=>> Building biology/freebayes build started at Fri Mar 29 13:21:28 GMT 2024 port directory: /usr/ports/biology/freebayes package name: freebayes-1.3.6_2 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1718 Mar 8 2023 /usr/ports/biology/freebayes/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: c014f9c79a Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 20 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.99.20240122_1 MASTERMNT=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/20/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=13-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.99.20240122_1 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix /usr/local --infodir share/info --auto-features=enabled -Dpython.bytecompile=-1 -Db_colorout=never --buildtype release --optimization plain --strip _build --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- 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=/ccache/libexec/ccache:/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" LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 CCACHE_DIR="/root/.ccache" --End CONFIGURE_ENV-- --MAKE_ENV-- NINJA_STATUS="[%p %s/%t] " 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=/ccache/libexec/ccache:/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 LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -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 " CCACHE_DIR="/root/.ccache" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=13.2 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 mysql=8.0 imagemagick=7 samba=4.13 java=18 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache NO_CCACHE_DEPEND=1 CCACHE_WRAPPER_PATH= /ccache/libexec/ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> freebayes-1.3.6_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_1: .......... done ===> freebayes-1.3.6_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of freebayes-1.3.6_2 =========================================================================== =================================================== ===== 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-1.3.6_2 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by freebayes-1.3.6_2 for building => SHA256 Checksum OK for ekg-freebayes-v1.3.6_GH0.tar.gz. => SHA256 Checksum OK for ekg-intervaltree-17ddd57_GH0.tar.gz. => SHA256 Checksum OK for ekg-vcflib-d4073c3_GH0.tar.gz. => SHA256 Checksum OK for ekg-fastahack-bb33265_GH0.tar.gz. => SHA256 Checksum OK for ekg-filevercmp-1a9b779_GH0.tar.gz. => SHA256 Checksum OK for ekg-fsom-a6ef318_GH0.tar.gz. => SHA256 Checksum OK for google-googletest-d225acc_GH0.tar.gz. => SHA256 Checksum OK for edawson-libVCFH-615a06b_GH0.tar.gz. => SHA256 Checksum OK for ekg-multichoose-68733cd_GH0.tar.gz. => SHA256 Checksum OK for ekg-smithwaterman-2610e25_GH0.tar.gz. => SHA256 Checksum OK for ekg-tabixpp-b255df1_GH0.tar.gz. => SHA256 Checksum OK for simd-everywhere-simde-no-tests-2931676_GH0.tar.gz. => SHA256 Checksum OK for ingydotnet-test-simple-bash-124673f_GH0.tar.gz. => SHA256 Checksum OK for illusori-bash-tap-c38fbfa_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-1.3.6_2 for building ===> Extracting for freebayes-1.3.6_2 => SHA256 Checksum OK for ekg-freebayes-v1.3.6_GH0.tar.gz. => SHA256 Checksum OK for ekg-intervaltree-17ddd57_GH0.tar.gz. => SHA256 Checksum OK for ekg-vcflib-d4073c3_GH0.tar.gz. => SHA256 Checksum OK for ekg-fastahack-bb33265_GH0.tar.gz. => SHA256 Checksum OK for ekg-filevercmp-1a9b779_GH0.tar.gz. => SHA256 Checksum OK for ekg-fsom-a6ef318_GH0.tar.gz. => SHA256 Checksum OK for google-googletest-d225acc_GH0.tar.gz. => SHA256 Checksum OK for edawson-libVCFH-615a06b_GH0.tar.gz. => SHA256 Checksum OK for ekg-multichoose-68733cd_GH0.tar.gz. => SHA256 Checksum OK for ekg-smithwaterman-2610e25_GH0.tar.gz. => SHA256 Checksum OK for ekg-tabixpp-b255df1_GH0.tar.gz. => SHA256 Checksum OK for simd-everywhere-simde-no-tests-2931676_GH0.tar.gz. => SHA256 Checksum OK for ingydotnet-test-simple-bash-124673f_GH0.tar.gz. => SHA256 Checksum OK for illusori-bash-tap-c38fbfa_GH0.tar.gz. cp -f -r /wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.3.6/vcflib-temp/* /wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.3.6/vcflib =========================================================================== =================================================== ===== 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-1.3.6_2 ===> Applying FreeBSD patches for freebayes-1.3.6_2 from /usr/ports/biology/freebayes/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> freebayes-1.3.6_2 depends on executable: meson - not found ===> Installing existing package /packages/All/meson-1.4.0.pkg [pkg-builder.dan.net.uk] Installing meson-1.4.0... [pkg-builder.dan.net.uk] `-- Installing ninja-1.11.1,2... [pkg-builder.dan.net.uk] | `-- Installing python39-3.9.18_1... [pkg-builder.dan.net.uk] | | `-- Installing gettext-runtime-0.22.3_1... [pkg-builder.dan.net.uk] | | `-- Installing indexinfo-0.3.1... [pkg-builder.dan.net.uk] | | `-- Extracting