=>> Building biology/abyss build started at Sun May 4 15:28:56 BST 2025 port directory: /usr/ports/biology/abyss package name: abyss-2.3.10 building for: FreeBSD pkg-builder.dan.net.uk 14.2-RELEASE FreeBSD 14.2-RELEASE amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1587 Dec 29 14:16 /usr/ports/biology/abyss/Makefile Ports top last git commit: 5529c5919b Ports top unclean checkout: yes Port dir last git commit: 1a35b19e6d Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1402000 Jail OSVERSION: 1402000 Job Id: 04 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1402000 UNAME_v=FreeBSD 14.2-RELEASE UNAME_r=14.2-RELEASE BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/14-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/04/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=14-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for abyss-2.3.10: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --without-sparsehash --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/abyss/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/abyss/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/abyss/work/.cache HOME=/wrkdirs/usr/ports/biology/abyss/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/abyss/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/abyss/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh DEFAULT_AUTOCONF=2.72 CMAKE_PREFIX_PATH="/usr/local" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/abyss/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/abyss/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/abyss/work/.cache HOME=/wrkdirs/usr/ports/biology/abyss/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/abyss/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/abyss/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 DEFAULT_AUTOCONF=2.72 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -Wno-error=unused-but-set-variable -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-- PORTDOCS="" OSREL=14.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/abyss" EXAMPLESDIR="share/examples/abyss" DATADIR="share/abyss" WWWDIR="www/abyss" ETCDIR="etc/abyss" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/abyss DOCSDIR=/usr/local/share/doc/abyss EXAMPLESDIR=/usr/local/share/examples/abyss WWWDIR=/usr/local/www/abyss ETCDIR=/usr/local/etc/abyss --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl apache=2.4 imagemagick=7 java=21 linux=c7 mysql=8.0 php=8.3 samba=4.19 varnish=7 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE ALLOW_UNSUPPORTED_SYSTEM=yes WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> abyss-2.3.10 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.1.2.pkg [pkg-builder.dan.net.uk] Installing pkg-2.1.2... [pkg-builder.dan.net.uk] Extracting pkg-2.1.2: .......... done ===> abyss-2.3.10 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of abyss-2.3.10 =========================================================================== =================================================== ===== 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 abyss-2.3.10 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by abyss-2.3.10 for building => SHA256 Checksum OK for bcgsc-abyss-2.3.10_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 abyss-2.3.10 for building ===> Extracting for abyss-2.3.10 => SHA256 Checksum OK for bcgsc-abyss-2.3.10_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 abyss-2.3.10 ===> Applying FreeBSD patches for abyss-2.3.10 from /usr/ports/biology/abyss/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> abyss-2.3.10 depends on file: /usr/local/include/boost/version.hpp - not found ===> Installing existing package /packages/All/boost-libs-1.87.0_1.pkg [pkg-builder.dan.net.uk] Installing boost-libs-1.87.0_1... [pkg-builder.dan.net.uk] `-- Installing icu-76.1,1... [pkg-builder.dan.net.uk] `-- Extracting icu-76.1,1: .......... done [pkg-builder.dan.net.uk] Extracting boost-libs-1.87.0_1: .......... done ===== Message from boost-libs-1.87.0_1: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===> abyss-2.3.10 depends on file: /usr/local/include/boost/version.hpp - found ===> Returning to build of abyss-2.3.10 ===> abyss-2.3.10 depends on executable: ghc - not found ===> Installing existing package /packages/All/ghc-9.6.6_2.pkg [pkg-builder.dan.net.uk] Installing ghc-9.6.6_2... [pkg-builder.dan.net.uk] `-- Installing gmp-6.3.0... [pkg-builder.dan.net.uk] | `-- Installing indexinfo-0.3.1_1... [pkg-builder.dan.net.uk] | `-- Extracting indexinfo-0.3.1_1: . done [pkg-builder.dan.net.uk] `-- Extracting gmp-6.3.0: .......... done [pkg-builder.dan.net.uk] `-- Installing libffi-3.4.8... [pkg-builder.dan.net.uk] `-- Extracting libffi-3.4.8: .......... done [pkg-builder.dan.net.uk] Extracting ghc-9.6.6_2: .......... done ===> abyss-2.3.10 depends on executable: ghc - found ===> Returning to build of abyss-2.3.10 ===> abyss-2.3.10 depends on executable: pandoc - not found ===> Installing existing package /packages/All/hs-pandoc-3.6.4.pkg [pkg-builder.dan.net.uk] Installing hs-pandoc-3.6.4... [pkg-builder.dan.net.uk] Extracting hs-pandoc-3.6.4: .......... done ===> abyss-2.3.10 depends on executable: pandoc - found ===> Returning to build of abyss-2.3.10 ===> abyss-2.3.10 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg-builder.dan.net.uk] Installing gmake-4.4.1... [pkg-builder.dan.net.uk] `-- Installing gettext-runtime-0.23.1... [pkg-builder.dan.net.uk] `-- Extracting gettext-runtime-0.23.1: .......... done [pkg-builder.dan.net.uk] Extracting gmake-4.4.1: .......... done ===> abyss-2.3.10 depends on package: gmake>=4.4.1 - found ===> Returning to build of abyss-2.3.10 ===> abyss-2.3.10 depends on package: autoconf>=2.72 - not found ===> Installing existing package /packages/All/autoconf-2.72.pkg [pkg-builder.dan.net.uk] Installing autoconf-2.72... [pkg-builder.dan.net.uk] `-- Installing autoconf-switch-20220527... [pkg-builder.dan.net.uk] `-- Extracting autoconf-switch-20220527: ....... done [pkg-builder.dan.net.uk] `-- Installing m4-1.4.19_1,1... [pkg-builder.dan.net.uk] | `-- Installing libsigsegv-2.14... [pkg-builder.dan.net.uk] | `-- Extracting libsigsegv-2.14: ..... done [pkg-builder.dan.net.uk] `-- Extracting m4-1.4.19_1,1: .......... done [pkg-builder.dan.net.uk] `-- Installing perl5-5.36.3_3... [pkg-builder.dan.net.uk] `-- Extracting perl5-5.36.3_3: .......... done [pkg-builder.dan.net.uk] Extracting autoconf-2.72: .......... done ===== Message from libsigsegv-2.14: -- Note that the stackoverflow handling functions of this library need procfs mounted on /proc. ===> abyss-2.3.10 depends on package: autoconf>=2.72 - found ===> Returning to build of abyss-2.3.10 ===> abyss-2.3.10 depends on package: automake>=1.17 - not found ===> Installing existing package /packages/All/automake-1.17.pkg [pkg-builder.dan.net.uk] Installing automake-1.17... [pkg-builder.dan.net.uk] Extracting automake-1.17: .......... done ===> abyss-2.3.10 depends on package: automake>=1.17 - found ===> Returning to build of abyss-2.3.10 ===> abyss-2.3.10 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg-builder.dan.net.uk] Installing ccache-3.7.12_8... [pkg-builder.dan.net.uk] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> abyss-2.3.10 depends on file: /usr/local/bin/ccache - found ===> Returning to build of abyss-2.3.10 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> abyss-2.3.10 depends on shared library: libbtllib.so - not found ===> Installing existing package /packages/All/btllib-1.7.5.pkg [pkg-builder.dan.net.uk] Installing btllib-1.7.5... [pkg-builder.dan.net.uk] `-- Installing samtools-1.21... [pkg-builder.dan.net.uk] | `-- Installing htslib-1.21... [pkg-builder.dan.net.uk] | | `-- Installing curl-8.13.0_1... [pkg-builder.dan.net.uk] | | `-- Installing brotli-1.1.0,1... [pkg-builder.dan.net.uk] | | `-- Extracting brotli-1.1.0,1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libidn2-2.3.8... [pkg-builder.dan.net.uk] | | | `-- Installing libunistring-1.3... [pkg-builder.dan.net.uk] | | | `-- Extracting libunistring-1.3: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libidn2-2.3.8: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libnghttp2-1.65.0... [pkg-builder.dan.net.uk] | | `-- Extracting libnghttp2-1.65.0: ....... done [pkg-builder.dan.net.uk] | | `-- Installing libssh2-1.11.1,3... [pkg-builder.dan.net.uk] | | | `-- Installing openssl-3.0.16,1... [pkg-builder.dan.net.uk] | | | `-- Extracting openssl-3.0.16,1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libssh2-1.11.1,3: .......... done [pkg-builder.dan.net.uk] | | `-- Installing zstd-1.5.7... [pkg-builder.dan.net.uk] | | | `-- Installing liblz4-1.10.0,1... [pkg-builder.dan.net.uk] | | | `-- Extracting liblz4-1.10.0,1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting zstd-1.5.7: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting curl-8.13.0_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libdeflate-1.22... [pkg-builder.dan.net.uk] | | `-- Extracting libdeflate-1.22: .......... done [pkg-builder.dan.net.uk] | `-- Extracting htslib-1.21: .......... done [pkg-builder.dan.net.uk] `-- Extracting samtools-1.21: .......... done [pkg-builder.dan.net.uk] `-- Installing sdsl-lite-2.1.1.137... [pkg-builder.dan.net.uk] `-- Extracting sdsl-lite-2.1.1.137: .......... done [pkg-builder.dan.net.uk] Extracting btllib-1.7.5: .......... done ===> abyss-2.3.10 depends on shared library: libbtllib.so - found (/usr/local/lib/libbtllib.so) ===> Returning to build of abyss-2.3.10 ===> abyss-2.3.10 depends on shared library: libffi.so - found (/usr/local/lib/libffi.so) ===> abyss-2.3.10 depends on shared library: libgmp.so - found (/usr/local/lib/libgmp.so) ===> abyss-2.3.10 depends on shared library: libmpich.so - not found ===> Installing existing package /packages/All/mpich-4.3.0.pkg [pkg-builder.dan.net.uk] Installing mpich-4.3.0... [pkg-builder.dan.net.uk] `-- Installing gcc13-13.3.0_2... [pkg-builder.dan.net.uk] | `-- Installing binutils-2.44,1... [pkg-builder.dan.net.uk] | `-- Extracting binutils-2.44,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing mpc-1.3.1_1... [pkg-builder.dan.net.uk] | | `-- Installing mpfr-4.2.2,1... [pkg-builder.dan.net.uk] | | `-- Extracting mpfr-4.2.2,1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting mpc-1.3.1_1: ...... done [pkg-builder.dan.net.uk] `-- Extracting gcc13-13.3.0_2: .......... done create symlink for gcc13 create symlink for gcc13 (world) create symlink for g++13 create symlink for g++13 (world) create symlink for cpp13 create symlink for cpp13 (world) [pkg-builder.dan.net.uk] `-- Installing hwloc2-2.11.2... [pkg-builder.dan.net.uk] | `-- Installing level-zero-1.21.9... [pkg-builder.dan.net.uk] | | `-- Installing libfmt-10.2.1... [pkg-builder.dan.net.uk] | | `-- Extracting libfmt-10.2.1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing spdlog-1.15.2... [pkg-builder.dan.net.uk] | | `-- Extracting spdlog-1.15.2: .......... done [pkg-builder.dan.net.uk] | `-- Extracting level-zero-1.21.9: .......... done [pkg-builder.dan.net.uk] | `-- Installing libpciaccess-0.18.1_1... [pkg-builder.dan.net.uk] | | `-- Installing hwdata-0.394,1... [pkg-builder.dan.net.uk] | | `-- Extracting hwdata-0.394,1: ...... done [pkg-builder.dan.net.uk] | `-- Extracting libpciaccess-0.18.1_1: ..... done [pkg-builder.dan.net.uk] | `-- Installing libxml2-2.11.9... [pkg-builder.dan.net.uk] | | `-- Installing readline-8.2.13_2... [pkg-builder.dan.net.uk] | | `-- Extracting readline-8.2.13_2: .......... done [pkg-builder.dan.net.uk] | `-- Extracting libxml2-2.11.9: .......... done [pkg-builder.dan.net.uk] `-- Extracting hwloc2-2.11.2: .......... done [pkg-builder.dan.net.uk] `-- Installing json-c-0.18... [pkg-builder.dan.net.uk] `-- Extracting json-c-0.18: .......... done [pkg-builder.dan.net.uk] `-- Installing libepoll-shim-0.0.20240608... [pkg-builder.dan.net.uk] `-- Extracting libepoll-shim-0.0.20240608: .......... done [pkg-builder.dan.net.uk] `-- Installing libfabric-1.15.1_4... [pkg-builder.dan.net.uk] `-- Extracting libfabric-1.15.1_4: .......... done [pkg-builder.dan.net.uk] Extracting mpich-4.3.0: .......... done ===== Message from gcc13-13.3.0_2: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc13 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> abyss-2.3.10 depends on shared library: libmpich.so - found (/usr/local/lib/libmpich.so) ===> Returning to build of abyss-2.3.10 ===> abyss-2.3.10 depends on shared library: libiconv.so - not found ===> Installing existing package /packages/All/libiconv-1.17_1.pkg [pkg-builder.dan.net.uk] Installing libiconv-1.17_1... [pkg-builder.dan.net.uk] Extracting libiconv-1.17_1: .......... done ===> abyss-2.3.10 depends on shared library: libiconv.so - found (/usr/local/lib/libiconv.so) ===> Returning to build of abyss-2.3.10 ===> abyss-2.3.10 depends on shared library: libsqlite3.so - not found ===> Installing existing package /packages/All/sqlite3-3.46.1_1,1.pkg [pkg-builder.dan.net.uk] Installing sqlite3-3.46.1_1,1... [pkg-builder.dan.net.uk] `-- Installing libedit-3.1.20250104,1... [pkg-builder.dan.net.uk] `-- Extracting libedit-3.1.20250104,1: .......... done [pkg-builder.dan.net.uk] Extracting sqlite3-3.46.1_1,1: ......... done ===> abyss-2.3.10 depends on shared library: libsqlite3.so - found (/usr/local/lib/libsqlite3.so) ===> Returning to build of abyss-2.3.10 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for abyss-2.3.10 configure.ac:25: installing './ar-lib' configure.ac:16: installing './compile' configure.ac:80: installing './config.guess' configure.ac:80: installing './config.sub' configure.ac:10: installing './install-sh' configure.ac:10: installing './missing' ABYSS/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' configure: loading site script /usr/ports/Templates/config.site checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether c++ accepts -g... yes checking for c++ option to enable C++11 features... none needed checking whether c++ supports C++11 features with -std=c++11... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether /usr/local/bin/gmake sets $(MAKE)... yes checking whether /usr/local/bin/gmake supports the include directive... yes (GNU style) checking whether /usr/local/bin/gmake supports nested variables... yes checking xargs -n works... yes checking whether UID '0' is supported by ustar format... yes checking whether GID '0' is supported by ustar format... yes checking how to create a ustar tar archive... (cached) /usr/bin/tar checking dependency style of c++ -std=c++11... gcc3 checking for gawk... (cached) /usr/bin/awk checking for gcc... cc checking whether the compiler supports GNU C... yes checking whether cc accepts -g... yes checking for cc option to enable C11 features... none needed checking whether cc understands -c and -o together... yes checking dependency style of cc... gcc3 checking how to run the C preprocessor... cpp checking whether the compiler supports GNU C++... (cached) yes checking whether c++ -std=c++11 accepts -g... (cached) yes checking for c++ -std=c++11 option to enable C++11 features... (cached) none needed checking for ranlib... ranlib checking for ghc... ghc checking for pandoc... yes checking for ar... ar checking the archiver (ar) interface... ar checking for stdio.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for strings.h... (cached) yes checking for sys/stat.h... (cached) yes checking for sys/types.h... (cached) yes checking for unistd.h... (cached) yes checking for vfork.h... (cached) no checking for dlfcn.h... (cached) yes checking for fcntl.h... (cached) yes checking for float.h... (cached) yes checking for limits.h... (cached) yes checking for stddef.h... (cached) yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for sys/param.h... (cached) yes checking for _Bool... (cached) yes checking for stdbool.h that conforms to C99 or later... (cached) yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for inline... inline checking for ptrdiff_t... (cached) yes checking for mode_t... (cached) yes checking for pid_t... (cached) yes checking for size_t... (cached) yes checking for ssize_t... (cached) yes checking for int64_t... (cached) yes checking for uint8_t... (cached) yes checking for uint16_t... (cached) yes checking for uint32_t... (cached) yes checking for uint64_t... (cached) yes checking for std::hash... yes checking for std::tr1::hash... no checking for std::tr1::tuple... no checking for dup2... (cached) yes checking for gethostname... (cached) yes checking for getopt_long... yes checking for getpagesize... (cached) yes checking for memset... (cached) yes checking for strdup... (cached) yes checking for strerror... (cached) yes checking for strtoul... (cached) yes checking for fork... (cached) yes checking for vfork... (cached) yes checking for vprintf... (cached) yes checking for working fork... yes checking for working vfork... (cached) yes checking build system type... amd64-portbld-freebsd14.2 checking host system type... amd64-portbld-freebsd14.2 checking for GNU libc compatible malloc... (cached) yes checking for working memcmp... yes checking for GNU libc compatible realloc... yes checking for cc options needed to detect all undeclared functions... -fno-builtin checking whether HOST_NAME_MAX is declared... no checking if compiler needs -Werror to reject unknown flags... yes checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... -D_THREAD_SAFE checking for PTHREAD_PRIO_INHERIT... yes checking for mpi.h... yes checking for MPI_Init in -lmpi... yes checking for sqrt in -lm... yes checking for pow... yes checking for sqrt... yes checking for ceilf... yes checking for dlsym in -ldl... yes checking for functional... yes checking for tr1/functional... no checking for boost/functional/hash.hpp... yes checking for boost/property_map/property_map.hpp... yes checking for google/sparse_hash_map... no checking for unordered_map... yes checking for tr1/unordered_map... no checking for unordered_set... yes checking for tr1/unordered_set... no checking for boost/unordered_set.hpp... yes checking for btllib/bloom_filter.hpp... yes checking for sqlite3.h... yes checking for main in -lsqlite3... yes checking for c++ -std=c++11 option to support OpenMP... -fopenmp checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating ABYSS/Makefile config.status: creating Align/Makefile config.status: creating Assembly/Makefile config.status: creating Common/Makefile config.status: creating DataLayer/Makefile config.status: creating FMIndex/Makefile config.status: creating Graph/Makefile config.status: creating Parallel/Makefile config.status: creating bin/Makefile config.status: creating doc/Makefile config.status: creating dialign/Makefile config.status: creating kmerprint/Makefile config.status: creating AdjList/Makefile config.status: creating Konnector/Makefile config.status: creating DAssembler/Makefile config.status: creating DistanceEst/Makefile config.status: creating Layout/Makefile config.status: creating Map/Makefile config.status: creating Overlap/Makefile config.status: creating PopBubbles/Makefile config.status: creating Scaffold/Makefile config.status: creating SimpleGraph/Makefile config.status: