=>> Building biology/freebayes build started at Sun Nov 9 22:57:43 EST 2025 port directory: /usr/ports/biology/freebayes package name: freebayes-1.3.9 building for: FreeBSD pkg.DaveG.ca 15.0-ALPHA3 FreeBSD 15.0-ALPHA3 1500064 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1144 Mar 7 2025 /usr/ports/biology/freebayes/Makefile Ports top last git commit: ec159283c191 Ports top unclean checkout: no Port dir last git commit: bac90e855c13 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1500064 Job Id: 12 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500064 UNAME_v=FreeBSD 15.0-ALPHA3 1500064 UNAME_r=15.0-ALPHA3 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/freebsd_15_c_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_15_c_x64-HEAD-ALL/12/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_15_c_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_15_c_x64-HEAD-ALL/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 " 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=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.42.0 PERL_VER=5.42 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/5.42 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--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 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 #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---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-2.4.2_1.pkg [pkg.DaveG.ca] Installing pkg-2.4.2_1... [pkg.DaveG.ca] Extracting pkg-2.4.2_1: .......... 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.DaveG.ca] Installing fastahack-1.0.0... [pkg.DaveG.ca] 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.DaveG.ca] Installing multichoose-1.0.3.2... [pkg.DaveG.ca] `-- Installing python311-3.11.14... [pkg.DaveG.ca] | `-- Installing gettext-runtime-0.23.1... [pkg.DaveG.ca] | | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] | `-- Extracting gettext-runtime-0.23.1: .......... done [pkg.DaveG.ca] | `-- Installing libffi-3.5.1... [pkg.DaveG.ca] | `-- Extracting libffi-3.5.1: .......... done [pkg.DaveG.ca] | `-- Installing mpdecimal-4.0.1... [pkg.DaveG.ca] | `-- Extracting mpdecimal-4.0.1: .......... done [pkg.DaveG.ca] | `-- Installing readline-8.3.1... [pkg.DaveG.ca] | `-- Extracting readline-8.3.1: .......... done [pkg.DaveG.ca] `-- Extracting python311-3.11.14: .......... done [pkg.DaveG.ca] Extracting multichoose-1.0.3.2: ....... done ===== Message from python311-3.11.14: -- 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.DaveG.ca] Installing simde-0.8.2... [pkg.DaveG.ca] 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.DaveG.ca] Installing vcflib-1.0.13... [pkg.DaveG.ca] `-- Installing curl-8.16.0... [pkg.DaveG.ca] | `-- Installing brotli-1.1.0,1... [pkg.DaveG.ca] | `-- Extracting brotli-1.1.0,1: .......... done [pkg.DaveG.ca] | `-- Installing libidn2-2.3.8... [pkg.DaveG.ca] | | `-- Installing libunistring-1.4.1... [pkg.DaveG.ca] | | `-- Extracting libunistring-1.4.1: .......... done [pkg.DaveG.ca] | `-- Extracting libidn2-2.3.8: .......... done [pkg.DaveG.ca] | `-- Installing libnghttp2-1.68.0... [pkg.DaveG.ca] | `-- Extracting libnghttp2-1.68.0: ....... done [pkg.DaveG.ca] | `-- Installing libpsl-0.21.5_2... [pkg.DaveG.ca] | `-- Extracting libpsl-0.21.5_2: ........ done [pkg.DaveG.ca] | `-- Installing libssh2-1.11.1,3... [pkg.DaveG.ca] | `-- Extracting libssh2-1.11.1,3: .......... done [pkg.DaveG.ca] | `-- Installing zstd-1.5.7... [pkg.DaveG.ca] | | `-- Installing liblz4-1.10.0_2,1... [pkg.DaveG.ca] | | `-- Extracting liblz4-1.10.0_2,1: .......... done [pkg.DaveG.ca] | `-- Extracting zstd-1.5.7: .......... done [pkg.DaveG.ca] `-- Extracting curl-8.16.0: .......... done [pkg.DaveG.ca] `-- Installing htslib-1.22... [pkg.DaveG.ca] | `-- Installing libdeflate-1.24... [pkg.DaveG.ca] | `-- Extracting libdeflate-1.24: .......... done [pkg.DaveG.ca] `-- Extracting htslib-1.22: .......... done [pkg.DaveG.ca] `-- Installing wfa2-lib-2.3.5... [pkg.DaveG.ca] `-- Extracting wfa2-lib-2.3.5: .......... done [pkg.DaveG.ca] 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.DaveG.ca] Installing intervaltree-0.1.2... [pkg.DaveG.ca] 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.DaveG.ca] Installing smithwaterman-g20160702... [pkg.DaveG.ca] 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.DaveG.ca] Installing tabixpp-1.1.2... [pkg.DaveG.ca] 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.DaveG.ca] Installing meson-1.7.0... [pkg.DaveG.ca] `-- Installing ninja-1.13.1,4... [pkg.DaveG.ca] `-- Extracting ninja-1.13.1,4: ..... done [pkg.DaveG.ca] 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-2.4.3,1.pkg [pkg.DaveG.ca] Installing pkgconf-2.4.3,1... [pkg.DaveG.ca] Extracting pkgconf-2.4.3,1: .......... 