpbbam.so.0.18.0.p/ZmwTypeMap.cpp.o.d -o src/libpbbam.so.0.18.0.p/ZmwTypeMap.cpp.o -c ../src/ZmwTypeMap.cpp
[67/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/vcf_VcfVariant.cpp.o -MF src/libpbbam.so.0.18.0.p/vcf_VcfVariant.cpp.o.d -o src/libpbbam.so.0.18.0.p/vcf_VcfVariant.cpp.o -c ../src/vcf/VcfVariant.cpp
[68/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/SubreadLengthQuery.cpp.o -MF src/libpbbam.so.0.18.0.p/SubreadLengthQuery.cpp.o.d -o src/libpbbam.so.0.18.0.p/SubreadLengthQuery.cpp.o -c ../src/SubreadLengthQuery.cpp
[69/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/pugixml_pugixml.cpp.o -MF src/libpbbam.so.0.18.0.p/pugixml_pugixml.cpp.o.d -o src/libpbbam.so.0.18.0.p/pugixml_pugixml.cpp.o -c ../src/pugixml/pugixml.cpp
[70/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/ReadGroupInfo.cpp.o -MF src/libpbbam.so.0.18.0.p/ReadGroupInfo.cpp.o.d -o src/libpbbam.so.0.18.0.p/ReadGroupInfo.cpp.o -c ../src/ReadGroupInfo.cpp
[71/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/vcf_VcfQuery.cpp.o -MF src/libpbbam.so.0.18.0.p/vcf_VcfQuery.cpp.o.d -o src/libpbbam.so.0.18.0.p/vcf_VcfQuery.cpp.o -c ../src/vcf/VcfQuery.cpp
[72/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/ReadAccuracyQuery.cpp.o -MF src/libpbbam.so.0.18.0.p/ReadAccuracyQuery.cpp.o.d -o src/libpbbam.so.0.18.0.p/ReadAccuracyQuery.cpp.o -c ../src/ReadAccuracyQuery.cpp
[73/102] c++ -Itools/pbbamify.p -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbbamify.p/common_OptionParser.cpp.o -MF tools/pbbamify.p/common_OptionParser.cpp.o.d -o tools/pbbamify.p/common_OptionParser.cpp.o -c ../tools/common/OptionParser.cpp
[74/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/vcf_VcfFormat.cpp.o -MF src/libpbbam.so.0.18.0.p/vcf_VcfFormat.cpp.o.d -o src/libpbbam.so.0.18.0.p/vcf_VcfFormat.cpp.o -c ../src/vcf/VcfFormat.cpp
[75/102] c++ -Itools/pbindexdump.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindexdump.p/pbindexdump_src_main.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_main.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_main.cpp.o -c ../tools/pbindexdump/src/main.cpp
[76/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/vcf_VcfSort.cpp.o -MF src/libpbbam.so.0.18.0.p/vcf_VcfSort.cpp.o.d -o src/libpbbam.so.0.18.0.p/vcf_VcfSort.cpp.o -c ../src/vcf/VcfSort.cpp
[77/102] c++ -Itools/pbindexdump.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindexdump.p/pbindexdump_src_PbIndexDump.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_PbIndexDump.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_PbIndexDump.cpp.o -c ../tools/pbindexdump/src/PbIndexDump.cpp
[78/102] c++ -Itools/pbmerge.p -Itools -I../tools -Iinclude -I../include -I../tools/pbmerge -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbmerge.p/common_OptionParser.cpp.o -MF tools/pbmerge.p/common_OptionParser.cpp.o.d -o tools/pbmerge.p/common_OptionParser.cpp.o -c ../tools/common/OptionParser.cpp