creating MergePaths/Makefile config.status: creating KAligner/Makefile config.status: creating PairedDBG/Makefile config.status: creating ParseAligns/Makefile config.status: creating PathOverlap/Makefile config.status: creating Consensus/Makefile config.status: creating FilterGraph/Makefile config.status: creating GapFiller/Makefile config.status: creating Sealer/Makefile config.status: creating vendor/gtest-1.7.0/Makefile config.status: creating RResolver/Makefile config.status: creating Unittest/Makefile config.status: creating LogKmerCount/Makefile config.status: creating Bloom/Makefile config.status: creating BloomDBG/Makefile config.status: creating DataBase/Makefile config.status: creating vendor/Makefile config.status: creating config.h config.status: executing depfiles commands =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for abyss-2.3.10 /usr/local/bin/gmake all-recursive gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10' Making all in bin gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/bin' gmake[2]: Nothing to be done for 'all'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/bin' Making all in doc gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/doc' gmake[2]: Nothing to be done for 'all'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/doc' Making all in Common gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Common' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-ContigID.o -MD -MP -MF .deps/libcommon_a-ContigID.Tpo -c -o libcommon_a-ContigID.o `test -f 'ContigID.cpp' || echo './'`ContigID.cpp mv -f .deps/libcommon_a-ContigID.Tpo .deps/libcommon_a-ContigID.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Fcontrol.o -MD -MP -MF .deps/libcommon_a-Fcontrol.Tpo -c -o libcommon_a-Fcontrol.o `test -f 'Fcontrol.cpp' || echo './'`Fcontrol.cpp mv -f .deps/libcommon_a-Fcontrol.Tpo .deps/libcommon_a-Fcontrol.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Histogram.o -MD -MP -MF .deps/libcommon_a-Histogram.Tpo -c -o libcommon_a-Histogram.o `test -f 'Histogram.cpp' || echo './'`Histogram.cpp mv -f .deps/libcommon_a-Histogram.Tpo .deps/libcommon_a-Histogram.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Kmer.o -MD -MP -MF .deps/libcommon_a-Kmer.Tpo -c -o libcommon_a-Kmer.o `test -f 'Kmer.cpp' || echo './'`Kmer.cpp mv -f .deps/libcommon_a-Kmer.Tpo .deps/libcommon_a-Kmer.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Log.o -MD -MP -MF .deps/libcommon_a-Log.Tpo -c -o libcommon_a-Log.o `test -f 'Log.cpp' || echo './'`Log.cpp mv -f .deps/libcommon_a-Log.Tpo .deps/libcommon_a-Log.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Options.o -MD -MP -MF .deps/libcommon_a-Options.Tpo -c -o libcommon_a-Options.o `test -f 'Options.cpp' || echo './'`Options.cpp mv -f .deps/libcommon_a-Options.Tpo .deps/libcommon_a-Options.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Sequence.o -MD -MP -MF .deps/libcommon_a-Sequence.Tpo -c -o libcommon_a-Sequence.o `test -f 'Sequence.cpp' || echo './'`Sequence.cpp mv -f .deps/libcommon_a-Sequence.Tpo .deps/libcommon_a-Sequence.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-SignalHandler.o -MD -MP -MF .deps/libcommon_a-SignalHandler.Tpo -c -o libcommon_a-SignalHandler.o `test -f 'SignalHandler.cpp' || echo './'`SignalHandler.cpp mv -f .deps/libcommon_a-SignalHandler.Tpo .deps/libcommon_a-SignalHandler.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Timer.o -MD -MP -MF .deps/libcommon_a-Timer.Tpo -c -o libcommon_a-Timer.o `test -f 'Timer.cpp' || echo './'`Timer.cpp mv -f .deps/libcommon_a-Timer.Tpo .deps/libcommon_a-Timer.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Uncompress.o -MD -MP -MF .deps/libcommon_a-Uncompress.Tpo -c -o libcommon_a-Uncompress.o `test -f 'Uncompress.cpp' || echo './'`Uncompress.cpp mv -f .deps/libcommon_a-Uncompress.Tpo .deps/libcommon_a-Uncompress.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-city.o -MD -MP -MF .deps/libcommon_a-city.Tpo -c -o libcommon_a-city.o `test -f 'city.cc' || echo './'`city.cc mv -f .deps/libcommon_a-city.Tpo .deps/libcommon_a-city.Po rm -f libcommon.a ar cr libcommon.a libcommon_a-ContigID.o libcommon_a-Fcontrol.o libcommon_a-Histogram.o libcommon_a-Kmer.o libcommon_a-Log.o libcommon_a-Options.o libcommon_a-Sequence.o libcommon_a-SignalHandler.o libcommon_a-Timer.o libcommon_a-Uncompress.o libcommon_a-city.o ranlib libcommon.a gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Common' Making all in Graph gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Graph' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT abyss_gc-gc.o -MD -MP -MF .deps/abyss_gc-gc.Tpo -c -o abyss_gc-gc.o `test -f 'gc.cc' || echo './'`gc.cc mv -f .deps/abyss_gc-gc.Tpo .deps/abyss_gc-gc.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -fstack-protector-strong -L/usr/local/lib -o abyss-gc abyss_gc-gc.o ../Common/libcommon.a -ldl -lm c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT abyss_todot-todot.o -MD -MP -MF .deps/abyss_todot-todot.Tpo -c -o abyss_todot-todot.o `test -f 'todot.cc' || echo './'`todot.cc mv -f .deps/abyss_todot-todot.Tpo .deps/abyss_todot-todot.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -L. -fstack-protector-strong -L/usr/local/lib -o abyss-todot abyss_todot-todot.o ../Common/libcommon.a -ldl -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Graph' Making all in DataLayer gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/DataLayer' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_fac-fac.o -MD -MP -MF .deps/abyss_fac-fac.Tpo -c -o abyss_fac-fac.o `test -f 'fac.cc' || echo './'`fac.cc mv -f .deps/abyss_fac-fac.Tpo .deps/abyss_fac-fac.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libdatalayer_a-FastaReader.o -MD -MP -MF .deps/libdatalayer_a-FastaReader.Tpo -c -o libdatalayer_a-FastaReader.o `test -f 'FastaReader.cpp' || echo './'`FastaReader.cpp mv -f .deps/libdatalayer_a-FastaReader.Tpo .deps/libdatalayer_a-FastaReader.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libdatalayer_a-FastaWriter.o -MD -MP -MF .deps/libdatalayer_a-FastaWriter.Tpo -c -o libdatalayer_a-FastaWriter.o `test -f 'FastaWriter.cpp' || echo './'`FastaWriter.cpp mv -f .deps/libdatalayer_a-FastaWriter.Tpo .deps/libdatalayer_a-FastaWriter.Po rm -f libdatalayer.a ar cr libdatalayer.a libdatalayer_a-FastaReader.o libdatalayer_a-FastaWriter.o ranlib libdatalayer.a c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-fac abyss_fac-fac.o libdatalayer.a ../Common/libcommon.a -ldl -lm c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_tofastq-abyss-tofastq.o -MD -MP -MF .deps/abyss_tofastq-abyss-tofastq.Tpo -c -o abyss_tofastq-abyss-tofastq.o `test -f 'abyss-tofastq.cc' || echo './'`abyss-tofastq.cc mv -f .deps/abyss_tofastq-abyss-tofastq.Tpo .deps/abyss_tofastq-abyss-tofastq.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-tofastq abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/DataLayer' Making all in DataBase gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/DataBase' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_db_csv-DB.o -MD -MP -MF .deps/abyss_db_csv-DB.Tpo -c -o abyss_db_csv-DB.o `test -f 'DB.cc' || echo './'`DB.cc mv -f .deps/abyss_db_csv-DB.Tpo .deps/abyss_db_csv-DB.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_db_csv-db-csv.o -MD -MP -MF .deps/abyss_db_csv-db-csv.Tpo -c -o abyss_db_csv-db-csv.o `test -f 'db-csv.cc' || echo './'`db-csv.cc mv -f .deps/abyss_db_csv-db-csv.Tpo .deps/abyss_db_csv-db-csv.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-db-csv abyss_db_csv-DB.o abyss_db_csv-db-csv.o -lsqlite3 -ldl -lm c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libdb_a-DB.o -MD -MP -MF .deps/libdb_a-DB.Tpo -c -o libdb_a-DB.o `test -f 'DB.cc' || echo './'`DB.cc mv -f .deps/libdb_a-DB.Tpo .deps/libdb_a-DB.Po rm -f libdb.a ar cr libdb.a libdb_a-DB.o ../Common/libcommon_a-ContigID.o ../Common/libcommon_a-Fcontrol.o ../Common/libcommon_a-Histogram.o ../Common/libcommon_a-Kmer.o ../Common/libcommon_a-Log.o ../Common/libcommon_a-Options.o ../Common/libcommon_a-Sequence.o ../Common/libcommon_a-SignalHandler.o ../Common/libcommon_a-Timer.o ../Common/libcommon_a-Uncompress.o ../Common/libcommon_a-city.o ranlib libdb.a gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/DataBase' Making all in FMIndex gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/FMIndex' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT abyss_count-count.o -MD -MP -MF .deps/abyss_count-count.Tpo -c -o abyss_count-count.o `test -f 'count.cc' || echo './'`count.cc mv -f .deps/abyss_count-count.Tpo .deps/abyss_count-count.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT libfmindex_a-bit_array.o -MD -MP -MF .deps/libfmindex_a-bit_array.Tpo -c -o libfmindex_a-bit_array.o `test -f 'bit_array.cc' || echo './'`bit_array.cc mv -f .deps/libfmindex_a-bit_array.Tpo .deps/libfmindex_a-bit_array.Po rm -f libfmindex.a ar cr libfmindex.a libfmindex_a-bit_array.o ranlib libfmindex.a c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -fstack-protector-strong -L/usr/local/lib -o abyss-count abyss_count-count.o libfmindex.a ../Common/libcommon.a -ldl -lm c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT abyss_dawg-abyss-dawg.o -MD -MP -MF .deps/abyss_dawg-abyss-dawg.Tpo -c -o abyss_dawg-abyss-dawg.o `test -f 'abyss-dawg.cc' || echo './'`abyss-dawg.cc mv -f .deps/abyss_dawg-abyss-dawg.Tpo .deps/abyss_dawg-abyss-dawg.