indexinfo-0.3.1: . done [pkg-builder.dan.net.uk] | | `-- Extracting gettext-runtime-0.22.3_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libffi-3.4.4_1... [pkg-builder.dan.net.uk] | | `-- Extracting libffi-3.4.4_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing mpdecimal-2.5.1... [pkg-builder.dan.net.uk] | | `-- Extracting mpdecimal-2.5.1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing openssl-3.0.13_1,1... [pkg-builder.dan.net.uk] | | `-- Extracting openssl-3.0.13_1,1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing readline-8.2.10... [pkg-builder.dan.net.uk] | | `-- Extracting readline-8.2.10: .......... done [pkg-builder.dan.net.uk] | `-- Extracting python39-3.9.18_1: .......... done [pkg-builder.dan.net.uk] `-- Extracting ninja-1.11.1,2: ..... done [pkg-builder.dan.net.uk] Extracting meson-1.4.0: .......... done ===== Message from python39-3.9.18_1: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 ===> freebayes-1.3.6_2 depends on executable: meson - found ===> Returning to build of freebayes-1.3.6_2 ===> freebayes-1.3.6_2 depends on executable: ninja - found ===> freebayes-1.3.6_2 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-2.1.1,1.pkg [pkg-builder.dan.net.uk] Installing pkgconf-2.1.1,1... [pkg-builder.dan.net.uk] Extracting pkgconf-2.1.1,1: .......... done ===> freebayes-1.3.6_2 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of freebayes-1.3.6_2 ===> freebayes-1.3.6_2 depends on package: perl5>=5.36<5.37 - not found ===> Installing existing package /packages/All/perl5-5.36.3_1.pkg [pkg-builder.dan.net.uk] Installing perl5-5.36.3_1... [pkg-builder.dan.net.uk] Extracting perl5-5.36.3_1: .......... done ===> freebayes-1.3.6_2 depends on package: perl5>=5.36<5.37 - found ===> Returning to build of freebayes-1.3.6_2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> freebayes-1.3.6_2 depends on shared library: libhts.so - not found ===> Installing existing package /packages/All/htslib-1.17_1.pkg [pkg-builder.dan.net.uk] Installing htslib-1.17_1... [pkg-builder.dan.net.uk] `-- Installing curl-8.6.0... [pkg-builder.dan.net.uk] | `-- Installing brotli-1.1.0,1... [pkg-builder.dan.net.uk] | `-- Extracting brotli-1.1.0,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libidn2-2.3.7... [pkg-builder.dan.net.uk] | | `-- Installing libunistring-1.2... [pkg-builder.dan.net.uk] | | `-- Extracting libunistring-1.2: .......... done [pkg-builder.dan.net.uk] | `-- Extracting libidn2-2.3.7: .......... done [pkg-builder.dan.net.uk] | `-- Installing libnghttp2-1.60.0... [pkg-builder.dan.net.uk] | `-- Extracting libnghttp2-1.60.0: ....... done [pkg-builder.dan.net.uk] | `-- Installing librtmp-2.4.20190330_1... [pkg-builder.dan.net.uk] | `-- Extracting librtmp-2.4.20190330_1: ......... done [pkg-builder.dan.net.uk] | `-- Installing libssh2-1.11.0_1,3... [pkg-builder.dan.net.uk] | `-- Extracting libssh2-1.11.0_1,3: .......... done [pkg-builder.dan.net.uk] | `-- Installing zstd-1.5.5_1... [pkg-builder.dan.net.uk] | | `-- Installing liblz4-1.9.4_1,1... [pkg-builder.dan.net.uk] | | `-- Extracting liblz4-1.9.4_1,1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting zstd-1.5.5_1: .......... done [pkg-builder.dan.net.uk] `-- Extracting curl-8.6.0: .......... done [pkg-builder.dan.net.uk] `-- Installing libdeflate-1.19... [pkg-builder.dan.net.uk] `-- Extracting libdeflate-1.19: .......... done [pkg-builder.dan.net.uk] Extracting htslib-1.17_1: .......... done ===> freebayes-1.3.6_2 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of freebayes-1.3.6_2 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for freebayes-1.3.6_2 WARNING: Recommend using either -Dbuildtype or -Doptimization + -Ddebug. Using both is redundant since they override each other. See: https://mesonbuild.com/Builtin-options.html#build-type-options The Meson build system Version: 1.4.0 Source dir: /wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.3.6 Build dir: /wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.3.6/_build Build type: native build Project name: freebayes Project version: 1.3.6 C compiler for the host machine: cc (clang 14.0.5 "FreeBSD clang version 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc12386ae247c)") C linker for the host machine: cc ld.lld 14.0.5 C++ compiler for the host machine: c++ (clang 14.0.5 "FreeBSD clang version 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc12386ae247c)") C++ linker for the host machine: c++ ld.lld 14.0.5 Host machine cpu family: x86_64 Host machine cpu: x86_64 Found pkg-config: YES (/usr/local/bin/pkgconf) 2.1.1 Run-time dependency zlib found: YES 1.2.13 Run-time dependency liblzma found: YES 5.4.1 Run-time dependency threads found: YES Library tabixpp found: NO Run-time dependency htslib found: YES 1.17 Library tabixpp found: NO Did not find CMake 'cmake' Found CMake: NO Run-time dependency libvcflib found: NO (tried pkgconfig and cmake) Run-time dependency libseqlib found: NO (tried pkgconfig and cmake) 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: 