=>> Building biology/pbbam build started at Sat Apr 6 16:41:54 BST 2024 port directory: /usr/ports/biology/pbbam package name: pbbam-0.18.0_8 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: ports@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1054 Mar 8 2023 /usr/ports/biology/pbbam/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: c014f9c79a Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 07 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.99.20240122_1 MASTERMNT=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/07/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=13-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.99.20240122_1 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- ports@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix /usr/local --infodir share/info --auto-features=enabled -Dpython.bytecompile=-1 -Db_colorout=never --buildtype release --optimization plain --strip _build --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PKG_CONFIG=pkgconf PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/pbbam/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/pbbam/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/pbbam/work/.cache HOME=/wrkdirs/usr/ports/biology/pbbam/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/pbbam/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/pbbam/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 CCACHE_DIR="/root/.ccache" --End CONFIGURE_ENV-- --MAKE_ENV-- NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/biology/pbbam/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/pbbam/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/pbbam/work/.cache HOME=/wrkdirs/usr/ports/biology/pbbam/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/pbbam/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/pbbam/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DESTDIR=/wrkdirs/usr/ports/biology/pbbam/work/stage LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -fstack-protector-strong " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " CCACHE_DIR="/root/.ccache" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" OSREL=13.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/pbbam" EXAMPLESDIR="share/examples/pbbam" DATADIR="share/pbbam" WWWDIR="www/pbbam" ETCDIR="etc/pbbam" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" 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 --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl mysql=8.0 imagemagick=7 samba=4.13 java=18 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache NO_CCACHE_DEPEND=1 CCACHE_WRAPPER_PATH= /ccache/libexec/ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> 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 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> pbbam-0.18.0_8 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_1: .......... done ===> pbbam-0.18.0_8 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of pbbam-0.18.0_8 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> 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 ===> Fetching all distfiles required by pbbam-0.18.0_8 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> 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 ===> Fetching all distfiles required by pbbam-0.18.0_8 for building => SHA256 Checksum OK for PacificBiosciences-pbbam-0.18.0_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> 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 ===> Fetching all distfiles required by pbbam-0.18.0_8 for building ===> Extracting for pbbam-0.18.0_8 => SHA256 Checksum OK for PacificBiosciences-pbbam-0.18.0_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for pbbam-0.18.0_8 ===> Applying FreeBSD patches for pbbam-0.18.0_8 from /usr/ports/biology/pbbam/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> pbbam-0.18.0_8 depends on executable: meson - not found ===> Installing existing package /packages/All/meson-1.4.0.pkg [pkg-builder.dan.net.uk] Installing meson-1.4.0... [pkg-builder.dan.net.uk] `-- Installing ninja-1.11.1,2... [pkg-builder.dan.net.uk] | `-- Installing python39-3.9.18_1... [pkg-builder.dan.net.uk] | | `-- Installing gettext-runtime-0.22.3_1... [pkg-builder.dan.net.uk] | | `-- Installing indexinfo-0.3.1... [pkg-builder.dan.net.uk] | | `-- Extracting indexinfo-0.3.1: . done [pkg-builder.dan.net.uk] | | `-- Extracting gettext-runtime-0.22.3_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libffi-3.4.4_1... [pkg-builder.dan.net.uk] | | `-- Extracting libffi-3.4.4_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing mpdecimal-2.5.1... [pkg-builder.dan.net.uk] | | `-- Extracting mpdecimal-2.5.1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing openssl-3.0.13_1,1... [pkg-builder.dan.net.uk] | | `-- Extracting openssl-3.0.13_1,1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing readline-8.2.10... [pkg-builder.dan.net.uk] | | `-- Extracting readline-8.2.10: .......... done [pkg-builder.dan.net.uk] | `-- Extracting python39-3.9.18_1: .......... done [pkg-builder.dan.net.uk] `-- Extracting ninja-1.11.1,2: ..... done [pkg-builder.dan.net.uk] Extracting meson-1.4.0: .......... done ===== Message from python39-3.9.18_1: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 ===> pbbam-0.18.0_8 depends on executable: meson - found ===> Returning to build of pbbam-0.18.0_8 ===> pbbam-0.18.0_8 depends on executable: ninja - found ===> pbbam-0.18.0_8 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-2.1.1,1.pkg [pkg-builder.dan.net.uk] Installing pkgconf-2.1.1,1... [pkg-builder.dan.net.uk] Extracting pkgconf-2.1.1,1: .......... done ===> pbbam-0.18.0_8 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of pbbam-0.18.0_8 ===> pbbam-0.18.0_8 depends on file: /usr/local/bin/python3.9 - found =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> pbbam-0.18.0_8 depends on shared library: libhts.so - not found ===> Installing existing package /packages/All/htslib-1.17_1.pkg [pkg-builder.dan.net.uk] Installing htslib-1.17_1... [pkg-builder.dan.net.uk] `-- Installing curl-8.6.0... [pkg-builder.dan.net.uk] | `-- Installing brotli-1.1.0,1... [pkg-builder.dan.net.uk] | `-- Extracting brotli-1.1.0,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libidn2-2.3.7... [pkg-builder.dan.net.uk] | | `-- Installing