[79/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/ZmwReadStitcher.cpp.o -MF src/libpbbam.so.0.18.0.p/ZmwReadStitcher.cpp.o.d -o src/libpbbam.so.0.18.0.p/ZmwReadStitcher.cpp.o -c ../src/ZmwReadStitcher.cpp
[80/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/SamTagCodec.cpp.o -MF src/libpbbam.so.0.18.0.p/SamTagCodec.cpp.o.d -o src/libpbbam.so.0.18.0.p/SamTagCodec.cpp.o -c ../src/SamTagCodec.cpp
[81/102] c++ -Itools/pbindexdump.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindexdump.p/pbindexdump_src_CppFormatter.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_CppFormatter.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_CppFormatter.cpp.o -c ../tools/pbindexdump/src/CppFormatter.cpp
[82/102] c++ -Itools/pbindex.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindex.p/pbindex_src_PbIndex.cpp.o -MF tools/pbindex.p/pbindex_src_PbIndex.cpp.o.d -o tools/pbindex.p/pbindex_src_PbIndex.cpp.o -c ../tools/pbindex/src/PbIndex.cpp
[83/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/ZmwGroupQuery.cpp.o -MF src/libpbbam.so.0.18.0.p/ZmwGroupQuery.cpp.o.d -o src/libpbbam.so.0.18.0.p/ZmwGroupQuery.cpp.o -c ../src/ZmwGroupQuery.cpp
[84/102] c++ -Itools/bam2sam.p -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/bam2sam.p/bam2sam_src_Bam2Sam.cpp.o -MF tools/bam2sam.p/bam2sam_src_Bam2Sam.cpp.o.d -o tools/bam2sam.p/bam2sam_src_Bam2Sam.cpp.o -c ../tools/bam2sam/src/Bam2Sam.cpp
[85/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/WhitelistedZmwReadStitcher.cpp.o -MF src/libpbbam.so.0.18.0.p/WhitelistedZmwReadStitcher.cpp.o.d -o src/libpbbam.so.0.18.0.p/WhitelistedZmwReadStitcher.cpp.o -c ../src/WhitelistedZmwReadStitcher.cpp
[86/102] c++ -Itools/pbindex.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindex.p/pbindex_src_main.cpp.o -MF tools/pbindex.p/pbindex_src_main.cpp.o.d -o tools/pbindex.p/pbindex_src_main.cpp.o -c ../tools/pbindex/src/main.cpp
[87/102] c++ -Itools/bam2sam.p -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/bam2sam.p/bam2sam_src_main.cpp.o -MF tools/bam2sam.p/bam2sam_src_main.cpp.o.d -o tools/bam2sam.p/bam2sam_src_main.cpp.o -c ../tools/bam2sam/src/main.cpp
[88/102] c++  -o tools/bam2sam tools/bam2sam.p/common_OptionParser.cpp.o tools/bam2sam.p/bam2sam_src_main.cpp.o tools/bam2sam.p/bam2sam_src_Bam2Sam.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,origin -Wl,-rpath,/usr/local/lib -Wl,--start-group /usr/local/lib/libhts.so -pthread /usr/lib/libz.so -Wl,--end-group
[89/102] c++ -Itools/pbindexdump.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindexdump.p/common_OptionParser.cpp.o -MF tools/pbindexdump.p/common_OptionParser.cpp.o.d -o tools/pbindexdump.p/common_OptionParser.cpp.o -c ../tools/common/OptionParser.cpp
[90/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.0.18.0.p/ZmwQuery.cpp.o -MF src/libpbbam.so.0.18.0.p/ZmwQuery.cpp.o.d -o src/libpbbam.so.0.18.0.p/ZmwQuery.cpp.o -c ../src/ZmwQuery.cpp