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -fstack-protector-strong -L/usr/local/lib -o abyss-dawg abyss_dawg-abyss-dawg.o libfmindex.a ../Common/libcommon.a -ldl -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/FMIndex' Making all in Assembly gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Assembly' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libassembly_a-AssemblyAlgorithms.o -MD -MP -MF .deps/libassembly_a-AssemblyAlgorithms.Tpo -c -o libassembly_a-AssemblyAlgorithms.o `test -f 'AssemblyAlgorithms.cc' || echo './'`AssemblyAlgorithms.cc mv -f .deps/libassembly_a-AssemblyAlgorithms.Tpo .deps/libassembly_a-AssemblyAlgorithms.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libassembly_a-Options.o -MD -MP -MF .deps/libassembly_a-Options.Tpo -c -o libassembly_a-Options.o `test -f 'Options.cc' || echo './'`Options.cc mv -f .deps/libassembly_a-Options.Tpo .deps/libassembly_a-Options.Po rm -f libassembly.a ar cr libassembly.a libassembly_a-AssemblyAlgorithms.o libassembly_a-Options.o ../Common/libcommon_a-ContigID.o ../Common/libcommon_a-Fcontrol.o ../Common/libcommon_a-Histogram.o ../Common/libcommon_a-Kmer.o ../Common/libcommon_a-Log.o ../Common/libcommon_a-Options.o ../Common/libcommon_a-Sequence.o ../Common/libcommon_a-SignalHandler.o ../Common/libcommon_a-Timer.o ../Common/libcommon_a-Uncompress.o ../Common/libcommon_a-city.o ranlib libassembly.a gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Assembly' Making all in dialign gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/dialign' depbase=`echo museq.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT museq.o -MD -MP -MF $depbase.Tpo -c -o museq.o museq.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo alig.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT alig.o -MD -MP -MF $depbase.Tpo -c -o alig.o alig.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo assemble.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT assemble.o -MD -MP -MF $depbase.Tpo -c -o assemble.o assemble.c &&\ mv -f $depbase.Tpo $depbase.Po assemble.c:37:32: warning: inline function 'find_eqc' is not defined [-Wundefined-inline] 37 | extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos); | ^ assemble.c:115:9: note: used here 115 | tap = find_eqc(ap, s1, sp1); | ^ assemble.c:13:20: warning: inline function 'calc_weight' is not defined [-Wundefined-inline] 13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, | ^ assemble.c:459:4: note: used here 459 | calc_weight(dg, smatrix, pdist); | ^ assemble.c:40:20: warning: inline function 'align_diag' is not defined [-Wundefined-inline] 40 | extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); | ^ assemble.c:532:24: note: used here 532 | alignedSomething = align_diag(algn, smatrix, dg) || alignedSomething; | ^ 3 warnings generated. depbase=`echo diag.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT diag.o -MD -MP -MF $depbase.Tpo -c -o diag.o diag.c &&\ mv -f $depbase.Tpo $depbase.Po diag.c:739:9: warning: equality comparison result unused [-Wunused-comparison] 739 | sdg == NULL; | ~~~~^~~~~~~ diag.c:739:9: note: use '=' to turn this equality comparison into an assignment 739 | sdg == NULL; | ^~ | = 1 warning generated. depbase=`echo io.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT io.o -MD -MP -MF $depbase.Tpo -c -o io.o io.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo orf.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT orf.o -MD -MP -MF $depbase.Tpo -c -o orf.o orf.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo parameters.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT parameters.o -MD -MP -MF $depbase.Tpo -c -o parameters.o parameters.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo prob.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT prob.o -MD -MP -MF $depbase.Tpo -c -o prob.o prob.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo translate.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT translate.o -MD -MP -MF $depbase.Tpo -c -o translate.o translate.c &&\ mv -f $depbase.Tpo $depbase.Po rm -f libdialign.a ar cr libdialign.a alig.o assemble.o diag.o io.o orf.o parameters.o prob.o translate.o ranlib libdialign.a cc -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -L/usr/local/lib -o dialign museq.o libdialign.a -ldl -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/dialign' Making all in Align gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Align' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_align-align.o -MD -MP -MF .deps/abyss_align-align.Tpo -c -o abyss_align-align.o `test -f 'align.cc' || echo './'`align.cc mv -f .deps/abyss_align-align.Tpo .deps/abyss_align-align.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libalign_a-alignGlobal.o -MD -MP -MF .deps/libalign_a-alignGlobal.Tpo -c -o libalign_a-alignGlobal.o `test -f 'alignGlobal.cc' || echo './'`alignGlobal.cc mv -f .deps/libalign_a-alignGlobal.Tpo .deps/libalign_a-alignGlobal.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libalign_a-dialign.o -MD -MP -MF .deps/libalign_a-dialign.Tpo -c -o libalign_a-dialign.o `test -f 'dialign.cpp' || echo './'`dialign.cpp mv -f .deps/libalign_a-dialign.Tpo .deps/libalign_a-dialign.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libalign_a-dna_diag_prob.o -MD -MP -MF .deps/libalign_a-dna_diag_prob.Tpo -c -o libalign_a-dna_diag_prob.o `test -f 'dna_diag_prob.cc' || echo './'`dna_diag_prob.cc mv -f .deps/libalign_a-dna_diag_prob.Tpo .deps/libalign_a-dna_diag_prob.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libalign_a-smith_waterman.o -MD -MP -MF .deps/libalign_a-smith_waterman.Tpo -c -o libalign_a-smith_waterman.o `test -f 'smith_waterman.cpp' || echo './'`smith_waterman.cpp mv -f .deps/libalign_a-smith_waterman.Tpo .deps/libalign_a-smith_waterman.Po rm -f libalign.a ar cr libalign.a libalign_a-alignGlobal.o libalign_a-dialign.o libalign_a-dna_diag_prob.o libalign_a-smith_waterman.o ranlib libalign.a c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-align abyss_align-align.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_mergepairs-mergepairs.o -MD -MP -MF .deps/abyss_mergepairs-mergepairs.Tpo -c -o abyss_mergepairs-mergepairs.o `test -f 'mergepairs.cc' || echo './'`mergepairs.cc mv -f .deps/abyss_mergepairs-mergepairs.Tpo .deps/abyss_mergepairs-mergepairs.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-mergepairs abyss_mergepairs-mergepairs.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Align' Making all in ABYSS gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/ABYSS' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT ABYSS-abyss.o -MD -MP -MF .deps/ABYSS-abyss.Tpo -c -o ABYSS-abyss.o `test -f 'abyss.cc' || echo './'`abyss.cc mv -f .deps/ABYSS-abyss.Tpo .deps/ABYSS-abyss.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -fstack-protector-strong -L/usr/local/lib -o ABYSS ABYSS-abyss.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/ABYSS' Making all in Parallel gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Parallel' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT ABYSS_P-parallelAbyss.o -MD -MP -MF .deps/ABYSS_P-parallelAbyss.Tpo -c -o ABYSS_P-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp mv -f .deps/ABYSS_P-parallelAbyss.Tpo .deps/ABYSS_P-parallelAbyss.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT ABYSS_P-CommLayer.o -MD -MP -MF .deps/ABYSS_P-CommLayer.Tpo -c -o ABYSS_P-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp mv -f .deps/ABYSS_P-CommLayer.Tpo .deps/ABYSS_P-CommLayer.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT ABYSS_P-NetworkSequenceCollection.o -MD -MP -MF .deps/ABYSS_P-NetworkSequenceCollection.Tpo -c -o ABYSS_P-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp mv -f .deps/ABYSS_P-NetworkSequenceCollection.Tpo .deps/ABYSS_P-NetworkSequenceCollection.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT ABYSS_P-MessageBuffer.o -MD -MP -MF .deps/ABYSS_P-MessageBuffer.Tpo -c -o ABYSS_P-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp mv -f .deps/ABYSS_P-MessageBuffer.Tpo .deps/ABYSS_P-MessageBuffer.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT ABYSS_P-Messages.o -MD -MP -MF .deps/ABYSS_P-Messages.Tpo -c -o ABYSS_P-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp mv -f .deps/ABYSS_P-Messages.Tpo .deps/ABYSS_P-Messages.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -fstack-protector-strong -L/usr/local/lib -o ABYSS-P ABYSS_P-parallelAbyss.o ABYSS_P-CommLayer.o ABYSS_P-NetworkSequenceCollection.o ABYSS_P-MessageBuffer.o ABYSS_P-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT abyss_paired_dbg_mpi-parallelAbyss.o -MD -MP -MF .deps/abyss_paired_dbg_mpi-parallelAbyss.Tpo -c -o abyss_paired_dbg_mpi-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp mv -f .deps/abyss_paired_dbg_mpi-parallelAbyss.Tpo .deps/abyss_paired_dbg_mpi-parallelAbyss.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT abyss_paired_dbg_mpi-CommLayer.o -MD -MP -MF .deps/abyss_paired_dbg_mpi-CommLayer.Tpo -c -o abyss_paired_dbg_mpi-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp mv -f .deps/abyss_paired_dbg_mpi-CommLayer.Tpo .deps/abyss_paired_dbg_mpi-CommLayer.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT abyss_paired_dbg_mpi-NetworkSequenceCollection.o -MD -MP -MF .deps/abyss_paired_dbg_mpi-NetworkSequenceCollection.Tpo -c -o abyss_paired_dbg_mpi-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp mv -f .deps/abyss_paired_dbg_mpi-NetworkSequenceCollection.Tpo .deps/abyss_paired_dbg_mpi-NetworkSequenceCollection.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT abyss_paired_dbg_mpi-MessageBuffer.o -MD -MP -MF .deps/abyss_paired_dbg_mpi-MessageBuffer.Tpo -c -o abyss_paired_dbg_mpi-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp mv -f .deps/abyss_paired_dbg_mpi-MessageBuffer.Tpo .deps/abyss_paired_dbg_mpi-MessageBuffer.