=>> Building biology/pbbam build started at Tue May 6 10:06:56 BST 2025 port directory: /usr/ports/biology/pbbam package name: pbbam-0.18.0_11 building for: FreeBSD pkg-builder.dan.net.uk 14.2-RELEASE FreeBSD 14.2-RELEASE amd64 maintained by: ports@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1055 Feb 16 09:27 /usr/ports/biology/pbbam/Makefile Ports top last git commit: 5529c5919b Ports top unclean checkout: yes Port dir last git commit: fa53920e72 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1402000 Jail OSVERSION: 1402000 Job Id: 05 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1402000 UNAME_v=FreeBSD 14.2-RELEASE UNAME_r=14.2-RELEASE 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=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/14-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/14-amd64-default-dan/05/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=14-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 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 --localstatedir /var --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/python3.11" 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=/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" --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=/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 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 " 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/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_EXT_SUFFIX=.cpython-311 PYTHON_VER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=14.2 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/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_EXT_SUFFIX=.cpython-311 PYTHON_VER=3.11 PYTHON_VERSION=python3.11 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 apache=2.4 imagemagick=7 java=21 linux=c7 mysql=8.0 php=8.3 samba=4.19 varnish=7 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE ALLOW_UNSUPPORTED_SYSTEM=yes WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.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 pipebuf (-y) 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_11 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.1.2.pkg [pkg-builder.dan.net.uk] Installing pkg-2.1.2... [pkg-builder.dan.net.uk] Extracting pkg-2.1.2: .......... done ===> pbbam-0.18.0_11 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of pbbam-0.18.0_11 =========================================================================== =================================================== ===== 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_11 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_11 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_11 for building ===> Extracting for pbbam-0.18.0_11 => 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_11 ===> Applying FreeBSD patches for pbbam-0.18.0_11 from /usr/ports/biology/pbbam/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> pbbam-0.18.0_11 depends on executable: meson - not found ===> Installing existing package /packages/All/meson-1.7.0.pkg [pkg-builder.dan.net.uk] Installing meson-1.7.0... [pkg-builder.dan.net.uk] `-- Installing ninja-1.11.1,4... [pkg-builder.dan.net.uk] | `-- Installing python311-3.11.12... [pkg-builder.dan.net.uk] | | `-- Installing gettext-runtime-0.23.1... [pkg-builder.dan.net.uk] | | `-- Installing indexinfo-0.3.1_1... [pkg-builder.dan.net.uk] | | `-- Extracting indexinfo-0.3.1_1: . done [pkg-builder.dan.net.uk] | | `-- Extracting gettext-runtime-0.23.1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libffi-3.4.8... [pkg-builder.dan.net.uk] | | `-- Extracting libffi-3.4.8: .......... done [pkg-builder.dan.net.uk] | | `-- Installing mpdecimal-4.0.0... [pkg-builder.dan.net.uk] | | `-- Extracting mpdecimal-4.0.0: .......... done [pkg-builder.dan.net.uk] | | `-- Installing openssl-3.0.16,1... [pkg-builder.dan.net.uk] | | `-- Extracting openssl-3.0.16,1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing readline-8.2.13_2... [pkg-builder.dan.net.uk] | | `-- Extracting readline-8.2.13_2: .......... done [pkg-builder.dan.net.uk] | `-- Extracting python311-3.11.12: .......... done [pkg-builder.dan.net.uk] `-- Extracting ninja-1.11.1,4: ..... done [pkg-builder.dan.net.uk] Extracting meson-1.7.0: .......... done ===== Message from python311-3.11.12: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===> pbbam-0.18.0_11 depends on executable: meson - found ===> Returning to build of pbbam-0.18.0_11 ===> pbbam-0.18.0_11 depends on executable: ninja - found ===> pbbam-0.18.0_11 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-2.3.0_1,1.pkg [pkg-builder.dan.net.uk] Installing pkgconf-2.3.0_1,1... [pkg-builder.dan.net.uk] Extracting pkgconf-2.3.0_1,1: .......... done ===> pbbam-0.18.0_11 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of pbbam-0.18.0_11 ===> pbbam-0.18.0_11 depends on file: /usr/local/bin/python3.11 - found ===> pbbam-0.18.0_11 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg-builder.dan.net.uk] Installing ccache-3.7.12_8... [pkg-builder.dan.net.uk] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> pbbam-0.18.0_11 depends on file: /usr/local/bin/ccache - found ===> Returning to build of pbbam-0.18.0_11 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> pbbam-0.18.0_11 depends on shared library: libhts.so - not found ===> Installing existing package /packages/All/htslib-1.21.pkg [pkg-builder.dan.net.uk] Installing htslib-1.21... [pkg-builder.dan.net.uk] `-- Installing curl-8.13.0_1... [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 libidn2-2.3.8... [pkg-builder.dan.net.uk] | | `-- Installing libunistring-1.3... [pkg-builder.dan.net.uk] | | `-- Extracting libunistring-1.3: .......... done [pkg-builder.dan.net.uk] | `-- Extracting libidn2-2.3.8: .......... done [pkg-builder.dan.net.uk] | `-- Installing libnghttp2-1.65.0... [pkg-builder.dan.net.uk] | `-- Extracting libnghttp2-1.65.0: ....... done [pkg-builder.dan.net.uk] | `-- Installing libssh2-1.11.1,3... [pkg-builder.dan.net.uk] | `-- Extracting libssh2-1.11.1,3: .......... done [pkg-builder.dan.net.uk] | `-- Installing zstd-1.5.7... [pkg-builder.dan.net.uk] | | `-- Installing liblz4-1.10.0,1... [pkg-builder.dan.net.uk] | | `-- Extracting liblz4-1.10.0,1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting zstd-1.5.7: .......... done [pkg-builder.dan.net.uk] `-- Extracting curl-8.13.0_1: .......... done [pkg-builder.dan.net.uk] `-- Installing libdeflate-1.22... [pkg-builder.dan.net.uk] `-- Extracting libdeflate-1.22: .......... done [pkg-builder.dan.net.uk] Extracting htslib-1.21: .......... done ===> pbbam-0.18.0_11 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of pbbam-0.18.0_11 ===> pbbam-0.18.0_11 depends on shared library: libboost_regex.so - not found ===> Installing existing package /packages/All/boost-libs-1.87.0_1.pkg [pkg-builder.dan.net.uk] Installing boost-libs-1.87.0_1... [pkg-builder.dan.net.uk] `-- Installing icu-76.1,1... [pkg-builder.dan.net.uk] `-- Extracting icu-76.1,1: .......... done [pkg-builder.dan.net.uk] Extracting boost-libs-1.87.0_1: .......... done ===== Message from boost-libs-1.87.0_1: -- 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_11 depends on shared library: libboost_regex.so - found (/usr/local/lib/libboost_regex.so) ===> Returning to build of pbbam-0.18.0_11 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for pbbam-0.18.0_11 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: 1.7.0 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 18.1.6 "FreeBSD clang version 18.1.6 (https://github.com/llvm/llvm-project.git llvmorg-18.1.6-0-g1118c2e05e67)") C++ linker for the host machine: c++ ld.lld 18.1.6 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) 2.3.0 Run-time dependency Boost found: YES 1.87.0 (/usr/local) Run-time dependency zlib found: YES 1.3.1 Run-time dependency htslib found: YES 1.21 Program python3.11 found: YES (/usr/local/bin/python3.11) 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 b_colorout : never buildtype : release infodir : share/info localstatedir : /var optimization : plain prefix : /usr/local python.bytecompile: -1 strip : true 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_11 [ 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] 44 | 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 70 | const std::unique_ptr ifr_; | ^ /usr/include/c++/v1/__memory/unique_ptr.h:190:55: note: copy constructor is implicitly deleted because 'unique_ptr' has a user-declared move constructor 190 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX23 unique_ptr(unique_ptr&& __u) _NOEXCEPT | ^ ../include/pbbam/AlignmentPrinter.h:44:44: note: replace 'default' with 'delete' 44 | AlignmentPrinter(AlignmentPrinter&&) = default; | ^~~~~~~ | delete ../include/pbbam/AlignmentPrinter.h:46:23: warning: explicitly defaulted move assignment operator is implicitly deleted [-Wdefaulted-function-deleted] 46 | 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 70 | const std::unique_ptr ifr_; | ^ ../include/pbbam/AlignmentPrinter.h:46:55: note: replace 'default' with 