[91/102] c++  -o src/libpbbam.so.0.18.0 src/libpbbam.so.0.18.0.p/Accuracy.cpp.o src/libpbbam.so.0.18.0.p/AlignmentPrinter.cpp.o src/libpbbam.so.0.18.0.p/BaiIndexedBamReader.cpp.o src/libpbbam.so.0.18.0.p/BamFile.cpp.o src/libpbbam.so.0.18.0.p/BamHeader.cpp.o src/libpbbam.so.0.18.0.p/BamReader.cpp.o src/libpbbam.so.0.18.0.p/BamRecord.cpp.o src/libpbbam.so.0.18.0.p/BamRecordBuilder.cpp.o src/libpbbam.so.0.18.0.p/BamRecordImpl.cpp.o src/libpbbam.so.0.18.0.p/BamRecordTags.cpp.o src/libpbbam.so.0.18.0.p/BamTagCodec.cpp.o src/libpbbam.so.0.18.0.p/BamWriter.cpp.o src/libpbbam.so.0.18.0.p/BarcodeQuery.cpp.o src/libpbbam.so.0.18.0.p/ChemistryTable.cpp.o src/libpbbam.so.0.18.0.p/Cigar.cpp.o src/libpbbam.so.0.18.0.p/CigarOperation.cpp.o src/libpbbam.so.0.18.0.p/Compare.cpp.o src/libpbbam.so.0.18.0.p/Config.cpp.o src/libpbbam.so.0.18.0.p/DataSet.cpp.o src/libpbbam.so.0.18.0.p/DataSetBaseTypes.cpp.o src/libpbbam.so.0.18.0.p/DataSetElement.cpp.o src/libpbbam.so.0.18.0.p/DataSetIO.cpp.o src/libpbbam.so.0.18.0.p/DataSetTypes.cpp.o src/libpbbam.so.0.18.0.p/DataSetXsd.cpp.o src/libpbbam.so.0.18.0.p/EntireFileQuery.cpp.o src/libpbbam.so.0.18.0.p/FastaReader.cpp.o src/libpbbam.so.0.18.0.p/FastaSequenceQuery.cpp.o src/libpbbam.so.0.18.0.p/FastqReader.cpp.o src/libpbbam.so.0.18.0.p/FileProducer.cpp.o src/libpbbam.so.0.18.0.p/FileUtils.cpp.o src/libpbbam.so.0.18.0.p/FofnReader.cpp.o src/libpbbam.so.0.18.0.p/Frames.cpp.o src/libpbbam.so.0.18.0.p/GenomicInterval.cpp.o src/libpbbam.so.0.18.0.p/GenomicIntervalQuery.cpp.o src/libpbbam.so.0.18.0.p/IndexedBamWriter.cpp.o src/libpbbam.so.0.18.0.p/IndexedFastaReader.cpp.o src/libpbbam.so.0.18.0.p/MD5.cpp.o src/libpbbam.so.0.18.0.p/MemoryUtils.cpp.o src/libpbbam.so.0.18.0.p/PbiBuilder.cpp.o src/libpbbam.so.0.18.0.p/PbiFile.cpp.o src/libpbbam.so.0.18.0.p/PbiFilter.cpp.o src/libpbbam.so.0.18.0.p/PbiFilterQuery.cpp.o src/libpbbam.so.0.18.0.p/PbiFilterTypes.cpp.o src/libpbbam.so.0.18.0.p/PbiIndexedBamReader.cpp.o src/libpbbam.so.0.18.0.p/PbiIndexIO.cpp.o src/libpbbam.so.0.18.0.p/PbiRawData.cpp.o src/libpbbam.so.0.18.0.p/ProgramInfo.cpp.o src/libpbbam.so.0.18.0.p/QNameQuery.cpp.o src/libpbbam.so.0.18.0.p/QualityValue.cpp.o src/libpbbam.so.0.18.0.p/ReadAccuracyQuery.cpp.o src/libpbbam.so.0.18.0.p/ReadGroupInfo.cpp.o src/libpbbam.so.0.18.0.p/SamTagCodec.cpp.o src/libpbbam.so.0.18.0.p/SamWriter.cpp.o src/libpbbam.so.0.18.0.p/SequenceInfo.cpp.o src/libpbbam.so.0.18.0.p/SubreadLengthQuery.cpp.o src/libpbbam.so.0.18.0.p/Validator.cpp.o src/libpbbam.so.0.18.0.p/ValidationErrors.cpp.o src/libpbbam.so.0.18.0.p/ValidationException.cpp.o src/libpbbam.so.0.18.0.p/Version.cpp.o src/libpbbam.so.0.18.0.p/VirtualZmwBamRecord.cpp.o src/libpbbam.so.0.18.0.p/VirtualZmwCompositeReader.cpp.o src/libpbbam.so.0.18.0.p/VirtualZmwReader.cpp.o src/libpbbam.so.0.18.0.p/VirtualRegionTypeMap.cpp.o