=>> Building biology/freebayes build started at Sat May 3 01:47:43 BST 2025 port directory: /usr/ports/biology/freebayes package name: freebayes-1.3.9 building for: FreeBSD pkg-builder.dan.net.uk 14.2-RELEASE FreeBSD 14.2-RELEASE amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1144 Feb 22 19:12 /usr/ports/biology/freebayes/Makefile Ports top last git commit: 5529c5919b Ports top unclean checkout: yes Port dir last git commit: bac90e855c Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1402000 Jail OSVERSION: 1402000 Job Id: 06 ---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/06/.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-- jwb@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-- ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/biology/freebayes/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/freebayes/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/freebayes/work/.cache HOME=/wrkdirs/usr/ports/biology/freebayes/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/freebayes/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/freebayes/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] " PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/freebayes/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/freebayes/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/freebayes/work/.cache HOME=/wrkdirs/usr/ports/biology/freebayes/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/freebayes/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/freebayes/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/freebayes/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=" -lexecinfo -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-- OSREL=14.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.36.3 PERL_VER=5.36 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.36 DOCSDIR="share/doc/freebayes" EXAMPLESDIR="share/examples/freebayes" DATADIR="share/freebayes" WWWDIR="www/freebayes" ETCDIR="etc/freebayes" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/freebayes DOCSDIR=/usr/local/share/doc/freebayes EXAMPLESDIR=/usr/local/share/examples/freebayes WWWDIR=/usr/local/www/freebayes ETCDIR=/usr/local/etc/freebayes --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 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> freebayes-1.3.9 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 ===> freebayes-1.3.9 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of freebayes-1.3.9 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by freebayes-1.3.9 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by freebayes-1.3.9 for building => SHA256 Checksum OK for ekg-freebayes-v1.3.9_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 ===> Fetching all distfiles required by freebayes-1.3.9 for building ===> Extracting for freebayes-1.3.9 => SHA256 Checksum OK for ekg-freebayes-v1.3.9_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 freebayes-1.3.9 ===> Applying FreeBSD patches for freebayes-1.3.9 from /usr/ports/biology/freebayes/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> freebayes-1.3.9 depends on package: fastahack>=1.0.0 - not found ===> Installing existing package /packages/All/fastahack-1.0.0.pkg [pkg-builder.dan.net.uk] Installing fastahack-1.0.0... [pkg-builder.dan.net.uk] Extracting fastahack-1.0.0: ....... done ===> freebayes-1.3.9 depends on package: fastahack>=1.0.0 - found ===> Returning to build of freebayes-1.3.9 ===> freebayes-1.3.9 depends on package: multichoose>=1.0.3.2 - not found ===> Installing existing package /packages/All/multichoose-1.0.3.2.pkg [pkg-builder.dan.net.uk] Installing multichoose-1.0.3.2... [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 multichoose-1.0.3.2: ....... 