libunistring-1.2... [pkg-builder.dan.net.uk] | | `-- Extracting libunistring-1.2: .......... done [pkg-builder.dan.net.uk] | `-- Extracting libidn2-2.3.7: .......... done [pkg-builder.dan.net.uk] | `-- Installing libnghttp2-1.60.0... [pkg-builder.dan.net.uk] | `-- Extracting libnghttp2-1.60.0: ....... done [pkg-builder.dan.net.uk] | `-- Installing librtmp-2.4.20190330_1... [pkg-builder.dan.net.uk] | `-- Extracting librtmp-2.4.20190330_1: ......... done [pkg-builder.dan.net.uk] | `-- Installing libssh2-1.11.0_1,3... [pkg-builder.dan.net.uk] | `-- Extracting libssh2-1.11.0_1,3: .......... done [pkg-builder.dan.net.uk] | `-- Installing zstd-1.5.5_1... [pkg-builder.dan.net.uk] | | `-- Installing liblz4-1.9.4_1,1... [pkg-builder.dan.net.uk] | | `-- Extracting liblz4-1.9.4_1,1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting zstd-1.5.5_1: .......... done [pkg-builder.dan.net.uk] `-- Extracting curl-8.6.0: .......... done [pkg-builder.dan.net.uk] `-- Installing libdeflate-1.19... [pkg-builder.dan.net.uk] `-- Extracting libdeflate-1.19: .......... done [pkg-builder.dan.net.uk] Extracting htslib-1.17_1: .......... done ===> pbbam-0.18.0_8 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of pbbam-0.18.0_8 ===> pbbam-0.18.0_8 depends on shared library: libboost_regex.so - not found ===> Installing existing package /packages/All/boost-libs-1.84.0.pkg [pkg-builder.dan.net.uk] Installing boost-libs-1.84.0... [pkg-builder.dan.net.uk] `-- Installing icu-74.2,1... [pkg-builder.dan.net.uk] `-- Extracting icu-74.2,1: .......... done [pkg-builder.dan.net.uk] Extracting boost-libs-1.84.0: .......... done ===== Message from boost-libs-1.84.0: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===> pbbam-0.18.0_8 depends on shared library: libboost_regex.so - found (/usr/local/lib/libboost_regex.so) ===> Returning to build of pbbam-0.18.0_8 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for pbbam-0.18.0_8 WARNING: Recommend using either -Dbuildtype or -Doptimization + -Ddebug. Using both is redundant since they override each other. See: https://mesonbuild.com/Builtin-options.html#build-type-options The Meson build system Version: 1.4.0 Source dir: /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0 Build dir: /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/_build Build type: native build Project name: PacBioBAM Project version: 0.18.0 C++ compiler for the host machine: c++ (clang 14.0.5 "FreeBSD clang version 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc12386ae247c)") C++ linker for the host machine: c++ ld.lld 14.0.5 Host machine cpu family: x86_64 Host machine cpu: x86_64 Compiler for C++ supports arguments -Wduplicated-cond: NO Compiler for C++ supports arguments -Wduplicated-branches: NO Compiler for C++ supports arguments -Wlogical-op: NO Compiler for C++ supports arguments -Wrestrict: NO Compiler for C++ supports arguments -Wnull-dereference: YES Compiler for C++ supports arguments -Wuseless-cast: NO Compiler for C++ supports arguments -Wdouble-promotion: YES Compiler for C++ supports arguments -Wshadow: YES Compiler for C++ supports arguments -Wformat=1: NO Run-time dependency threads found: YES Found pkg-config: YES (/usr/local/bin/pkgconf) 2.1.1 Run-time dependency Boost found: YES 1.84.0 (/usr/local) Run-time dependency zlib found: YES 1.2.13 Run-time dependency htslib found: YES 1.17 Program python3.9 found: YES (/usr/local/bin/python3.9) 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 NOTICE: Future-deprecated features used: * 0.56.0: {'dependency.get_pkgconfig_variable'} PacBioBAM 0.18.0 User defined options auto_features : enabled buildtype : release infodir : share/info optimization : plain prefix : /usr/local strip : true python.bytecompile: -1 b_colorout : never Found ninja-1.11.1 at /usr/local/bin/ninja WARNING: Running the setup command as `meson [options]` instead of `meson setup [options]` is ambiguous and deprecated. =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for pbbam-0.18.0_8 [ 0% 1/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 1% 2/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 In file included from ../src/AlignmentPrinter.cpp:9: ../include/pbbam/AlignmentPrinter.h:44:5: warning: explicitly defaulted move constructor is implicitly deleted [-Wdefaulted-function-deleted] AlignmentPrinter(AlignmentPrinter&&) = default; ^ ../include/pbbam/AlignmentPrinter.h:70:47: note: move constructor of 'AlignmentPrinter' is implicitly deleted because field 'ifr_' has a deleted move constructor const std::unique_ptr ifr_; ^ /usr/include/c++/v1/__memory/unique_ptr.h:210:3: note: copy constructor is implicitly deleted because 'unique_ptr' has a user-declared move constructor unique_ptr(unique_ptr&& __u) _NOEXCEPT ^ In file included from ../src/AlignmentPrinter.cpp:9: ../include/pbbam/AlignmentPrinter.h:46:23: warning: explicitly defaulted move assignment operator is implicitly deleted [-Wdefaulted-function-deleted] AlignmentPrinter& operator=(AlignmentPrinter&&) = default; ^ ../include/pbbam/AlignmentPrinter.h:70:47: note: move assignment operator of 'AlignmentPrinter' is implicitly deleted because field 'ifr_' has no move assignment operator const std::unique_ptr ifr_; ^ 2 warnings generated. [ 2% 3/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 3% 4/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 4% 5/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 5% 6/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 6% 7/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 7% 8/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 8% 9/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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:93:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bam_copy1(d_.get(), other.d_.get()); ^~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~ ../src/BamRecordImpl.cpp:233:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bam_copy1(result.d_.get(), rawData.get()); ^~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2 warnings generated. [ 9% 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 10% 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 11% 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 12% 