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT abyss_paired_dbg_mpi-Messages.o -MD -MP -MF .deps/abyss_paired_dbg_mpi-Messages.Tpo -c -o abyss_paired_dbg_mpi-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp mv -f .deps/abyss_paired_dbg_mpi-Messages.Tpo .deps/abyss_paired_dbg_mpi-Messages.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -fstack-protector-strong -L/usr/local/lib -o abyss-paired-dbg-mpi abyss_paired_dbg_mpi-parallelAbyss.o abyss_paired_dbg_mpi-CommLayer.o abyss_paired_dbg_mpi-NetworkSequenceCollection.o abyss_paired_dbg_mpi-MessageBuffer.o abyss_paired_dbg_mpi-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Parallel' Making all in Bloom gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Bloom' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../vendor -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT abyss_bloom-bloom.o -MD -MP -MF .deps/abyss_bloom-bloom.Tpo -c -o abyss_bloom-bloom.o `test -f 'bloom.cc' || echo './'`bloom.cc mv -f .deps/abyss_bloom-bloom.Tpo .deps/abyss_bloom-bloom.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -fstack-protector-strong -L/usr/local/lib -o abyss-bloom abyss_bloom-bloom.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Bloom' Making all in BloomDBG gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/BloomDBG' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../vendor -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT abyss_bloom_dbg-bloom-dbg.o -MD -MP -MF .deps/abyss_bloom_dbg-bloom-dbg.Tpo -c -o abyss_bloom_dbg-bloom-dbg.o `test -f 'bloom-dbg.cc' || echo './'`bloom-dbg.cc mv -f .deps/abyss_bloom_dbg-bloom-dbg.Tpo .deps/abyss_bloom_dbg-bloom-dbg.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -fstack-protector-strong -L/usr/local/lib -o abyss-bloom-dbg abyss_bloom_dbg-bloom-dbg.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/BloomDBG' Making all in Konnector gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Konnector' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT konnector-konnector.o -MD -MP -MF .deps/konnector-konnector.Tpo -c -o konnector-konnector.o `test -f 'konnector.cc' || echo './'`konnector.cc mv -f .deps/konnector-konnector.Tpo .deps/konnector-konnector.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -fstack-protector-strong -L/usr/local/lib -o konnector konnector-konnector.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Konnector' Making all in Consensus gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Consensus' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT Consensus-Consensus.o -MD -MP -MF .deps/Consensus-Consensus.Tpo -c -o Consensus-Consensus.o `test -f 'Consensus.cpp' || echo './'`Consensus.cpp Consensus.cpp:379:11: warning: variable 'numIgnored' set but not used [-Wunused-but-set-variable] 379 | unsigned numIgnored = 0; | ^ 1 warning generated. mv -f .deps/Consensus-Consensus.Tpo .deps/Consensus-Consensus.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o Consensus Consensus-Consensus.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Consensus' Making all in DAssembler gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/DAssembler' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT DAssembler-DAssembler.o -MD -MP -MF .deps/DAssembler-DAssembler.Tpo -c -o DAssembler-DAssembler.o `test -f 'DAssembler.cpp' || echo './'`DAssembler.cpp mv -f .deps/DAssembler-DAssembler.Tpo .deps/DAssembler-DAssembler.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT DAssembler-RotatedRead.o -MD -MP -MF .deps/DAssembler-RotatedRead.Tpo -c -o DAssembler-RotatedRead.o `test -f 'RotatedRead.cpp' || echo './'`RotatedRead.cpp mv -f .deps/DAssembler-RotatedRead.Tpo .deps/DAssembler-RotatedRead.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o DAssembler DAssembler-DAssembler.o DAssembler-RotatedRead.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/DAssembler' Making all in DistanceEst gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/DistanceEst' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT DistanceEst-DistanceEst.o -MD -MP -MF .deps/DistanceEst-DistanceEst.Tpo -c -o DistanceEst-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp mv -f .deps/DistanceEst-DistanceEst.Tpo .deps/DistanceEst-DistanceEst.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT DistanceEst-MLE.o -MD -MP -MF .deps/DistanceEst-MLE.Tpo -c -o DistanceEst-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp mv -f .deps/DistanceEst-MLE.Tpo .deps/DistanceEst-MLE.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o DistanceEst DistanceEst-DistanceEst.o DistanceEst-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT DistanceEst_ssq-DistanceEst.o -MD -MP -MF .deps/DistanceEst_ssq-DistanceEst.Tpo -c -o DistanceEst_ssq-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp mv -f .deps/DistanceEst_ssq-DistanceEst.Tpo .deps/DistanceEst_ssq-DistanceEst.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT DistanceEst_ssq-MLE.o -MD -MP -MF .deps/DistanceEst_ssq-MLE.Tpo -c -o DistanceEst_ssq-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp mv -f .deps/DistanceEst_ssq-MLE.Tpo .deps/DistanceEst_ssq-MLE.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o DistanceEst-ssq DistanceEst_ssq-DistanceEst.o DistanceEst_ssq-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/DistanceEst' Making all in KAligner gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/KAligner' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT KAligner-KAligner.o -MD -MP -MF .deps/KAligner-KAligner.Tpo -c -o KAligner-KAligner.o `test -f 'KAligner.cpp' || echo './'`KAligner.cpp mv -f .deps/KAligner-KAligner.Tpo .deps/KAligner-KAligner.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT KAligner-Aligner.o -MD -MP -MF .deps/KAligner-Aligner.Tpo -c -o KAligner-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp mv -f .deps/KAligner-Aligner.Tpo .deps/KAligner-Aligner.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -fstack-protector-strong -L/usr/local/lib -o KAligner KAligner-KAligner.o KAligner-Aligner.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -lpthread -ldl -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/KAligner' Making all in Layout gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Layout' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT abyss_layout-layout.o -MD -MP -MF .deps/abyss_layout-layout.Tpo -c -o abyss_layout-layout.o `test -f 'layout.cc' || echo './'`layout.cc mv -f .deps/abyss_layout-layout.Tpo .deps/abyss_layout-layout.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -fstack-protector-strong -L/usr/local/lib -o abyss-layout abyss_layout-layout.o ../Common/libcommon.a -ldl -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Layout' Making all in LogKmerCount gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/LogKmerCount' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT logcounter-logcounter.o -MD -MP -MF .deps/logcounter-logcounter.Tpo -c -o logcounter-logcounter.o `test -f 'logcounter.cc' || echo './'`logcounter.cc mv -f .deps/logcounter-logcounter.Tpo .deps/logcounter-logcounter.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o logcounter logcounter-logcounter.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/LogKmerCount' Making all in Map gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Map' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT abyss_index-index.o -MD -MP -MF .deps/abyss_index-index.Tpo -c -o abyss_index-index.o `test -f 'index.cc' || echo './'`index.cc mv -f .deps/abyss_index-index.Tpo .deps/abyss_index-index.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -fstack-protector-strong -L/usr/local/lib -o abyss-index abyss_index-index.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT abyss_map-map.o -MD -MP -MF .deps/abyss_map-map.Tpo -c -o abyss_map-map.o `test -f 'map.cc' || echo './'`map.cc mv -f .deps/abyss_map-map.Tpo .deps/abyss_map-map.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -fstack-protector-strong -L/usr/local/lib -o abyss-map abyss_map-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -D SAM_SEQ_QUAL=1 -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT abyss_map_ssq-map.o -MD -MP -MF .deps/abyss_map_ssq-map.Tpo -c -o abyss_map_ssq-map.o `test -f 'map.cc' || echo './'`map.cc mv -f .deps/abyss_map_ssq-map.Tpo .deps/abyss_map_ssq-map.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -fstack-protector-strong -L/usr/local/lib -o abyss-map-ssq abyss_map_ssq-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT abyss_overlap-overlap.o -MD -MP -MF .deps/abyss_overlap-overlap.Tpo -c -o abyss_overlap-overlap.o `test -f 'overlap.cc' || echo './'`overlap.cc mv -f .deps/abyss_overlap-overlap.Tpo .deps/abyss_overlap-overlap.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -fstack-protector-strong -L/usr/local/lib -o abyss-overlap abyss_overlap-overlap.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Map' Making all in MergePaths gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/MergePaths' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT MergePaths-MergePaths.o -MD -MP -MF .deps/MergePaths-MergePaths.Tpo -c -o MergePaths-MergePaths.o `test -f 'MergePaths.cpp' || echo './'`MergePaths.cpp mv -f .deps/MergePaths-MergePaths.Tpo .deps/MergePaths-MergePaths.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -fstack-protector-strong -L/usr/local/lib -o MergePaths MergePaths-MergePaths.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT MergeContigs-MergeContigs.o -MD -MP -MF .deps/MergeContigs-MergeContigs.Tpo -c -o MergeContigs-MergeContigs.o `test -f 'MergeContigs.cpp' || echo './'`MergeContigs.cpp mv -f .deps/MergeContigs-MergeContigs.Tpo .deps/MergeContigs-MergeContigs.