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 ===> freebayes-1.3.9 depends on package: multichoose>=1.0.3.2 - found ===> Returning to build of freebayes-1.3.9 ===> freebayes-1.3.9 depends on package: simde>=0.8.2 - not found ===> Installing existing package /packages/All/simde-0.8.2.pkg [pkg-builder.dan.net.uk] Installing simde-0.8.2... [pkg-builder.dan.net.uk] Extracting simde-0.8.2: .......... done ===> freebayes-1.3.9 depends on package: simde>=0.8.2 - found ===> Returning to build of freebayes-1.3.9 ===> freebayes-1.3.9 depends on package: vcflib>=1.0.12 - not found ===> Installing existing package /packages/All/vcflib-1.0.13.pkg [pkg-builder.dan.net.uk] Installing vcflib-1.0.13... [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 htslib-1.21... [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 [pkg-builder.dan.net.uk] `-- Installing wfa2-lib-2.3.5... [pkg-builder.dan.net.uk] `-- Extracting wfa2-lib-2.3.5: .......... done [pkg-builder.dan.net.uk] Extracting vcflib-1.0.13: .......... done ===> freebayes-1.3.9 depends on package: vcflib>=1.0.12 - found ===> Returning to build of freebayes-1.3.9 ===> freebayes-1.3.9 depends on package: intervaltree>=0.1.2 - not found ===> Installing existing package /packages/All/intervaltree-0.1.2.pkg [pkg-builder.dan.net.uk] Installing intervaltree-0.1.2... [pkg-builder.dan.net.uk] Extracting intervaltree-0.1.2: .. done ===> freebayes-1.3.9 depends on package: intervaltree>=0.1.2 - found ===> Returning to build of freebayes-1.3.9 ===> freebayes-1.3.9 depends on package: smithwaterman>=g20160702 - not found ===> Installing existing package /packages/All/smithwaterman-g20160702.pkg [pkg-builder.dan.net.uk] Installing smithwaterman-g20160702... [pkg-builder.dan.net.uk] Extracting smithwaterman-g20160702: .......... done ===> freebayes-1.3.9 depends on package: smithwaterman>=g20160702 - found ===> Returning to build of freebayes-1.3.9 ===> freebayes-1.3.9 depends on package: wfa2-lib>=2.3.5 - found ===> freebayes-1.3.9 depends on package: tabixpp>=1.1.2 - not found ===> Installing existing package /packages/All/tabixpp-1.1.2.pkg [pkg-builder.dan.net.uk] Installing tabixpp-1.1.2... [pkg-builder.dan.net.uk] Extracting tabixpp-1.1.2: ..... done ===> freebayes-1.3.9 depends on package: tabixpp>=1.1.2 - found ===> Returning to build of freebayes-1.3.9 ===> freebayes-1.3.9 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] `-- Extracting ninja-1.11.1,4: ..... done [pkg-builder.dan.net.uk] Extracting meson-1.7.0: .......... done ===> freebayes-1.3.9 depends on executable: meson - found ===> Returning to build of freebayes-1.3.9 ===> freebayes-1.3.9 depends on executable: ninja - found ===> freebayes-1.3.9 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 ===> freebayes-1.3.9 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of freebayes-1.3.9 ===> freebayes-1.3.9 depends on package: perl5>=5.36<5.37 - not found ===> Installing existing package /packages/All/perl5-5.36.3_3.pkg [pkg-builder.dan.net.uk] Installing perl5-5.36.3_3... [pkg-builder.dan.net.uk] Extracting perl5-5.36.3_3: .......... done ===> freebayes-1.3.9 depends on package: perl5>=5.36<5.37 - found ===> Returning to build of freebayes-1.3.9 ===> freebayes-1.3.9 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. ===> freebayes-1.3.9 depends on file: /usr/local/bin/ccache - found ===> Returning to build of freebayes-1.3.9 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> freebayes-1.3.9 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for freebayes-1.3.9 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/freebayes/work/freebayes-1.3.9 Build dir: /wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.3.9/_build Build type: native build Project name: freebayes Project version: 1.3.9 C compiler for the host machine: cc (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: cc ld.lld 18.1.6 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 Found pkg-config: YES (/usr/local/bin/pkgconf) 2.3.0 Run-time dependency liblzma found: YES 5.4.5 Run-time dependency threads found: YES Run-time dependency zlib found: YES 1.3.1 Run-time dependency htslib found: YES 1.21 Did not find CMake 'cmake' Found CMake: NO Run-time dependency libseqlib found: NO (tried pkgconfig and cmake) Library tabixpp found: NO Compiler for C++ supports arguments -fpermissive: YES Compiler for C++ supports arguments -Wno-reorder: YES Compiler for C++ supports arguments -Wno-sign-compare: YES Compiler for C++ supports arguments -Wno-unused-variable: YES Compiler for C++ supports arguments -Wno-unused-but-set-variable: YES Program prove found: YES (/usr/local/bin/prove) Build targets in project: 4 freebayes 1.3.9 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 freebayes-1.3.9 [ 2% 1/35] c++ -Ilibcustom_seqlib.a.p -I. -I.. -I../contrib/SeqLib -fdiagnostics-color=never -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -std=c++14 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -MD -MQ libcustom_seqlib.a.p/contrib_SeqLib_src_BamReader.cpp.o -MF libcustom_seqlib.a.p/contrib_SeqLib_src_BamReader.cpp.o.d -o libcustom_seqlib.a.p/contrib_SeqLib_src_BamReader.cpp.o -c ../contrib/SeqLib/src/BamReader.cpp [ 5% 2/35] c++ -Ilibcustom_seqlib.a.p -I. -I.. -I../contrib/SeqLib -fdiagnostics-color=never -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -std=c++14 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -MD -MQ libcustom_seqlib.a.p/contrib_SeqLib_src_BamRecord.cpp.o -MF libcustom_seqlib.a.p/contrib_SeqLib_src_BamRecord.cpp.o.d -o libcustom_seqlib.a.p/contrib_SeqLib_src_BamRecord.cpp.o -c ../contrib/SeqLib/src/BamRecord.cpp [ 8% 3/35] c++ -Ilibcustom_seqlib.a.p -I. -I.. -I../contrib/SeqLib -fdiagnostics-color=never -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -std=c++14 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -MD -MQ libcustom_seqlib.a.p/contrib_SeqLib_src_BamHeader.cpp.o -MF libcustom_seqlib.a.p/contrib_SeqLib_src_BamHeader.cpp.o.d -o libcustom_seqlib.a.p/contrib_SeqLib_src_BamHeader.cpp.o -c ../contrib/SeqLib/src/BamHeader.cpp [ 11% 4/35] c++ -Ilibcustom_seqlib.a.p -I. -I.. -I../contrib/SeqLib -fdiagnostics-color=never -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -std=c++14 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -MD -MQ libcustom_seqlib.a.p/contrib_SeqLib_src_BamWriter.cpp.o -MF libcustom_seqlib.a.p/contrib_SeqLib_src_BamWriter.cpp.o.d -o libcustom_seqlib.a.p/contrib_SeqLib_src_BamWriter.cpp.o -c ../contrib/SeqLib/src/BamWriter.cpp [ 14% 5/35] c++ -Ilibcustom_seqlib.a.p -I. -I.. -I../contrib/SeqLib -fdiagnostics-color=never -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -std=c++14 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -MD -MQ libcustom_seqlib.a.p/contrib_SeqLib_src_GenomicRegion.cpp.o -MF libcustom_seqlib.a.p/contrib_SeqLib_src_GenomicRegion.cpp.o.d -o libcustom_seqlib.a.p/contrib_SeqLib_src_GenomicRegion.cpp.o -c ../contrib/SeqLib/src/GenomicRegion.cpp [ 17% 6/35] c++ -Ilibcustom_seqlib.a.p -I. -I.. -I../contrib/SeqLib -fdiagnostics-color=never -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -std=c++14 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -MD -MQ libcustom_seqlib.a.p/contrib_SeqLib_src_ssw_cpp.cpp.o -MF libcustom_seqlib.a.p/contrib_SeqLib_src_ssw_cpp.cpp.o.d -o libcustom_seqlib.a.p/contrib_SeqLib_src_ssw_cpp.cpp.o -c ../contrib/SeqLib/src/ssw_cpp.cpp [ 20% 7/35] cc -Ilibcustom_seqlib.a.p -I. -I.. -I../contrib/SeqLib -fdiagnostics-color=never -D_FILE_OFFSET_BITS=64 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -MD -MQ libcustom_seqlib.a.p/contrib_SeqLib_src_ssw.c.o -MF libcustom_seqlib.a.p/contrib_SeqLib_src_ssw.c.o.d -o libcustom_seqlib.a.p/contrib_SeqLib_src_ssw.c.o -c ../contrib/SeqLib/src/ssw.c [ 22% 8/35] rm -f libcustom_seqlib.a && llvm-ar csrDT libcustom_seqlib.a libcustom_seqlib.a.p/contrib_SeqLib_src_BamReader.cpp.o libcustom_seqlib.a.p/contrib_SeqLib_src_BamRecord.cpp.o libcustom_seqlib.a.p/contrib_SeqLib_src_BamHeader.cpp.o libcustom_seqlib.a.p/contrib_SeqLib_src_BamWriter.cpp.o libcustom_seqlib.a.p/contrib_SeqLib_src_GenomicRegion.cpp.o libcustom_seqlib.a.p/contrib_SeqLib_src_ssw_cpp.cpp.o libcustom_seqlib.a.p/contrib_SeqLib_src_ssw.c.o [ 25% 9/35] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/local/include/fastahack -I/usr/local/include/vcflib -I/usr/local/include/wfa2lib -I../contrib/SeqLib -I/usr/local/include/multichoose -I/usr/local/include -fdiagnostics-color=never -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Allele.cpp.o -MF libfreebayes_common.a.p/src_Allele.cpp.o.d -o libfreebayes_common.a.p/src_Allele.cpp.o -c ../src/Allele.cpp [ 28% 10/35] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/local/include/fastahack -I/usr/local/include/vcflib -I/usr/local/include/wfa2lib -I../contrib/SeqLib -I/usr/local/include/multichoose -I/usr/local/include -fdiagnostics-color=never -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_AlleleParser.cpp.o -MF libfreebayes_common.a.p/src_AlleleParser.cpp.o.d -o libfreebayes_common.a.p/src_AlleleParser.cpp.o -c ../src/AlleleParser.cpp [ 31% 11/35] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/local/include/fastahack -I/usr/local/include/vcflib -I/usr/local/include/wfa2lib -I../contrib/SeqLib -I/usr/local/include/multichoose -I/usr/local/include -fdiagnostics-color=never -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_BedReader.cpp.o -MF libfreebayes_common.a.p/src_BedReader.cpp.o.d -o libfreebayes_common.a.p/src_BedReader.cpp.o -c ../src/BedReader.cpp [ 34% 12/35] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/local/include/fastahack -I/usr/local/include/vcflib -I/usr/local/include/wfa2lib -I../contrib/SeqLib -I/usr/local/include/multichoose -I/usr/local/include -fdiagnostics-color=never -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Bias.cpp.o -MF libfreebayes_common.a.p/src_Bias.cpp.o.d -o libfreebayes_common.a.p/src_Bias.cpp.o -c ../src/Bias.cpp [ 37% 13/35] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/local/include/fastahack -I/usr/local/include/vcflib -I/usr/local/include/wfa2lib -I../contrib/SeqLib -I/usr/local/include/multichoose -I/usr/local/include -fdiagnostics-color=never -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_CNV.cpp.o -MF libfreebayes_common.a.p/src_CNV.cpp.o.d -o libfreebayes_common.a.p/src_CNV.cpp.o -c ../src/CNV.cpp [ 40% 14/35] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/local/include/fastahack -I/usr/local/include/vcflib -I/usr/local/include/wfa2lib -I../contrib/SeqLib -I/usr/local/include/multichoose -I/usr/local/include -fdiagnostics-color=never -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Contamination.cpp.o -MF libfreebayes_common.a.p/src_Contamination.cpp.o.d -o libfreebayes_common.a.p/src_Contamination.cpp.o -c ../src/Contamination.cpp [ 42% 15/35] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/local/include/fastahack -I/usr/local/include/vcflib -I/usr/local/include/wfa2lib -I../contrib/SeqLib -I/usr/local/include/multichoose -I/usr/local/include -fdiagnostics-color=never -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_DataLikelihood.cpp.o -MF libfreebayes_common.a.p/src_DataLikelihood.cpp.o.d -o libfreebayes_common.a.p/src_DataLikelihood.cpp.o -c ../src/DataLikelihood.cpp [ 45% 16/35] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/local/include/fastahack -I/usr/local/include/vcflib -I/usr/local/include/wfa2lib -I../contrib/SeqLib -I/usr/local/include/multichoose -I/usr/local/include -fdiagnostics-color=never -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Dirichlet.cpp.o -MF libfreebayes_common.a.p/src_Dirichlet.cpp.o.d -o libfreebayes_common.a.p/src_Dirichlet.cpp.o -c ../src/Dirichlet.cpp [ 48% 17/35] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/local/include/fastahack -I/usr/local/include/vcflib -I/usr/local/include/wfa2lib -I../contrib/SeqLib -I/usr/local/include/multichoose -I/usr/local/include -fdiagnostics-color=never -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Ewens.cpp.o -MF libfreebayes_common.a.p/src_Ewens.cpp.o.d -o libfreebayes_common.a.p/src_Ewens.cpp.o -c ../src/Ewens.cpp [ 51% 18/35] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/local/include/fastahack -I/usr/local/include/vcflib -I/usr/local/include/wfa2lib -I../contrib/SeqLib -I/usr/local/include/multichoose -I/usr/local/include -fdiagnostics-color=never -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_FBFasta.cpp.o -MF libfreebayes_common.a.p/src_FBFasta.cpp.o.d -o libfreebayes_common.a.p/src_FBFasta.cpp.o -c ../src/FBFasta.cpp [ 54% 19/35] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/local/include/fastahack -I/usr/local/include/vcflib -I/usr/local/include/wfa2lib -I../contrib/SeqLib -I/usr/local/include/multichoose -I/usr/local/include -fdiagnostics-color=never -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Genotype.cpp.o -MF libfreebayes_common.a.p/src_Genotype.cpp.o.d -o libfreebayes_common.a.p/src_Genotype.cpp.o -c ../src/Genotype.cpp [ 57% 