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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% 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 14% 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 15% 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 16% 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 17% 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 18% 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 19% 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 20% 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 21% 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 22% 23/102] c++ 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-DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 37% 38/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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:37:14: warning: 'cigar_tab' is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations] rawData->cigar_tab = nullptr; ^ /usr/local/include/htslib/sam.h:84:29: note: 'cigar_tab' has been explicitly marked deprecated here const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead"); ^ /usr/local/include/htslib/hts_defs.h:75:49: note: expanded from macro 'HTS_DEPRECATED' #define HTS_DEPRECATED(message) __attribute__ ((__deprecated__ (message))) ^ 1 warning generated. 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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 [ 48% 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 49% 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 50% 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 50% 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 51% 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 52% 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 53% 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 54% 56/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 55% 57/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 56% 58/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 57% 59/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 58% 60/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 59% 61/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 60% 62/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 61% 63/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 62% 64/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 63% 65/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 ../src/XmlWriter.cpp:129:21: warning: loop variable 'prefixIter' creates a copy from type 'const std::__map_iterator, std::__tree_node, void *> *, long>>::value_type' (aka 'const pair') [-Wrange-loop-construct] for (const auto prefixIter : xsdPrefixesUsed) { ^ ../src/XmlWriter.cpp:129:10: note: use reference type 'const std::__map_iterator, std::__tree_node, void *> *, long>>::value_type &' (aka 'const pair &') to prevent copying for (const auto prefixIter : xsdPrefixesUsed) { ^~~~~~~~~~~~~~~~~~~~~~~ & 1 warning generated. [ 64% 66/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 65% 67/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 66% 68/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 67% 69/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 68% 70/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 69% 71/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 70% 72/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 ../src/vcf/VcfFormat.cpp:481:29: warning: loop variable 'fieldValue' creates a copy from type 'const std::string' [-Wrange-loop-construct] for (const auto fieldValue : fieldValues) { ^ ../src/vcf/VcfFormat.cpp:481:18: note: use reference type 'const std::string &' to prevent copying for (const auto fieldValue : fieldValues) { ^~~~~~~~~~~~~~~~~~~~~~~ & ../src/vcf/VcfFormat.cpp:521:21: warning: loop variable 'field' creates a copy from type 'const PacBio::VCF::InfoField' [-Wrange-loop-construct] for (const auto field : fields) { ^ ../src/vcf/VcfFormat.cpp:521:10: note: use reference type 'const PacBio::VCF::InfoField &' to prevent copying for (const auto field : fields) { ^~~~~~~~~~~~~~~~~~ & ../src/vcf/VcfFormat.cpp:541:25: warning: loop variable 'id' creates a copy from type 'const std::string' [-Wrange-loop-construct] for (const auto id : genotypeIds) { ^ ../src/vcf/VcfFormat.cpp:541:14: note: use reference type 'const std::string &' to prevent copying for (const auto id : genotypeIds) { ^~~~~~~~~~~~~~~ & ../src/vcf/VcfFormat.cpp:548:25: warning: loop variable 'sampleGenotype' creates a copy from type 'const PacBio::VCF::GenotypeField' [-Wrange-loop-construct] for (const auto sampleGenotype : sampleGenotypes) { ^ ../src/vcf/VcfFormat.cpp:548:14: note: use reference type 'const PacBio::VCF::GenotypeField &' to prevent copying for (const auto sampleGenotype : sampleGenotypes) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~ & 4 warnings generated. [ 71% 73/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 72% 74/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 73% 75/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 In file included from ../src/vcf/VcfSort.cpp:11: ../include/pbbam/vcf/VcfQuery.h:23:5: warning: explicitly defaulted default constructor is implicitly deleted [-Wdefaulted-function-deleted] VcfQuery() = default; ^ ../include/pbbam/vcf/VcfQuery.h:39:15: note: default constructor of 'VcfQuery' is implicitly deleted because field 'reader_' has a deleted default constructor VcfReader reader_; ^ ../include/pbbam/vcf/VcfReader.h:26:5: note: 'VcfReader' has been explicitly marked deleted here VcfReader() = delete; ^ 1 warning generated. [ 74% 76/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 In file included from ../src/vcf/VcfQuery.cpp:1: ../include/pbbam/vcf/VcfQuery.h:23:5: warning: explicitly defaulted default constructor is implicitly deleted [-Wdefaulted-function-deleted] VcfQuery() = default; ^ ../include/pbbam/vcf/VcfQuery.h:39:15: note: default constructor of 'VcfQuery' is implicitly deleted because field 'reader_' has a deleted default constructor VcfReader reader_; ^ ../include/pbbam/vcf/VcfReader.h:26:5: note: 'VcfReader' has been explicitly marked deleted here VcfReader() = delete; ^ 1 warning generated. [ 75% 77/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 76% 