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -fstack-protector-strong -L/usr/local/lib -o MergeContigs MergeContigs-MergeContigs.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I../SimpleGraph -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT PathConsensus-PathConsensus.o -MD -MP -MF .deps/PathConsensus-PathConsensus.Tpo -c -o PathConsensus-PathConsensus.o `test -f 'PathConsensus.cpp' || echo './'`PathConsensus.cpp mv -f .deps/PathConsensus-PathConsensus.Tpo .deps/PathConsensus-PathConsensus.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -fstack-protector-strong -L/usr/local/lib -o PathConsensus PathConsensus-PathConsensus.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/MergePaths' Making all in Overlap gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Overlap' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT Overlap-Overlap.o -MD -MP -MF .deps/Overlap-Overlap.Tpo -c -o Overlap-Overlap.o `test -f 'Overlap.cpp' || echo './'`Overlap.cpp mv -f .deps/Overlap-Overlap.Tpo .deps/Overlap-Overlap.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -fstack-protector-strong -L/usr/local/lib -o Overlap Overlap-Overlap.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Overlap' Making all in PairedDBG gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/PairedDBG' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT abyss_paired_dbg-abyss-paired-dbg.o -MD -MP -MF .deps/abyss_paired_dbg-abyss-paired-dbg.Tpo -c -o abyss_paired_dbg-abyss-paired-dbg.o `test -f 'abyss-paired-dbg.cc' || echo './'`abyss-paired-dbg.cc mv -f .deps/abyss_paired_dbg-abyss-paired-dbg.Tpo .deps/abyss_paired_dbg-abyss-paired-dbg.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT abyss_paired_dbg-KmerPair.o -MD -MP -MF .deps/abyss_paired_dbg-KmerPair.Tpo -c -o abyss_paired_dbg-KmerPair.o `test -f 'KmerPair.cc' || echo './'`KmerPair.cc mv -f .deps/abyss_paired_dbg-KmerPair.Tpo .deps/abyss_paired_dbg-KmerPair.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -fstack-protector-strong -L/usr/local/lib -o abyss-paired-dbg abyss_paired_dbg-abyss-paired-dbg.o abyss_paired_dbg-KmerPair.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm depbase=`echo KmerPair.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT KmerPair.o -MD -MP -MF $depbase.Tpo -c -o KmerPair.o KmerPair.cc &&\ mv -f $depbase.Tpo $depbase.Po rm -f libpaireddbg.a ar cr libpaireddbg.a KmerPair.o ranlib libpaireddbg.a gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/PairedDBG' Making all in ParseAligns gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/ParseAligns' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_fixmate-abyss-fixmate.o -MD -MP -MF .deps/abyss_fixmate-abyss-fixmate.Tpo -c -o abyss_fixmate-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc mv -f .deps/abyss_fixmate-abyss-fixmate.Tpo .deps/abyss_fixmate-abyss-fixmate.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-fixmate abyss_fixmate-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_fixmate_ssq-abyss-fixmate.o -MD -MP -MF .deps/abyss_fixmate_ssq-abyss-fixmate.Tpo -c -o abyss_fixmate_ssq-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc mv -f .deps/abyss_fixmate_ssq-abyss-fixmate.Tpo .deps/abyss_fixmate_ssq-abyss-fixmate.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-fixmate-ssq abyss_fixmate_ssq-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ParseAligns-ParseAligns.o -MD -MP -MF .deps/ParseAligns-ParseAligns.Tpo -c -o ParseAligns-ParseAligns.o `test -f 'ParseAligns.cpp' || echo './'`ParseAligns.cpp mv -f .deps/ParseAligns-ParseAligns.Tpo .deps/ParseAligns-ParseAligns.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o ParseAligns ParseAligns-ParseAligns.o ../Common/libcommon.a -ldl -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/ParseAligns' Making all in PathOverlap gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/PathOverlap' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT PathOverlap-PathOverlap.o -MD -MP -MF .deps/PathOverlap-PathOverlap.Tpo -c -o PathOverlap-PathOverlap.o `test -f 'PathOverlap.cpp' || echo './'`PathOverlap.cpp mv -f .deps/PathOverlap-PathOverlap.Tpo .deps/PathOverlap-PathOverlap.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -fstack-protector-strong -L/usr/local/lib -o PathOverlap PathOverlap-PathOverlap.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/PathOverlap' Making all in PopBubbles gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/PopBubbles' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT PopBubbles-PopBubbles.o -MD -MP -MF .deps/PopBubbles-PopBubbles.Tpo -c -o PopBubbles-PopBubbles.o `test -f 'PopBubbles.cpp' || echo './'`PopBubbles.cpp mv -f .deps/PopBubbles-PopBubbles.Tpo .deps/PopBubbles-PopBubbles.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -fstack-protector-strong -L/usr/local/lib -o PopBubbles PopBubbles-PopBubbles.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/PopBubbles' Making all in Scaffold gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Scaffold' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT abyss_scaffold-scaffold.o -MD -MP -MF .deps/abyss_scaffold-scaffold.Tpo -c -o abyss_scaffold-scaffold.o `test -f 'scaffold.cc' || echo './'`scaffold.cc mv -f .deps/abyss_scaffold-scaffold.Tpo .deps/abyss_scaffold-scaffold.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -fstack-protector-strong -L/usr/local/lib -o abyss-scaffold abyss_scaffold-scaffold.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT abyss_junction-junction.o -MD -MP -MF .deps/abyss_junction-junction.Tpo -c -o abyss_junction-junction.o `test -f 'junction.cc' || echo './'`junction.cc mv -f .deps/abyss_junction-junction.Tpo .deps/abyss_junction-junction.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -fstack-protector-strong -L/usr/local/lib -o abyss-junction abyss_junction-junction.o ../Common/libcommon.a -ldl -lm c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT abyss_longseqdist-longseqdist.o -MD -MP -MF .deps/abyss_longseqdist-longseqdist.Tpo -c -o abyss_longseqdist-longseqdist.o `test -f 'longseqdist.cpp' || echo './'`longseqdist.cpp mv -f .deps/abyss_longseqdist-longseqdist.Tpo .deps/abyss_longseqdist-longseqdist.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -fstack-protector-strong -L/usr/local/lib -o abyss-longseqdist abyss_longseqdist-longseqdist.o ../Common/libcommon.a -ldl -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Scaffold' Making all in SimpleGraph gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/SimpleGraph' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-strict-aliasing -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT SimpleGraph-SimpleGraph.o -MD -MP -MF .deps/SimpleGraph-SimpleGraph.Tpo -c -o SimpleGraph-SimpleGraph.o `test -f 'SimpleGraph.cpp' || echo './'`SimpleGraph.cpp SimpleGraph.cpp:519:46: warning: variable 'ignoredCount' set but not used [-Wunused-but-set-variable] 519 | unsigned validCount = 0, invalidCount = 0, ignoredCount = 0; | ^ 1 warning generated. mv -f .deps/SimpleGraph-SimpleGraph.Tpo .deps/SimpleGraph-SimpleGraph.Po c++ -std=c++11 -Wall -Wextra -Werror -Wno-strict-aliasing -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -fstack-protector-strong -L/usr/local/lib -o SimpleGraph SimpleGraph-SimpleGraph.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -lpthread -ldl -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/SimpleGraph' Making all in kmerprint gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/kmerprint' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT kmerprint-kmerprint.o -MD -MP -MF .deps/kmerprint-kmerprint.Tpo -c -o kmerprint-kmerprint.o `test -f 'kmerprint.cc' || echo './'`kmerprint.cc mv -f .deps/kmerprint-kmerprint.Tpo .deps/kmerprint-kmerprint.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -fstack-protector-strong -L/usr/local/lib -o kmerprint kmerprint-kmerprint.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/kmerprint' Making all in FilterGraph gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/FilterGraph' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT abyss_filtergraph-FilterGraph.o -MD -MP -MF .deps/abyss_filtergraph-FilterGraph.Tpo -c -o abyss_filtergraph-FilterGraph.o `test -f 'FilterGraph.cc' || echo './'`FilterGraph.cc mv -f .deps/abyss_filtergraph-FilterGraph.Tpo .deps/abyss_filtergraph-FilterGraph.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -fstack-protector-strong -L/usr/local/lib -o abyss-filtergraph abyss_filtergraph-FilterGraph.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/FilterGraph' Making all in GapFiller gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/GapFiller' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../Align -D SAM_SEQ_QUAL=1 -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_gapfill-gapfill.o -MD -MP -MF .deps/abyss_gapfill-gapfill.Tpo -c -o abyss_gapfill-gapfill.o `test -f 'gapfill.cpp' || echo './'`gapfill.cpp mv -f .deps/abyss_gapfill-gapfill.Tpo .deps/abyss_gapfill-gapfill.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-gapfill abyss_gapfill-gapfill.o ../Align/libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/GapFiller' Making all in Sealer gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Sealer' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT abyss_sealer-sealer.o -MD -MP -MF .deps/abyss_sealer-sealer.Tpo -c -o abyss_sealer-sealer.o `test -f 'sealer.cc' || echo './'`sealer.cc mv -f .deps/abyss_sealer-sealer.Tpo .deps/abyss_sealer-sealer.