src/libpbbam.so.0.18.0.p/XmlReader.cpp.o src/libpbbam.so.0.18.0.p/XmlWriter.cpp.o src/libpbbam.so.0.18.0.p/WhitelistedZmwReadStitcher.cpp.o src/libpbbam.so.0.18.0.p/ZmwGroupQuery.cpp.o src/libpbbam.so.0.18.0.p/ZmwReadStitcher.cpp.o src/libpbbam.so.0.18.0.p/ZmwQuery.cpp.o src/libpbbam.so.0.18.0.p/ZmwTypeMap.cpp.o src/libpbbam.so.0.18.0.p/vcf_VcfVariant.cpp.o src/libpbbam.so.0.18.0.p/vcf_VcfFormat.cpp.o src/libpbbam.so.0.18.0.p/vcf_VcfHeader.cpp.o src/libpbbam.so.0.18.0.p/vcf_VcfReader.cpp.o src/libpbbam.so.0.18.0.p/vcf_VcfSort.cpp.o src/libpbbam.so.0.18.0.p/vcf_VcfQuery.cpp.o src/libpbbam.so.0.18.0.p/vcf_VcfWriter.cpp.o src/libpbbam.so.0.18.0.p/pugixml_pugixml.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -shared -fPIC -Wl,--start-group -Wl,-soname,libpbbam.so.0.18.0 -pthread /usr/lib/libz.so /usr/local/lib/libhts.so -Wl,--end-group
[92/102] c++ -Itools/pbindex.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindex.p/common_OptionParser.cpp.o -MF tools/pbindex.p/common_OptionParser.cpp.o.d -o tools/pbindex.p/common_OptionParser.cpp.o -c ../tools/common/OptionParser.cpp
[93/102] c++ -Itools/pbindexdump.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o -c ../tools/pbindexdump/src/JsonFormatter.cpp
[94/102] /usr/local/bin/meson --internal symbolextractor /construction/biology/pbbam/pbbam-0.18.0/_build src/libpbbam.so.0.18.0 src/libpbbam.so.0.18.0 src/libpbbam.so.0.18.0.p/libpbbam.so.0.18.0.symbols 
WARNING: Symbol extracting has not been implemented for this platform. Relinking will always happen on source changes.
[95/102] c++  -o tools/pbindex tools/pbindex.p/common_OptionParser.cpp.o tools/pbindex.p/pbindex_src_main.cpp.o tools/pbindex.p/pbindex_src_PbIndex.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,origin '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/construction/biology/pbbam/pbbam-0.18.0/_build/src -Wl,--start-group src/libpbbam.so.0.18.0 /usr/local/lib/libhts.so /usr/lib/libz.so -Wl,--end-group
[96/102] c++  -o tools/pbindexdump tools/pbindexdump.p/common_OptionParser.cpp.o tools/pbindexdump.p/pbindexdump_src_CppFormatter.cpp.o tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o tools/pbindexdump.p/pbindexdump_src_PbIndexDump.cpp.o tools/pbindexdump.p/pbindexdump_src_main.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,origin '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/construction/biology/pbbam/pbbam-0.18.0/_build/src -Wl,--start-group src/libpbbam.so.0.18.0 /usr/local/lib/libhts.so /usr/lib/libz.so -Wl,--end-group
[97/102] c++ -Itools/pbbamify.p -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbbamify.p/pbbamify_src_PbBamify.cpp.o -MF tools/pbbamify.p/pbbamify_src_PbBamify.cpp.o.d -o tools/pbbamify.p/pbbamify_src_PbBamify.cpp.o -c ../tools/pbbamify/src/PbBamify.cpp
