------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=6.1 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/python3.8" 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 -Db_colorout=never --buildtype release --strip _build SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- NINJA_STATUS="[%p %s/%t] " 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/python3.8 PYTHON_LIBDIR=lib/python3.8 PYTHON_PLATFORM=dragonfly6 PYTHON_SITELIBDIR=lib/python3.8/site-packages PYTHON_SUFFIX=38 PYTHON_EXT_SUFFIX=.cpython-38 PYTHON_VER=3.8 PYTHON_VERSION=python3.8 PYTHON2="@comment " PYTHON3="" OSREL=6.1 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=600102 OSVERSION=9999999 OSREL=6.1 _OSRELEASE=6.1-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-2.4.1.txz Installing /packages/All/mpdecimal-2.5.1.txz Installing /packages/All/ncurses-6.2.20210626.txz ===== Message from ncurses-6.2.20210626: -- { type: install message: < 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://docs.freebsd.org/en/articles/contributing/#ports-contributing 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 00:00:00 ------------------------------------------------------------------------------- -- 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://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> 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://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> 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 00:00:01 ------------------------------------------------------------------------------- -- 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://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> 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/python3.8 - 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/python3.8 - 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: 0.58.1 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 (1.7.4) 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 1.12 Program python3.8 found: YES (/usr/local/bin/python3.8) 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 00:00:05 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for pbbam-0.18.0_5 [ 0% 10/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -pipe -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 [ 1% 11/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -pipe -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 [ 2% 12/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -pipe -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 [ 3% 13/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -pipe -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 [ 4% 14/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -pipe -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 [ 5% 15/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -pipe -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 [ 6% 16/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -pipe -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 [ 7% 17/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -pipe -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 [ 8% 18/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -pipe -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 [ 9% 19/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -pipe -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 [ 10% 20/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -pipe -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 [ 11% 21/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -pipe -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&)': ../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()); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 12% 22/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -pipe -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 [ 13% 23/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -pipe -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 [ 14% 24/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -pipe -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 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src/libpbbam.so.0.18.0.p/PbiFilterQuery.cpp.o -c ../src/PbiFilterQuery.cpp [ 39% 49/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -pipe -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 [ 40% 50/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -pipe -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 [ 41% 51/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -pipe -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 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:77:29: 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:77:29: 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:77:29: note: declared here const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead"); ^~~~~~~~~~~~~~ [ 42% 52/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -pipe -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 [ 43% 53/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -pipe -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% 54/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -pipe -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 [ 45% 55/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic 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-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 [ 84% 95/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -pipe -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 [ 85% 95/102] c++ -Itools/pbindexdump.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -pipe -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 [ 86% 95/102] c++ -Itools/bam2sam.p -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -pipe -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 [ 87% 96/102] 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 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -Wl,-z,origin -Wl,-rpath,/usr/local/lib -Wl,--start-group /usr/local/lib/libhts.so -pthread /usr/lib/libz.so -Wl,--end-group [ 88% 96/102] c++ -Itools/pbindexdump.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -pipe -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 [ 89% 96/102] c++ -Itools/pbindex.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -pipe -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 [ 90% 96/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -pipe -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 [ 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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 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -pthread /usr/lib/libz.so /usr/local/lib/libhts.so -Wl,--end-group [ 92% 98/102] /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. [ 93% 100/102] 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 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -Wl,-z,origin '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/construction/biology/pbbam/pbbam-0.18.0/_build/src -Wl,--start-group src/libpbbam.so.0.18.0 /usr/local/lib/libhts.so /usr/lib/libz.so -Wl,--end-group [ 94% 100/102] c++ -o tools/pbindex tools/pbindex.p/common_OptionParser.cpp.o tools/pbindex.p/pbindex_src_main.cpp.o tools/pbindex.p/pbindex_src_PbIndex.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -Wl,-z,origin '-Wl,-rpath,$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 [ 95% 100/102] c++ -Itools/pbmerge.p -Itools -I../tools -Iinclude -I../include -I../tools/pbmerge -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -pipe -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 [ 96% 101/102] 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 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -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% 101/102] c++ -Itools/pbbamify.p -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -pipe -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 [ 98% 101/102] c++ -Itools/pbbamify.p -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -pipe -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 [ 99% 101/102] c++ -Itools/pbbamify.p -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -pipe -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 [100% 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 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -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 00:03:14 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> pbbam-0.18.0_5 depends on file: /usr/local/bin/python3.8 - 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/python3.8 - found ===> Generating temporary packing list [ 0% 1/1] /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 00:00:03 ------------------------------------------------------------------------------- -- 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 00:00:04 TOTAL TIME 00:04:01