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>=5.42.r<5.43 - not found ===> Installing existing package /packages/All/perl5-5.42.0_1.pkg [pkg.DaveG.ca] Installing perl5-5.42.0_1... [pkg.DaveG.ca] Extracting perl5-5.42.0_1: .......... done ===> freebayes-1.3.9 depends on package: perl5>=5.42.r<5.43 - 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.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] 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 19.1.7 "FreeBSD clang version 19.1.7 (https://github.com/llvm/llvm-project.git llvmorg-19.1.7-0-gcd708029e0b2)") C linker for the host machine: cc ld.lld 19.1.7 C++ compiler for the host machine: c++ (clang 19.1.7 "FreeBSD clang version 19.1.7 (https://github.com/llvm/llvm-project.git llvmorg-19.1.7-0-gcd708029e0b2)") C++ linker for the host machine: c++ ld.lld 19.1.7 Host machine cpu family: x86_64 Host machine cpu: x86_64 Found pkg-config: YES (/usr/local/bin/pkgconf) 2.4.3 Run-time dependency liblzma found: YES 5.8.1 Run-time dependency threads found: YES Run-time dependency zlib found: YES 1.3.1 Run-time dependency htslib found: YES 1.22 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-1.13.1 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% 31/35] 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 [ 5% 31/35] 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 [ 8% 31/35] 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 [ 11% 31/35] 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 [ 14% 31/35] 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 [ 17% 31/35] 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% 31/35] 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 [ 22% 31/35] 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 [ 25% 31/35] 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 [ 28% 31/35] 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 [ 31% 31/35] 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 [ 34% 31/35] 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 [ 37% 31/35] 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 [ 40% 31/35] 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 [ 42% 31/35] 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 [ 45% 31/35] 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 [ 48% 31/35] 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 [ 51% 31/35] 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 [ 54% 31/35] 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 [ 57% 31/35] 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 [ 60% 31/35] 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 [ 62% 31/35] 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 [ 65% 31/35] 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 [ 68% 32/35] 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 [ 71% 32/35] 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 [ 74% 32/35] 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 [ 77% 32/35] 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 [ 80% 32/35] 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 [ 82% 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 [ 85% 32/35] 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 [ 88% 32/35] 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 [ 91% 32/35] 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 [ 94% 33/35] 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 [ 97% 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 -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 [100% 35/35] 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 -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=2025-11-10T03:57:43+0000' 'PKG_NOTE_ports_top_git_hash=ec159283c191' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=bac90e855c13' '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 Sun Nov 9 22:58:49 EST 2025 build time: 00:01:07