[98/102] c++ -Itools/pbmerge.p -Itools -I../tools -Iinclude -I../include -I../tools/pbmerge -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbmerge.p/pbmerge_src_main.cpp.o -MF tools/pbmerge.p/pbmerge_src_main.cpp.o.d -o tools/pbmerge.p/pbmerge_src_main.cpp.o -c ../tools/pbmerge/src/main.cpp
[99/102] c++  -o tools/pbmerge tools/pbmerge.p/common_OptionParser.cpp.o tools/pbmerge.p/pbmerge_src_main.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,origin '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/construction/biology/pbbam/pbbam-0.18.0/_build/src -Wl,--start-group src/libpbbam.so.0.18.0 /usr/local/lib/libhts.so /usr/lib/libz.so -Wl,--end-group
[100/102] c++ -Itools/pbbamify.p -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o -MF tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o.d -o tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o -c ../tools/pbbamify/src/QueryLookup.cpp
[101/102] c++ -Itools/pbbamify.p -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -I/usr/local/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbbamify.p/pbbamify_src_main.cpp.o -MF tools/pbbamify.p/pbbamify_src_main.cpp.o.d -o tools/pbbamify.p/pbbamify_src_main.cpp.o -c ../tools/pbbamify/src/main.cpp
[102/102] c++  -o tools/pbbamify tools/pbbamify.p/common_OptionParser.cpp.o tools/pbbamify.p/pbbamify_src_main.cpp.o tools/pbbamify.p/pbbamify_src_PbBamify.cpp.o tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,origin '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/construction/biology/pbbam/pbbam-0.18.0/_build/src -Wl,--start-group src/libpbbam.so.0.18.0 /usr/local/lib/libhts.so /usr/lib/libz.so -Wl,--end-group

SUCCEEDED 00:02:11

-------------------------------------------------------------------------------
-- Phase: run-depends
-------------------------------------------------------------------------------

===>   pbbam-0.18.0_5 depends on file: /usr/local/bin/python3.7 - found

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: stage
-------------------------------------------------------------------------------

===>  Staging for pbbam-0.18.0_5
===>   pbbam-0.18.0_5 depends on file: /usr/local/bin/python3.7 - found
===>   Generating temporary packing list
[0/1] /usr/local/bin/meson install --no-rebuild
Installing src/libpbbam.so.0.18.0 to /construction/biology/pbbam/stage/usr/local/lib
Stripping target 'src/libpbbam.so.0.18.0' using strip.
Installing tools/bam2sam to /construction/biology/pbbam/stage/usr/local/bin
Stripping target 'tools/bam2sam' using strip.
Installing tools/pbindex to /construction/biology/pbbam/stage/usr/local/bin
Stripping target 'tools/pbindex' using strip.
Installing tools/pbindexdump to /construction/biology/pbbam/stage/usr/local/bin
Stripping target 'tools/pbindexdump' using strip.
Installing tools/pbmerge to /construction/biology/pbbam/stage/usr/local/bin
Stripping target 'tools/pbmerge' using strip.
Installing tools/pbbamify to /construction/biology/pbbam/stage/usr/local/bin
Stripping target 'tools/pbbamify' using strip.