'delete' 46 | AlignmentPrinter& operator=(AlignmentPrinter&&) = default; | ^~~~~~~ | delete 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] 93 | 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] 233 | 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 In file included from ../src/BarcodeQuery.cpp:13: In file included from ../include/pbbam/CompositeBamReader.h:226: ../include/pbbam/internal/CompositeBamReader.inl:171:30: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 171 | struct PositionSorter : std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 1 warning generated. [ 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++ -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/DataSetTypes.cpp.o -MF src/libpbbam.so.0.18.0.p/DataSetTypes.cpp.o.d -o src/libpbbam.so.0.18.0.p/DataSetTypes.cpp.o -c ../src/DataSetTypes.cpp [ 23% 24/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -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/DataSetXsd.cpp.o -MF src/libpbbam.so.0.18.0.p/DataSetXsd.cpp.o.d -o src/libpbbam.so.0.18.0.p/DataSetXsd.cpp.o -c ../src/DataSetXsd.cpp [ 24% 25/102] 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/EntireFileQuery.cpp.o -MF src/libpbbam.so.0.18.0.p/EntireFileQuery.cpp.o.d -o src/libpbbam.so.0.18.0.p/EntireFileQuery.cpp.o -c ../src/EntireFileQuery.cpp In file included from ../src/EntireFileQuery.cpp:11: In file included from ../include/pbbam/CompositeBamReader.h:226: ../include/pbbam/internal/CompositeBamReader.inl:171:30: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 171 | struct PositionSorter : std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 1 warning generated. [ 25% 26/102] 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/FastaReader.cpp.o -MF src/libpbbam.so.0.18.0.p/FastaReader.cpp.o.d -o src/libpbbam.so.0.18.0.p/FastaReader.cpp.o -c ../src/FastaReader.cpp [ 26% 27/102] 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/FastaSequenceQuery.cpp.o -MF src/libpbbam.so.0.18.0.p/FastaSequenceQuery.cpp.o.d -o src/libpbbam.so.0.18.0.p/FastaSequenceQuery.cpp.o -c ../src/FastaSequenceQuery.cpp [ 27% 28/102] 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/FastqReader.cpp.o -MF src/libpbbam.so.0.18.0.p/FastqReader.cpp.o.d -o src/libpbbam.so.0.18.0.p/FastqReader.cpp.o -c ../src/FastqReader.cpp [ 28% 29/102] 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/FileProducer.cpp.o -MF src/libpbbam.so.0.18.0.p/FileProducer.cpp.o.d -o src/libpbbam.so.0.18.0.p/FileProducer.cpp.o -c ../src/FileProducer.cpp [ 29% 30/102] 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/FileUtils.cpp.o -MF src/libpbbam.so.0.18.0.p/FileUtils.cpp.o.d -o src/libpbbam.so.0.18.0.p/FileUtils.cpp.o -c ../src/FileUtils.cpp [ 30% 31/102] 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/FofnReader.cpp.o -MF src/libpbbam.so.0.18.0.p/FofnReader.cpp.o.d -o src/libpbbam.so.0.18.0.p/FofnReader.cpp.o -c ../src/FofnReader.cpp [ 31% 32/102] 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/Frames.cpp.o -MF src/libpbbam.so.0.18.0.p/Frames.cpp.o.d -o src/libpbbam.so.0.18.0.p/Frames.cpp.o -c ../src/Frames.cpp [ 32% 33/102] 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/GenomicInterval.cpp.o -MF src/libpbbam.so.0.18.0.p/GenomicInterval.cpp.o.d -o src/libpbbam.so.0.18.0.p/GenomicInterval.cpp.o -c ../src/GenomicInterval.cpp [ 33% 34/102] 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/GenomicIntervalQuery.cpp.o -MF src/libpbbam.so.0.18.0.p/GenomicIntervalQuery.cpp.o.d -o src/libpbbam.so.0.18.0.p/GenomicIntervalQuery.cpp.o -c ../src/GenomicIntervalQuery.cpp In file included from ../src/GenomicIntervalQuery.cpp:11: In file included from ../include/pbbam/CompositeBamReader.h:226: ../include/pbbam/internal/CompositeBamReader.inl:171:30: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 171 | struct PositionSorter : std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 1 warning generated. [ 34% 35/102] 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/IndexedBamWriter.cpp.o -MF src/libpbbam.so.0.18.0.p/IndexedBamWriter.cpp.o.d -o src/libpbbam.so.0.18.0.p/IndexedBamWriter.cpp.o -c ../src/IndexedBamWriter.cpp [ 35% 36/102] 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/IndexedFastaReader.cpp.o -MF src/libpbbam.so.0.18.0.p/IndexedFastaReader.cpp.o.d -o src/libpbbam.so.0.18.0.p/IndexedFastaReader.cpp.o -c ../src/IndexedFastaReader.cpp [ 36% 37/102] 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/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] 37 | rawData->cigar_tab = nullptr; | ^ /usr/local/include/htslib/sam.h:84:29: note: 'cigar_tab' has been explicitly marked deprecated here 84 | const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead"); | ^ /usr/local/include/htslib/hts_defs.h:90:49: note: expanded from macro 'HTS_DEPRECATED' 90 | #define HTS_DEPRECATED(message) __attribute__ ((__deprecated__ (message))) | ^ 1 warning generated. [ 38% 39/102] 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/PbiBuilder.cpp.o -MF src/libpbbam.so.0.18.0.p/PbiBuilder.cpp.o.d -o src/libpbbam.so.0.18.0.p/PbiBuilder.cpp.o -c ../src/PbiBuilder.cpp ../src/PbiBuilder.cpp:640:17: warning: variable 'i' set but not used [-Wunused-but-set-variable] 640 | for (size_t i = 0; totalNumRead < currentRow_; ++i) { | ^ 1 warning generated. [ 39% 40/102] 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/PbiFile.cpp.o -MF src/libpbbam.so.0.18.0.p/PbiFile.cpp.o.d -o src/libpbbam.so.0.18.0.p/PbiFile.cpp.o -c ../src/PbiFile.cpp [ 40% 41/102] 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/PbiFilter.cpp.o -MF src/libpbbam.so.0.18.0.p/PbiFilter.cpp.o.d -o src/libpbbam.so.0.18.0.p/PbiFilter.cpp.o -c ../src/PbiFilter.cpp [ 41% 42/102] 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/PbiFilterQuery.cpp.o -MF src/libpbbam.so.0.18.0.p/PbiFilterQuery.cpp.o.d -o src/libpbbam.so.0.18.0.p/PbiFilterQuery.cpp.o -c ../src/PbiFilterQuery.cpp In file included from ../src/PbiFilterQuery.cpp:13: In file included from ../include/pbbam/CompositeBamReader.h:226: ../include/pbbam/internal/CompositeBamReader.inl:171:30: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 171 | struct PositionSorter : std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 1 warning generated. [ 42% 43/102] 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/PbiFilterTypes.cpp.o -MF src/libpbbam.so.0.18.0.p/PbiFilterTypes.cpp.o.d -o src/libpbbam.so.0.18.0.p/PbiFilterTypes.cpp.o -c ../src/PbiFilterTypes.cpp [ 43% 44/102] 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/PbiIndexedBamReader.cpp.o -MF src/libpbbam.so.0.18.0.p/PbiIndexedBamReader.cpp.o.d -o src/libpbbam.so.0.18.0.p/PbiIndexedBamReader.cpp.o -c ../src/PbiIndexedBamReader.cpp [ 44% 45/102] 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/PbiIndexIO.cpp.o -MF src/libpbbam.so.0.18.0.p/PbiIndexIO.cpp.o.d -o src/libpbbam.so.0.18.0.p/PbiIndexIO.cpp.o -c ../src/PbiIndexIO.cpp [ 45% 46/102] 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/PbiRawData.cpp.o -MF src/libpbbam.so.0.18.0.p/PbiRawData.cpp.o.d -o src/libpbbam.so.0.18.0.p/PbiRawData.cpp.o -c ../src/PbiRawData.cpp [ 46% 47/102] 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/ProgramInfo.cpp.o -MF src/libpbbam.so.0.18.0.p/ProgramInfo.cpp.o.d -o src/libpbbam.so.0.18.0.p/ProgramInfo.cpp.o -c ../src/ProgramInfo.cpp [ 47% 48/102] 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/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 In file included from ../src/QNameQuery.cpp:15: In file included from ../include/pbbam/CompositeBamReader.h:226: ../include/pbbam/internal/CompositeBamReader.inl:171:30: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 171 | struct PositionSorter : std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 1 warning generated. [ 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 In file included from ../src/ReadAccuracyQuery.cpp:11: In file included from ../include/pbbam/CompositeBamReader.h:226: ../include/pbbam/internal/CompositeBamReader.inl:171:30: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 171 | struct PositionSorter : std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 1 warning generated. [ 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 In file included from ../src/SubreadLengthQuery.cpp:13: In file included from ../include/pbbam/CompositeBamReader.h:226: ../include/pbbam/internal/CompositeBamReader.inl:171:30: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 171 | struct PositionSorter : std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 1 warning generated. [ 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 value_type' (aka 'const pair') [-Wrange-loop-construct] 129 | for (const auto prefixIter : xsdPrefixesUsed) { | ^ ../src/XmlWriter.cpp:129:10: note: use reference type 'const value_type &' (aka 'const pair &') to prevent copying 129 | 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 In file included from ../src/ZmwGroupQuery.cpp:17: In file included from ../include/pbbam/CompositeBamReader.h:226: ../include/pbbam/internal/CompositeBamReader.inl:171:30: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 171 | struct PositionSorter : std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 1 warning generated. [ 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 In file included from ../src/ZmwQuery.cpp:13: In file included from ../include/pbbam/CompositeBamReader.h:226: ../include/pbbam/internal/CompositeBamReader.inl:171:30: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 171 | struct PositionSorter : std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 1 warning generated. [ 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] 481 | for (const auto fieldValue : fieldValues) { | ^ ../src/vcf/VcfFormat.cpp:481:18: note: use reference type 'const std::string &' to prevent copying 481 | 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] 521 | for (const auto field : fields) { | ^ ../src/vcf/VcfFormat.cpp:521:10: note: use reference type 'const PacBio::VCF::InfoField &' to prevent copying 521 | 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] 541 | for (const auto id : genotypeIds) { | ^ ../src/vcf/VcfFormat.cpp:541:14: note: use reference type 'const std::string &' to prevent copying 541 | 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] 548 | for (const auto sampleGenotype : sampleGenotypes) { | ^ ../src/vcf/VcfFormat.cpp:548:14: note: use reference type 'const PacBio::VCF::GenotypeField &' to prevent copying 548 | 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] 23 | 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 39 | VcfReader reader_; | ^ ../include/pbbam/vcf/VcfReader.h:26:5: note: 'VcfReader' has been explicitly marked deleted here 26 | VcfReader() = delete; | ^ ../include/pbbam/vcf/VcfQuery.h:23:18: note: replace 'default' with 'delete' 23 | VcfQuery() = default; | ^~~~~~~ | 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] 23 | 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 39 | VcfReader reader_; | ^ ../include/pbbam/vcf/VcfReader.h:26:5: note: 'VcfReader' has been explicitly marked deleted here 26 | VcfReader() = delete; | ^ ../include/pbbam/vcf/VcfQuery.h:23:18: note: replace 'default' with 'delete' 23 | VcfQuery() = default; | ^~~~~~~ | 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] 72 | for (const auto e : settings.errors_) | ^ ../tools/bam2sam/src/main.cpp:72:14: note: use reference type 'const std::string &' to prevent copying 72 | 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] 57 | for (const auto e : settings.errors_) | ^ ../tools/pbindex/src/main.cpp:57:14: note: use reference type 'const std::string &' to prevent copying 57 | 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] 93 | for (const auto e : settings.errors_) | ^ ../tools/pbindexdump/src/main.cpp:93:14: note: use reference type 'const std::string &' to prevent copying 93 | 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 In file included from ../tools/pbmerge/src/main.cpp:9: In file included from ../tools/pbmerge/../common/BamFileMerger.h:40: In file included from ../tools/pbmerge/../common/BamFileMerger.inl:9: In file included from ../include/pbbam/CompositeBamReader.h:226: ../include/pbbam/internal/CompositeBamReader.inl:171:30: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 171 | struct PositionSorter : std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ../tools/pbmerge/src/main.cpp:9: In file included from ../tools/pbmerge/../common/BamFileMerger.h:40: ../tools/pbmerge/../common/BamFileMerger.inl:75:27: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 75 | struct QNameSorter : std::binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ ../tools/pbmerge/src/main.cpp:95:25: warning: loop variable 'e' creates a copy from type 'const std::string' [-Wrange-loop-construct] 95 | for (const auto e : settings.errors_) | ^ ../tools/pbmerge/src/main.cpp:95:14: note: use reference type 'const std::string &' to prevent copying 95 | for (const auto e : settings.errors_) | ^~~~~~~~~~~~~~ | & 3 warnings 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_11 depends on file: /usr/local/bin/python3.11 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for pbbam-0.18.0_11 ===> 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=2025-05-06T09:06:56+0000' 'PKG_NOTE_ports_top_git_hash=5529c5919b' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=fa53920e72' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for pbbam-0.18.0_11 ===> Building pbbam-0.18.0_11 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for pbbam-0.18.0_11 build of biology/pbbam | pbbam-0.18.0_11 ended at Tue May 6 10:16:20 BST 2025 build time: 00:09:24