78/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 77% 79/102] 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 -shared -fPIC -Wl,-soname,libpbbam.so.0.18.0 -fstack-protector-strong -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -Wl,-rpath,/usr/local/lib -Wl,-rpath-link,/usr/local/lib -pthread -Wl,--start-group /usr/lib/libz.so /usr/local/lib/libhts.so -Wl,--end-group [ 78% 80/102] /usr/local/bin/meson --internal symbolextractor /wrkdirs/usr/ports/biology/pbbam/work/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 [ 79% 81/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 80% 82/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 ../tools/bam2sam/src/main.cpp:72:25: warning: loop variable 'e' creates a copy from type 'const std::string' [-Wrange-loop-construct] for (const auto e : settings.errors_) ^ ../tools/bam2sam/src/main.cpp:72:14: note: use reference type 'const std::string &' to prevent copying for (const auto e : settings.errors_) ^~~~~~~~~~~~~~ & 1 warning generated. [ 81% 83/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 82% 84/102] 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 -fstack-protector-strong -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -Wl,-rpath,/usr/local/lib -Wl,-rpath-link,/usr/local/lib -Wl,--start-group /usr/local/lib/libhts.so -pthread /usr/lib/libz.so -Wl,--end-group [ 83% 85/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 84% 86/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -Wnull-dereference -Wdouble-promotion -Wshadow -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 ../tools/pbindex/src/main.cpp:57:25: warning: loop variable 'e' creates a copy from type 'const std::string' [-Wrange-loop-construct] for (const auto e : settings.errors_) ^ ../tools/pbindex/src/main.cpp:57:14: note: use reference type 'const std::string &' to prevent copying for (const auto e : settings.errors_) ^~~~~~~~~~~~~~ & 1 warning generated. [ 85% 87/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 86% 88/102] 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 -fstack-protector-strong -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include '-Wl,-rpath,$ORIGIN/../src:/usr/local/lib' -Wl,-rpath-link,/wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/_build/src -Wl,-rpath-link,/usr/local/lib -Wl,--start-group src/libpbbam.so.0.18.0 /usr/local/lib/libhts.so /usr/lib/libz.so -Wl,--end-group [ 87% 89/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 88% 90/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 89% 91/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 90% 92/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 91% 93/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -Wnull-dereference -Wdouble-promotion -Wshadow -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 ../tools/pbindexdump/src/main.cpp:93:25: warning: loop variable 'e' creates a copy from type 'const std::string' [-Wrange-loop-construct] for (const auto e : settings.errors_) ^ ../tools/pbindexdump/src/main.cpp:93:14: note: use reference type 'const std::string &' to prevent copying for (const auto e : settings.errors_) ^~~~~~~~~~~~~~ & 1 warning generated. [ 92% 94/102] 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 -fstack-protector-strong -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include '-Wl,-rpath,$ORIGIN/../src:/usr/local/lib' -Wl,-rpath-link,/wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/_build/src -Wl,-rpath-link,/usr/local/lib -Wl,--start-group src/libpbbam.so.0.18.0 /usr/local/lib/libhts.so /usr/lib/libz.so -Wl,--end-group [ 93% 95/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -DBOOST_ALL_NO_LIB -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 94% 96/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -DBOOST_ALL_NO_LIB -Wnull-dereference -Wdouble-promotion -Wshadow -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 ../tools/pbmerge/src/main.cpp:95:25: warning: loop variable 'e' creates a copy from type 'const std::string' [-Wrange-loop-construct] for (const auto e : settings.errors_) ^ ../tools/pbmerge/src/main.cpp:95:14: note: use reference type 'const std::string &' to prevent copying for (const auto e : settings.errors_) ^~~~~~~~~~~~~~ & 1 warning generated. [ 95% 97/102] 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 -fstack-protector-strong -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include '-Wl,-rpath,$ORIGIN/../src:/usr/local/lib' -Wl,-rpath-link,/wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/_build/src -Wl,-rpath-link,/usr/local/lib -Wl,--start-group src/libpbbam.so.0.18.0 /usr/local/lib/libhts.so /usr/lib/libz.so -Wl,--end-group [ 96% 98/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -DBOOST_ALL_NO_LIB -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 97% 99/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -DBOOST_ALL_NO_LIB -Wnull-dereference -Wdouble-promotion -Wshadow -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% 100/102] 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -DBOOST_ALL_NO_LIB -Wnull-dereference -Wdouble-promotion -Wshadow -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 [ 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 -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -DBOOST_ALL_NO_LIB -Wnull-dereference -Wdouble-promotion -Wshadow -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 [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 -fstack-protector-strong -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include '-Wl,-rpath,$ORIGIN/../src:/usr/local/lib' -Wl,-rpath-link,/wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/_build/src -Wl,-rpath-link,/usr/local/lib -Wl,--start-group src/libpbbam.so.0.18.0 /usr/local/lib/libhts.so /usr/lib/libz.so -Wl,--end-group =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> pbbam-0.18.0_8 depends on file: /usr/local/bin/python3.9 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for pbbam-0.18.0_8 ===> Generating temporary packing list [ 0% 1/1] /usr/local/bin/meson install --no-rebuild Installing src/libpbbam.so.0.18.0 to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/lib Stripping target 'src/libpbbam.so.0.18.0'. Installing tools/bam2sam to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/bin Stripping target 'tools/bam2sam'. Installing tools/pbindex to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/bin Stripping target 'tools/pbindex'. Installing tools/pbindexdump to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/bin Stripping target 'tools/pbindexdump'. Installing tools/pbmerge to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/bin Stripping target 'tools/pbmerge'. Installing tools/pbbamify to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/bin Stripping target 'tools/pbbamify'. Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/Accuracy.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/AlignmentPrinter.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/BaiIndexedBamReader.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/BamFile.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/BamHeader.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/BamReader.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/BamRecord.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/BamRecordBuilder.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/BamRecordImpl.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/BamRecordTag.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/BamRecordView.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/BamTagCodec.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/BamWriter.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/BarcodeQuery.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/Cigar.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/CigarOperation.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/ClipType.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/Compare.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/CompositeBamReader.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/CompositeFastaReader.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/Config.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/DataSet.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/DataSetTypes.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/DataSetXsd.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/EntireFileQuery.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/FastaReader.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/FastaSequence.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/FastaSequenceQuery.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/FastqReader.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/FastqSequence.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/FrameEncodingType.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/Frames.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/GenomicInterval.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/GenomicIntervalQuery.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/IndexedBamWriter.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/IndexedFastaReader.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/Interval.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/IRecordWriter.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/LocalContextFlags.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/MakeUnique.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/MD5.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/MoveAppend.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/Orientation.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/PbiBasicTypes.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/PbiBuilder.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/PbiFile.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/PbiFilter.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/PbiFilterQuery.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/PbiFilterTypes.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/PbiIndexedBamReader.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/PbiRawData.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/Position.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/ProgramInfo.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/PulseBehavior.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/PulseExclusionReason.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/QNameQuery.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/QualityValue.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/QualityValues.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/ReadAccuracyQuery.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/ReadGroupInfo.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/RecordType.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/SamTagCodec.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/SamWriter.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/SequenceInfo.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/Strand.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/StringUtilities.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/SubreadLengthQuery.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/Tag.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/TagCollection.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/Unused.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/Validator.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/ZmwGroupQuery.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/ZmwQuery.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/ZmwType.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/ZmwTypeMap.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/exception/BundleChemistryMappingException.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/exception Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/exception/InvalidSequencingChemistryException.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/exception Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/exception/ValidationException.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/exception Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/Accuracy.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/BamHeader.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/BamRecord.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/BamRecordBuilder.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/BamRecordImpl.