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/Accuracy.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/AlignmentPrinter.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/BaiIndexedBamReader.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/BamFile.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/BamHeader.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/BamReader.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/BamRecord.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/BamRecordBuilder.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/BamRecordImpl.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/BamRecordTag.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/BamRecordView.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/BamTagCodec.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/BamWriter.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/BarcodeQuery.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/Cigar.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/CigarOperation.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/ClipType.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/Compare.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/CompositeBamReader.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/CompositeFastaReader.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/Config.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/DataSet.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/DataSetTypes.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/DataSetXsd.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/EntireFileQuery.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/FastaReader.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/FastaSequence.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/FastaSequenceQuery.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/FastqReader.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/FastqSequence.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/FrameEncodingType.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/Frames.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/GenomicInterval.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/GenomicIntervalQuery.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/IndexedBamWriter.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/IndexedFastaReader.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/Interval.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/IRecordWriter.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/LocalContextFlags.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/MakeUnique.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/MD5.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/MoveAppend.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/Orientation.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/PbiBasicTypes.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/PbiBuilder.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/PbiFile.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/PbiFilter.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/PbiFilterQuery.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/PbiFilterTypes.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/PbiIndexedBamReader.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/PbiRawData.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/Position.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/ProgramInfo.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/PulseBehavior.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/PulseExclusionReason.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/QNameQuery.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/QualityValue.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/QualityValues.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/ReadAccuracyQuery.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/ReadGroupInfo.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/RecordType.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/SamTagCodec.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/SamWriter.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/SequenceInfo.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/Strand.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/StringUtilities.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/SubreadLengthQuery.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/Tag.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/TagCollection.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/Unused.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/Validator.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/ZmwGroupQuery.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/ZmwQuery.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/ZmwType.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/ZmwTypeMap.h to /construction/biology/pbbam/stage/usr/local/include/pbbam
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/exception/BundleChemistryMappingException.h to /construction/biology/pbbam/stage/usr/local/include/pbbam/exception
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/exception/InvalidSequencingChemistryException.h to /construction/biology/pbbam/stage/usr/local/include/pbbam/exception
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/exception/ValidationException.h to /construction/biology/pbbam/stage/usr/local/include/pbbam/exception
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/Accuracy.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/BamHeader.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/BamRecord.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/BamRecordBuilder.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/BamRecordImpl.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/BamRecordView.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/Cigar.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/CigarOperation.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/Compare.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/CompositeBamReader.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/CompositeFastaReader.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/DataSet.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/DataSetBaseTypes.h to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/DataSetBaseTypes.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/DataSetElement.h to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/DataSetElement.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/DataSetListElement.h to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/DataSetListElement.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/DataSetTypes.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/FastaSequence.