6 freebayes 1.3.6 User defined options auto_features : enabled buildtype : release infodir : share/info optimization : plain prefix : /usr/local strip : true python.bytecompile: -1 b_colorout : never Found ninja-1.11.1 at /usr/local/bin/ninja WARNING: Running the setup command as `meson [options]` instead of `meson setup [options]` is ambiguous and deprecated. =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for freebayes-1.3.6_2 [ 2% 1/46] c++ -Ilibcustom_tabixpp.a.p -I. -I.. -I../vcflib/tabixpp -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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_tabixpp.a.p/vcflib_tabixpp_tabix.cpp.o -MF libcustom_tabixpp.a.p/vcflib_tabixpp_tabix.cpp.o.d -o libcustom_tabixpp.a.p/vcflib_tabixpp_tabix.cpp.o -c ../vcflib/tabixpp/tabix.cpp ../vcflib/tabixpp/tabix.cpp:15:10: warning: 'bgzf_is_bgzf' is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations] if ( bgzf_is_bgzf(cfilename)!=1 ) ^ /usr/local/include/htslib/bgzf.h:270:38: note: 'bgzf_is_bgzf' has been explicitly marked deprecated here int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead"); ^ /usr/local/include/htslib/hts_defs.h:75:49: note: expanded from macro 'HTS_DEPRECATED' #define HTS_DEPRECATED(message) __attribute__ ((__deprecated__ (message))) ^ 1 warning generated. [ 4% 2/46] rm -f libcustom_tabixpp.a && llvm-ar csrDT libcustom_tabixpp.a libcustom_tabixpp.a.p/vcflib_tabixpp_tabix.cpp.o [ 6% 3/46] c++ -Ilibcustom_vcflib.a.p -I. -I.. -I../vcflib/tabixpp -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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_vcflib.a.p/vcflib_src_Variant.cpp.o -MF libcustom_vcflib.a.p/vcflib_src_Variant.cpp.o.d -o libcustom_vcflib.a.p/vcflib_src_Variant.cpp.o -c ../vcflib/src/Variant.cpp [ 8% 4/46] c++ -Ilibcustom_vcflib.a.p -I. -I.. -I../vcflib/tabixpp -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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_vcflib.a.p/vcflib_smithwaterman_SmithWatermanGotoh.cpp.o -MF libcustom_vcflib.a.p/vcflib_smithwaterman_SmithWatermanGotoh.cpp.o.d -o libcustom_vcflib.a.p/vcflib_smithwaterman_SmithWatermanGotoh.cpp.o -c ../vcflib/smithwaterman/SmithWatermanGotoh.cpp [ 10% 5/46] c++ -Ilibcustom_vcflib.a.p -I. -I.. -I../vcflib/tabixpp -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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_vcflib.a.p/vcflib_smithwaterman_disorder.cpp.o -MF libcustom_vcflib.a.p/vcflib_smithwaterman_disorder.cpp.o.d -o libcustom_vcflib.a.p/vcflib_smithwaterman_disorder.cpp.o -c ../vcflib/smithwaterman/disorder.cpp [ 13% 6/46] c++ -Ilibcustom_vcflib.a.p -I. -I.. -I../vcflib/tabixpp -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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_vcflib.a.p/vcflib_smithwaterman_Repeats.cpp.o -MF libcustom_vcflib.a.p/vcflib_smithwaterman_Repeats.cpp.o.d -o libcustom_vcflib.a.p/vcflib_smithwaterman_Repeats.cpp.o -c ../vcflib/smithwaterman/Repeats.cpp [ 15% 7/46] c++ -Ilibcustom_vcflib.a.p -I. -I.. -I../vcflib/tabixpp -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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_vcflib.a.p/vcflib_smithwaterman_LeftAlign.cpp.o -MF libcustom_vcflib.a.p/vcflib_smithwaterman_LeftAlign.cpp.o.d -o libcustom_vcflib.a.p/vcflib_smithwaterman_LeftAlign.cpp.o -c ../vcflib/smithwaterman/LeftAlign.cpp [ 17% 8/46] c++ -Ilibcustom_vcflib.a.p -I. -I.. -I../vcflib/tabixpp -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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_vcflib.a.p/vcflib_smithwaterman_IndelAllele.cpp.o -MF libcustom_vcflib.a.p/vcflib_smithwaterman_IndelAllele.cpp.o.d -o libcustom_vcflib.a.p/vcflib_smithwaterman_IndelAllele.cpp.o -c ../vcflib/smithwaterman/IndelAllele.cpp [ 19% 9/46] c++ -Ilibcustom_vcflib.a.p -I. -I.. -I../vcflib/tabixpp -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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_vcflib.a.p/vcflib_fastahack_Fasta.cpp.o -MF libcustom_vcflib.a.p/vcflib_fastahack_Fasta.cpp.o.d -o libcustom_vcflib.a.p/vcflib_fastahack_Fasta.cpp.o -c ../vcflib/fastahack/Fasta.cpp [ 21% 10/46] c++ -Ilibcustom_vcflib.a.p -I. -I.. -I../vcflib/tabixpp -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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_vcflib.a.p/vcflib_src_split.cpp.o -MF libcustom_vcflib.a.p/vcflib_src_split.cpp.o.d -o libcustom_vcflib.a.p/vcflib_src_split.cpp.o -c ../vcflib/src/split.cpp [ 23% 11/46] rm -f libcustom_vcflib.a && llvm-ar csrDT libcustom_vcflib.a libcustom_vcflib.a.p/vcflib_src_Variant.cpp.o libcustom_vcflib.a.p/vcflib_smithwaterman_SmithWatermanGotoh.cpp.o libcustom_vcflib.a.p/vcflib_smithwaterman_disorder.cpp.o libcustom_vcflib.a.p/vcflib_smithwaterman_Repeats.cpp.o libcustom_vcflib.a.p/vcflib_smithwaterman_LeftAlign.cpp.o libcustom_vcflib.a.p/vcflib_smithwaterman_IndelAllele.cpp.o libcustom_vcflib.a.p/vcflib_fastahack_Fasta.cpp.o libcustom_vcflib.a.p/vcflib_src_split.cpp.o [ 26% 12/46] c++ -Ilibcustom_seqlib.a.p -I. -I.. -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -I../contrib -I../contrib/SeqLib -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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 [ 28% 13/46] c++ -Ilibcustom_seqlib.a.p -I. -I.. -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -I../contrib -I../contrib/SeqLib -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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 [ 30% 14/46] c++ -Ilibcustom_seqlib.a.p -I. -I.. -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -I../contrib -I../contrib/SeqLib -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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 [ 32% 15/46] c++ -Ilibcustom_seqlib.a.p -I. -I.. -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -I../contrib -I../contrib/SeqLib -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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 [ 34% 16/46] c++ -Ilibcustom_seqlib.a.p -I. -I.. -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -I../contrib -I../contrib/SeqLib -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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 [ 36% 17/46] c++ -Ilibcustom_seqlib.a.p -I. -I.. -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -I../contrib -I../contrib/SeqLib -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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 [ 39% 18/46] cc -Ilibcustom_seqlib.a.p -I. -I.. -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -I../contrib -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 [ 41% 19/46] 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 [ 43% 20/46] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I../vcflib/tabixpp -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -I../contrib -I../contrib/SeqLib -I/usr/local/include -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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 ../src/Allele.cpp:160:13: warning: enumeration values 'ALLELE_GENOTYPE' and 'ALLELE_NULL' not handled in switch [-Wswitch] switch (this->type) { ^~~~~~~~~~ 1 warning generated. [ 45% 21/46] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I../vcflib/tabixpp -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -I../contrib -I../contrib/SeqLib -I/usr/local/include -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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 [ 47% 22/46] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I../vcflib/tabixpp -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -I../contrib -I../contrib/SeqLib -I/usr/local/include -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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 [ 50% 23/46] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I../vcflib/tabixpp -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -I../contrib -I../contrib/SeqLib -I/usr/local/include -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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 [ 52% 24/46] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I../vcflib/tabixpp -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -I../contrib -I../contrib/SeqLib -I/usr/local/include -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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 [ 54% 25/46] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I../vcflib/tabixpp -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -I../contrib -I../contrib/SeqLib -I/usr/local/include -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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 [ 56% 26/46] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I../vcflib/tabixpp -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -I../contrib -I../contrib/SeqLib -I/usr/local/include -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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 [ 58% 27/46] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I../vcflib/tabixpp -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -I../contrib -I../contrib/SeqLib -I/usr/local/include -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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 [ 60% 28/46] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I../vcflib/tabixpp -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -I../contrib -I../contrib/SeqLib -I/usr/local/include -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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 [ 63% 29/46] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I../vcflib/tabixpp -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -I../contrib -I../contrib/SeqLib -I/usr/local/include -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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 [ 65% 30/46] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I../vcflib/tabixpp -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -I../contrib -I../contrib/SeqLib -I/usr/local/include -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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 [ 67% 31/46] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I../vcflib/tabixpp -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -I../contrib -I../contrib/SeqLib -I/usr/local/include -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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 [ 69% 32/46] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I../vcflib/tabixpp -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -I../contrib -I../contrib/SeqLib -I/usr/local/include -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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 [ 71% 33/46] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I../vcflib/tabixpp -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -I../contrib -I../contrib/SeqLib -I/usr/local/include -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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 [ 73% 34/46] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I../vcflib/tabixpp -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -I../contrib -I../contrib/SeqLib -I/usr/local/include -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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 [ 76% 35/46] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I../vcflib/tabixpp -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -I../contrib -I../contrib/SeqLib -I/usr/local/include -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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 [ 78% 36/46] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I../vcflib/tabixpp -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -I../contrib -I../contrib/SeqLib -I/usr/local/include -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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 [ 80% 37/46] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I../vcflib/tabixpp -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -I../contrib -I../contrib/SeqLib -I/usr/local/include -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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 [ 82% 38/46] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I../vcflib/tabixpp -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -I../contrib -I../contrib/SeqLib -I/usr/local/include -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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 [ 84% 39/46] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I../vcflib/tabixpp -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -I../contrib -I../contrib/SeqLib -I/usr/local/include -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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 [ 86% 40/46] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I../vcflib/tabixpp -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -I../contrib -I../contrib/SeqLib -I/usr/local/include -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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 [ 89% 41/46] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I../vcflib/tabixpp -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -I../contrib -I../contrib/SeqLib -I/usr/local/include -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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 [ 91% 42/46] 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 [ 93% 43/46] c++ -Ifreebayes.p -I. -I.. -I../src -I../ttmath -I../vcflib/tabixpp -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -I../contrib -I../contrib/SeqLib -I/usr/local/include -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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 [ 95% 44/46] c++ -o freebayes freebayes.p/src_freebayes.cpp.o -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_tabixpp.a libcustom_vcflib.a libcustom_seqlib.a /usr/lib/libz.so /usr/lib/liblzma.so -pthread /usr/local/lib/libhts.so -Wl,--end-group [ 97% 45/46] c++ -Ibamleftalign.p -I. -I.. -I../src -I../ttmath -I../vcflib/src -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I../vcflib/fastahack -I../contrib -I../contrib/SeqLib -I/usr/local/include -fdiagnostics-color=never -D_GLIBCXX_ASSERTIONS=1 -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% 46/46] c++ -o bamleftalign bamleftalign.p/src_bamleftalign.cpp.o -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_tabixpp.a libcustom_vcflib.a libcustom_seqlib.a /usr/lib/libz.so /usr/lib/liblzma.so -pthread /usr/local/lib/libhts.so -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-1.3.6_2 ===> 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=2024-03-29T13:21:28+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=c014f9c79a' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for freebayes-1.3.6_2 ===> Building freebayes-1.3.6_2 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for freebayes-1.3.6_2 build of biology/freebayes | freebayes-1.3.6_2 ended at Fri Mar 29 13:25:06 GMT 2024 build time: 00:03:39