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/BamRecordView.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/Cigar.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/CigarOperation.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/Compare.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/CompositeBamReader.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/CompositeFastaReader.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/DataSet.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/DataSetBaseTypes.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/DataSetBaseTypes.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/DataSetElement.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/DataSetElement.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/DataSetListElement.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/DataSetListElement.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/DataSetTypes.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/FastaSequence.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/FastqSequence.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/Frames.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/GenomicInterval.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/Interval.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/PbiBasicTypes.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/PbiFilter.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/PbiFilterTypes.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/PbiRawData.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/ProgramInfo.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/QualityValue.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/QualityValues.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/QueryBase.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/QueryBase.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/ReadGroupInfo.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/SequenceInfo.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/Tag.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/Validator.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/vcf/VcfVariant.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/vcf Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/vcf/VcfFile.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/vcf Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/vcf/VcfFormat.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/vcf Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/vcf/VcfHeader.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/vcf Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/vcf/VcfHeaderTypes.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/vcf Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/vcf/VcfReader.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/vcf Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/vcf/VcfSort.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/vcf Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/vcf/VcfQuery.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/vcf Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/vcf/VcfWriter.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/vcf Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/vcf/internal/VcfVariant.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/vcf/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/vcf/internal/VcfFile.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/vcf/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/vcf/internal/VcfHeader.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/vcf/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/vcf/internal/VcfHeaderTypes.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/vcf/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/virtual/VirtualPolymeraseBamRecord.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/virtual Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/virtual/VirtualPolymeraseCompositeReader.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/virtual Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/virtual/VirtualPolymeraseReader.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/virtual Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/virtual/VirtualRegion.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/virtual Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/virtual/VirtualRegionType.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/virtual Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/virtual/VirtualRegionTypeMap.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/virtual Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/virtual/VirtualZmwBamRecord.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/virtual Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/virtual/WhitelistedZmwReadStitcher.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/virtual Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/virtual/ZmwReadStitcher.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/virtual Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/virtual/ZmwWhitelistVirtualReader.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/virtual Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/_build/meson-private/pbbam.pc to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/libdata/pkgconfig Installing symlink pointing to libpbbam.so.0.18.0 to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/lib/libpbbam.so install -l rs /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/lib/libpbbam.so.0.18.0 /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/lib/libpbbam.so.0.18 install -l rs /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/lib/libpbbam.so.0.18.0 /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/lib/libpbbam.so.0 ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2024-04-06T15:41:54+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=c014f9c79a' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for pbbam-0.18.0_8 ===> Building pbbam-0.18.0_8 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for pbbam-0.18.0_8 build of biology/pbbam | pbbam-0.18.0_8 ended at Sat Apr 6 18:12:26 BST 2024 build time: 01:30:34