20/35] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/local/include/fastahack -I/usr/local/include/vcflib -I/usr/local/include/wfa2lib -I../contrib/SeqLib -I/usr/local/include/multichoose -I/usr/local/include -fdiagnostics-color=never -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_IndelAllele.cpp.o -MF libfreebayes_common.a.p/src_IndelAllele.cpp.o.d -o libfreebayes_common.a.p/src_IndelAllele.cpp.o -c ../src/IndelAllele.cpp [ 60% 21/35] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/local/include/fastahack -I/usr/local/include/vcflib -I/usr/local/include/wfa2lib -I../contrib/SeqLib -I/usr/local/include/multichoose -I/usr/local/include -fdiagnostics-color=never -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_LeftAlign.cpp.o -MF libfreebayes_common.a.p/src_LeftAlign.cpp.o.d -o libfreebayes_common.a.p/src_LeftAlign.cpp.o -c ../src/LeftAlign.cpp [ 62% 22/35] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/local/include/fastahack -I/usr/local/include/vcflib -I/usr/local/include/wfa2lib -I../contrib/SeqLib -I/usr/local/include/multichoose -I/usr/local/include -fdiagnostics-color=never -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Marginals.cpp.o -MF libfreebayes_common.a.p/src_Marginals.cpp.o.d -o libfreebayes_common.a.p/src_Marginals.cpp.o -c ../src/Marginals.cpp [ 65% 23/35] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/local/include/fastahack -I/usr/local/include/vcflib -I/usr/local/include/wfa2lib -I../contrib/SeqLib -I/usr/local/include/multichoose -I/usr/local/include -fdiagnostics-color=never -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Multinomial.cpp.o -MF libfreebayes_common.a.p/src_Multinomial.cpp.o.d -o libfreebayes_common.a.p/src_Multinomial.cpp.o -c ../src/Multinomial.cpp [ 68% 24/35] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/local/include/fastahack -I/usr/local/include/vcflib -I/usr/local/include/wfa2lib -I../contrib/SeqLib -I/usr/local/include/multichoose -I/usr/local/include -fdiagnostics-color=never -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_NonCall.cpp.o -MF libfreebayes_common.a.p/src_NonCall.cpp.o.d -o libfreebayes_common.a.p/src_NonCall.cpp.o -c ../src/NonCall.cpp [ 71% 25/35] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/local/include/fastahack -I/usr/local/include/vcflib -I/usr/local/include/wfa2lib -I../contrib/SeqLib -I/usr/local/include/multichoose -I/usr/local/include -fdiagnostics-color=never -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Parameters.cpp.o -MF libfreebayes_common.a.p/src_Parameters.cpp.o.d -o libfreebayes_common.a.p/src_Parameters.cpp.o -c ../src/Parameters.cpp [ 74% 26/35] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/local/include/fastahack -I/usr/local/include/vcflib -I/usr/local/include/wfa2lib -I../contrib/SeqLib -I/usr/local/include/multichoose -I/usr/local/include -fdiagnostics-color=never -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Result.cpp.o -MF libfreebayes_common.a.p/src_Result.cpp.o.d -o libfreebayes_common.a.p/src_Result.cpp.o -c ../src/Result.cpp [ 77% 27/35] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/local/include/fastahack -I/usr/local/include/vcflib -I/usr/local/include/wfa2lib -I../contrib/SeqLib -I/usr/local/include/multichoose -I/usr/local/include -fdiagnostics-color=never -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_ResultData.cpp.o -MF libfreebayes_common.a.p/src_ResultData.cpp.o.d -o libfreebayes_common.a.p/src_ResultData.cpp.o -c ../src/ResultData.cpp [ 80% 28/35] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/local/include/fastahack -I/usr/local/include/vcflib -I/usr/local/include/wfa2lib -I../contrib/SeqLib -I/usr/local/include/multichoose -I/usr/local/include -fdiagnostics-color=never -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Sample.cpp.o -MF libfreebayes_common.a.p/src_Sample.cpp.o.d -o libfreebayes_common.a.p/src_Sample.cpp.o -c ../src/Sample.cpp [ 82% 29/35] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/local/include/fastahack -I/usr/local/include/vcflib -I/usr/local/include/wfa2lib -I../contrib/SeqLib -I/usr/local/include/multichoose -I/usr/local/include -fdiagnostics-color=never -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_SegfaultHandler.cpp.o -MF libfreebayes_common.a.p/src_SegfaultHandler.cpp.o.d -o libfreebayes_common.a.p/src_SegfaultHandler.cpp.o -c ../src/SegfaultHandler.cpp [ 85% 30/35] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/local/include/fastahack -I/usr/local/include/vcflib -I/usr/local/include/wfa2lib -I../contrib/SeqLib -I/usr/local/include/multichoose -I/usr/local/include -fdiagnostics-color=never -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Utility.cpp.o -MF libfreebayes_common.a.p/src_Utility.cpp.o.d -o libfreebayes_common.a.p/src_Utility.cpp.o -c ../src/Utility.cpp [ 88% 31/35] rm -f libfreebayes_common.a && llvm-ar csrDT libfreebayes_common.a libfreebayes_common.a.p/src_Allele.cpp.o libfreebayes_common.a.p/src_AlleleParser.cpp.o libfreebayes_common.a.p/src_BedReader.cpp.o libfreebayes_common.a.p/src_Bias.cpp.o libfreebayes_common.a.p/src_CNV.cpp.o libfreebayes_common.a.p/src_Contamination.cpp.o libfreebayes_common.a.p/src_DataLikelihood.cpp.o libfreebayes_common.a.p/src_Dirichlet.cpp.o libfreebayes_common.a.p/src_Ewens.cpp.o libfreebayes_common.a.p/src_FBFasta.cpp.o libfreebayes_common.a.p/src_Genotype.cpp.o libfreebayes_common.a.p/src_IndelAllele.cpp.o libfreebayes_common.a.p/src_LeftAlign.cpp.o libfreebayes_common.a.p/src_Marginals.cpp.o libfreebayes_common.a.p/src_Multinomial.cpp.o libfreebayes_common.a.p/src_NonCall.cpp.o libfreebayes_common.a.p/src_Parameters.cpp.o libfreebayes_common.a.p/src_Result.cpp.o libfreebayes_common.a.p/src_ResultData.cpp.o libfreebayes_common.a.p/src_Sample.cpp.o libfreebayes_common.a.p/src_SegfaultHandler.cpp.o libfreebayes_common.a.p/src_Utility.cpp.o [ 91% 32/35] c++ -Ifreebayes.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/local/include/fastahack -I/usr/local/include/vcflib -I../contrib/SeqLib -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/wfa2lib -I/usr/local/include -fdiagnostics-color=never -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ freebayes.p/src_freebayes.cpp.o -MF freebayes.p/src_freebayes.cpp.o.d -o freebayes.p/src_freebayes.cpp.o -c ../src/freebayes.cpp [ 94% 33/35] c++ -o freebayes freebayes.p/src_freebayes.cpp.o -L/usr/local/lib -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,--start-group -lexecinfo -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 libfreebayes_common.a libcustom_seqlib.a /usr/lib/libz.so /usr/lib/liblzma.so -pthread /usr/local/lib/libhts.so -lvcflib -lvcflib -Wl,--end-group [ 97% 34/35] c++ -Ibamleftalign.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/local/include/fastahack -I/usr/local/include/vcflib -I../contrib/SeqLib -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/wfa2lib -I/usr/local/include -fdiagnostics-color=never -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ bamleftalign.p/src_bamleftalign.cpp.o -MF bamleftalign.p/src_bamleftalign.cpp.o.d -o bamleftalign.p/src_bamleftalign.cpp.o -c ../src/bamleftalign.cpp [100% 35/35] c++ -o bamleftalign bamleftalign.p/src_bamleftalign.cpp.o -L/usr/local/lib -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,--start-group -lexecinfo -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 libfreebayes_common.a libcustom_seqlib.a /usr/lib/libz.so /usr/lib/liblzma.so -pthread /usr/local/lib/libhts.so -lvcflib -lvcflib -Wl,--end-group =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for freebayes-1.3.9 ===> Generating temporary packing list [ 0% 1/1] /usr/local/bin/meson install --no-rebuild Installing freebayes to /wrkdirs/usr/ports/biology/freebayes/work/stage/usr/local/bin Stripping target 'freebayes'. Installing bamleftalign to /wrkdirs/usr/ports/biology/freebayes/work/stage/usr/local/bin Stripping target 'bamleftalign'. ====> 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=2025-05-03T00:47:43+0000' 'PKG_NOTE_ports_top_git_hash=5529c5919b' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=bac90e855c' '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 freebayes-1.3.9 ===> Building freebayes-1.3.9 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for freebayes-1.3.9 build of biology/freebayes | freebayes-1.3.9 ended at Sat May 3 01:50:36 BST 2025 build time: 00:02:53