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/FastqSequence.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/Frames.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/GenomicInterval.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/Interval.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/PbiBasicTypes.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/PbiFilter.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/PbiFilterTypes.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/PbiRawData.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/ProgramInfo.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/QualityValue.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/QualityValues.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/QueryBase.h to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/QueryBase.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/ReadGroupInfo.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/SequenceInfo.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/Tag.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/Validator.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/vcf/VcfVariant.h to /construction/biology/pbbam/stage/usr/local/include/pbbam/vcf
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/vcf/VcfFile.h to /construction/biology/pbbam/stage/usr/local/include/pbbam/vcf
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/vcf/VcfFormat.h to /construction/biology/pbbam/stage/usr/local/include/pbbam/vcf
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/vcf/VcfHeader.h to /construction/biology/pbbam/stage/usr/local/include/pbbam/vcf
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/vcf/VcfHeaderTypes.h to /construction/biology/pbbam/stage/usr/local/include/pbbam/vcf
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/vcf/VcfReader.h to /construction/biology/pbbam/stage/usr/local/include/pbbam/vcf
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/vcf/VcfSort.h to /construction/biology/pbbam/stage/usr/local/include/pbbam/vcf
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/vcf/VcfQuery.h to /construction/biology/pbbam/stage/usr/local/include/pbbam/vcf
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/vcf/VcfWriter.h to /construction/biology/pbbam/stage/usr/local/include/pbbam/vcf
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/vcf/internal/VcfVariant.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/vcf/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/vcf/internal/VcfFile.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/vcf/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/vcf/internal/VcfHeader.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/vcf/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/vcf/internal/VcfHeaderTypes.inl to /construction/biology/pbbam/stage/usr/local/include/pbbam/vcf/internal
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/virtual/VirtualPolymeraseBamRecord.h to /construction/biology/pbbam/stage/usr/local/include/pbbam/virtual
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/virtual/VirtualPolymeraseCompositeReader.h to /construction/biology/pbbam/stage/usr/local/include/pbbam/virtual
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/virtual/VirtualPolymeraseReader.h to /construction/biology/pbbam/stage/usr/local/include/pbbam/virtual
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/virtual/VirtualRegion.h to /construction/biology/pbbam/stage/usr/local/include/pbbam/virtual
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/virtual/VirtualRegionType.h to /construction/biology/pbbam/stage/usr/local/include/pbbam/virtual
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/virtual/VirtualRegionTypeMap.h to /construction/biology/pbbam/stage/usr/local/include/pbbam/virtual
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/virtual/VirtualZmwBamRecord.h to /construction/biology/pbbam/stage/usr/local/include/pbbam/virtual
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/virtual/WhitelistedZmwReadStitcher.h to /construction/biology/pbbam/stage/usr/local/include/pbbam/virtual
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/virtual/ZmwReadStitcher.h to /construction/biology/pbbam/stage/usr/local/include/pbbam/virtual
Installing /construction/biology/pbbam/pbbam-0.18.0/include/pbbam/virtual/ZmwWhitelistVirtualReader.h to /construction/biology/pbbam/stage/usr/local/include/pbbam/virtual
Installing /construction/biology/pbbam/pbbam-0.18.0/_build/meson-private/pbbam.pc to /construction/biology/pbbam/stage/usr/local/lib/pkgconfig
install -l rs /construction/biology/pbbam/stage/usr/local/lib/libpbbam.so.0.18.0  /construction/biology/pbbam/stage/usr/local/lib/libpbbam.so.0.18
install -l rs /construction/biology/pbbam/stage/usr/local/lib/libpbbam.so.0.18.0  /construction/biology/pbbam/stage/usr/local/lib/libpbbam.so.0
====> Compressing man pages (compress-man)
====> Running Q/A tests (stage-qa)
Error: /usr/local/lib/libpbbam.so.0.18.0 is linked to /usr/local/lib/libdeflate.so.0 from archivers/libdeflate but it is not declared as a dependency
Warning: you need LIB_DEPENDS+=libdeflate.so:archivers/libdeflate
Error: /usr/local/lib/libpbbam.so.0.18.0 is linked to /usr/local/lib/libcurl.so.4 from ftp/curl but it is not declared as a dependency
Warning: you need LIB_DEPENDS+=libcurl.so:ftp/curl
Error: /usr/local/lib/libpbbam.so.0.18.0 is linked to /usr/local/lib/libcrypto.so.11 from security/openssl but it is not declared as a dependency
Warning: you need USES=ssl
Error: /usr/local/lib/libpbbam.so.0.18.0 is linked to /usr/local/lib/libnghttp2.so.14 from www/libnghttp2 but it is not declared as a dependency
Warning: you need LIB_DEPENDS+=libnghttp2.so:www/libnghttp2
Error: /usr/local/lib/libpbbam.so.0.18.0 is linked to /usr/local/lib/libssl.so.11 from security/openssl but it is not declared as a dependency
Warning: you need USES=ssl
Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks

SUCCEEDED 00:00:08

-------------------------------------------------------------------------------
-- Phase: check-plist
-------------------------------------------------------------------------------

====> Checking for pkg-plist issues (check-plist)
===> Parsing plist
===> Checking for items in STAGEDIR missing from pkg-plist
===> Checking for items in pkg-plist which are not in STAGEDIR
===> No pkg-plist issues found (check-plist)

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: package
-------------------------------------------------------------------------------

===>  Building package for pbbam-0.18.0_5
file sizes/checksums   [148]:   0%
file sizes/checksums   [148]:  67%
file sizes/checksums   [148]: 100%
packing files          [148]:   0%
packing files          [148]:  67%
packing files          [148]: 100%
packing directories      [0]:   0%
packing directories      [0]: 100%

SUCCEEDED 00:00:10
TOTAL TIME 00:02:49