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -fstack-protector-strong -L/usr/local/lib -o abyss-sealer abyss_sealer-sealer.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm pandoc -s -o abyss-sealer.1 README.md gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Sealer' Making all in RResolver gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/RResolver' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -D_THREAD_SAFE -pthread -Wno-deprecated-declarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_rresolver_short-RResolverShort.o -MD -MP -MF .deps/abyss_rresolver_short-RResolverShort.Tpo -c -o abyss_rresolver_short-RResolverShort.o `test -f 'RResolverShort.cpp' || echo './'`RResolverShort.cpp mv -f .deps/abyss_rresolver_short-RResolverShort.Tpo .deps/abyss_rresolver_short-RResolverShort.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -D_THREAD_SAFE -pthread -Wno-deprecated-declarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_rresolver_short-Contigs.o -MD -MP -MF .deps/abyss_rresolver_short-Contigs.Tpo -c -o abyss_rresolver_short-Contigs.o `test -f 'Contigs.cpp' || echo './'`Contigs.cpp mv -f .deps/abyss_rresolver_short-Contigs.Tpo .deps/abyss_rresolver_short-Contigs.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -D_THREAD_SAFE -pthread -Wno-deprecated-declarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libralgorithmsshort_a-RAlgorithmsShort.o -MD -MP -MF .deps/libralgorithmsshort_a-RAlgorithmsShort.Tpo -c -o libralgorithmsshort_a-RAlgorithmsShort.o `test -f 'RAlgorithmsShort.cpp' || echo './'`RAlgorithmsShort.cpp mv -f .deps/libralgorithmsshort_a-RAlgorithmsShort.Tpo .deps/libralgorithmsshort_a-RAlgorithmsShort.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -D_THREAD_SAFE -pthread -Wno-deprecated-declarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libralgorithmsshort_a-BloomFilters.o -MD -MP -MF .deps/libralgorithmsshort_a-BloomFilters.Tpo -c -o libralgorithmsshort_a-BloomFilters.o `test -f 'BloomFilters.cpp' || echo './'`BloomFilters.cpp BloomFilters.cpp:144:6: warning: variable 'i' set but not used [-Wunused-but-set-variable] 144 | int i = 0; | ^ 1 warning generated. mv -f .deps/libralgorithmsshort_a-BloomFilters.Tpo .deps/libralgorithmsshort_a-BloomFilters.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -D_THREAD_SAFE -pthread -Wno-deprecated-declarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libralgorithmsshort_a-Contigs.o -MD -MP -MF .deps/libralgorithmsshort_a-Contigs.Tpo -c -o libralgorithmsshort_a-Contigs.o `test -f 'Contigs.cpp' || echo './'`Contigs.cpp mv -f .deps/libralgorithmsshort_a-Contigs.Tpo .deps/libralgorithmsshort_a-Contigs.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -D_THREAD_SAFE -pthread -Wno-deprecated-declarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libralgorithmsshort_a-SequenceTree.o -MD -MP -MF .deps/libralgorithmsshort_a-SequenceTree.Tpo -c -o libralgorithmsshort_a-SequenceTree.o `test -f 'SequenceTree.cpp' || echo './'`SequenceTree.cpp mv -f .deps/libralgorithmsshort_a-SequenceTree.Tpo .deps/libralgorithmsshort_a-SequenceTree.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -D_THREAD_SAFE -pthread -Wno-deprecated-declarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libralgorithmsshort_a-RUtils.o -MD -MP -MF .deps/libralgorithmsshort_a-RUtils.Tpo -c -o libralgorithmsshort_a-RUtils.o `test -f 'RUtils.cpp' || echo './'`RUtils.cpp mv -f .deps/libralgorithmsshort_a-RUtils.Tpo .deps/libralgorithmsshort_a-RUtils.Po rm -f libralgorithmsshort.a ar cr libralgorithmsshort.a libralgorithmsshort_a-RAlgorithmsShort.o libralgorithmsshort_a-BloomFilters.o libralgorithmsshort_a-Contigs.o libralgorithmsshort_a-SequenceTree.o libralgorithmsshort_a-RUtils.o ../DataLayer/abyss_fac-fac.o ../DataLayer/abyss_tofastq-abyss-tofastq.o ../DataLayer/libdatalayer_a-FastaReader.o ../DataLayer/libdatalayer_a-FastaWriter.o ../Common/libcommon_a-ContigID.o ../Common/libcommon_a-Fcontrol.o ../Common/libcommon_a-Histogram.o ../Common/libcommon_a-Kmer.o ../Common/libcommon_a-Log.o ../Common/libcommon_a-Options.o ../Common/libcommon_a-Sequence.o ../Common/libcommon_a-SignalHandler.o ../Common/libcommon_a-Timer.o ../Common/libcommon_a-Uncompress.o ../Common/libcommon_a-city.o ranlib libralgorithmsshort.a c++ -std=c++11 -Wall -Wextra -Werror -D_THREAD_SAFE -pthread -Wno-deprecated-declarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -pthread -o abyss-rresolver-short abyss_rresolver_short-RResolverShort.o abyss_rresolver_short-Contigs.o ../DataLayer/libdatalayer.a ../Common/libcommon.a libralgorithmsshort.a -lbtllib -ldl -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/RResolver' Making all in AdjList gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/AdjList' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -DPAIRED_DBG -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -MT AdjList-AdjList.o -MD -MP -MF .deps/AdjList-AdjList.Tpo -c -o AdjList-AdjList.o `test -f 'AdjList.cpp' || echo './'`AdjList.cpp mv -f .deps/AdjList-AdjList.Tpo .deps/AdjList-AdjList.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -Wno-error=unused-but-set-variable -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wno-deprecated-declarations -fstack-protector-strong -L/usr/local/lib -o AdjList AdjList-AdjList.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../PairedDBG/libpaireddbg.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/AdjList' Making all in vendor gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/vendor' gmake[2]: Nothing to be done for 'all'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/vendor' Making all in vendor/gtest-1.7.0 gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/vendor/gtest-1.7.0' gmake[2]: Nothing to be done for 'all'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/vendor/gtest-1.7.0' Making all in Unittest gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Unittest' gmake[2]: Nothing to be done for 'all'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Unittest' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10' pandoc -s -o README.html README.md gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10' =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> abyss-2.3.10 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-5.2.37.pkg [pkg-builder.dan.net.uk] Installing bash-5.2.37... [pkg-builder.dan.net.uk] Extracting bash-5.2.37: .......... done ===> abyss-2.3.10 depends on executable: bash - found ===> Returning to build of abyss-2.3.10 ===> abyss-2.3.10 depends on executable: gmake - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for abyss-2.3.10 ===> Generating temporary packing list Making install in bin gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/bin' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/bin' /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' install -m 555 abyss-bowtie abyss-bowtie2 abyss-bwa abyss-bwasw abyss-bwamem abyss-fatoagp abyss-kaligner abyss-pe abyss-samtoafg abyss-tabtomd abyss-bloom-dist.mk abyss-dida abyss-stack-size '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/bin' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/bin' Making install in doc gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/doc' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/doc' gmake[2]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/share/doc/abyss' install -m 0644 flowchart.pdf flowchart_simplified.pdf '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/share/doc/abyss' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/doc' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/doc' Making install in Common gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Common' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Common' gmake[2]: Nothing to be done for 'install-exec-am'. gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Common' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Common' Making install in Graph gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Graph' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Graph' /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' install -s -m 555 abyss-gc abyss-todot '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Graph' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Graph' Making install in DataLayer gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/DataLayer' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/DataLayer' /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' install -s -m 555 abyss-fac abyss-tofastq '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/DataLayer' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/DataLayer' Making install in DataBase gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/DataBase' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/DataBase' /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' install -s -m 555 abyss-db-csv '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' install -m 555 abyss-db-txt '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/DataBase' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/DataBase' Making install in FMIndex gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/FMIndex' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/FMIndex' gmake[2]: Nothing to be done for 'install-exec-am'. gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/FMIndex' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/FMIndex' Making install in Assembly gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Assembly' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Assembly' gmake[2]: Nothing to be done for 'install-exec-am'. gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Assembly' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Assembly' Making install in dialign gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/dialign' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/dialign' gmake[2]: Nothing to be done for 'install-exec-am'. gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/dialign' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/dialign' Making install in Align gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Align' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Align' /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' install -s -m 555 abyss-align abyss-mergepairs '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Align' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Align' Making install in ABYSS gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/ABYSS' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/ABYSS' /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' install -s -m 555 ABYSS '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/ABYSS' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/ABYSS' Making install in Parallel gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Parallel' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Parallel' /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' install -s -m 555 ABYSS-P abyss-paired-dbg-mpi '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Parallel' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Parallel' Making install in Bloom gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Bloom' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Bloom' /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' install -s -m 555 abyss-bloom '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Bloom' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Bloom' Making install in BloomDBG gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/BloomDBG' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/BloomDBG' /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' install -s -m 555 abyss-bloom-dbg '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/BloomDBG' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/BloomDBG' Making install in Konnector gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Konnector' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Konnector' /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' install -s -m 555 konnector '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Konnector' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Konnector' Making install in Consensus gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Consensus' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Consensus' /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' install -s -m 555 Consensus '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Consensus' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Consensus' Making install in DAssembler gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/DAssembler' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/DAssembler' /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' install -s -m 555 DAssembler '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/DAssembler' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/DAssembler' Making install in DistanceEst gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/DistanceEst' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/DistanceEst' /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' install -s -m 555 DistanceEst DistanceEst-ssq '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/DistanceEst' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/DistanceEst' Making install in KAligner gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/KAligner' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/KAligner' /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' install -s -m 555 KAligner '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/KAligner' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/KAligner' Making install in Layout gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Layout' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Layout' /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' install -s -m 555 abyss-layout '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Layout' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Layout' Making install in LogKmerCount gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/LogKmerCount' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/LogKmerCount' /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' install -s -m 555 logcounter '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/LogKmerCount' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/LogKmerCount' Making install in Map gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Map' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Map' /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' install -s -m 555 abyss-index abyss-map abyss-map-ssq abyss-overlap '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Map' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Map' Making install in MergePaths gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/MergePaths' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/MergePaths' /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' install -s -m 555 MergePaths MergeContigs PathConsensus '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/MergePaths' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/MergePaths' Making install in Overlap gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Overlap' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Overlap' /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' install -s -m 555 Overlap '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Overlap' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Overlap' Making install in PairedDBG gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/PairedDBG' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/PairedDBG' /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' install -s -m 555 abyss-paired-dbg '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/PairedDBG' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/PairedDBG' Making install in ParseAligns gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/ParseAligns' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/ParseAligns' /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' install -s -m 555 abyss-fixmate abyss-fixmate-ssq ParseAligns '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/ParseAligns' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/ParseAligns' Making install in PathOverlap gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/PathOverlap' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/PathOverlap' /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' install -s -m 555 PathOverlap '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/PathOverlap' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/PathOverlap' Making install in PopBubbles gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/PopBubbles' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/PopBubbles' /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' install -s -m 555 PopBubbles '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/PopBubbles' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/PopBubbles' Making install in Scaffold gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Scaffold' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Scaffold' /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' install -s -m 555 abyss-scaffold abyss-junction abyss-longseqdist '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Scaffold' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Scaffold' Making install in SimpleGraph gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/SimpleGraph' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/SimpleGraph' /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' install -s -m 555 SimpleGraph '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/SimpleGraph' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/SimpleGraph' Making install in kmerprint gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/kmerprint' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/kmerprint' gmake[2]: Nothing to be done for 'install-exec-am'. gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/kmerprint' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/kmerprint' Making install in FilterGraph gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/FilterGraph' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/FilterGraph' /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' install -s -m 555 abyss-filtergraph '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/FilterGraph' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/FilterGraph' Making install in GapFiller gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/GapFiller' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/GapFiller' /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' install -s -m 555 abyss-gapfill '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/GapFiller' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/GapFiller' Making install in Sealer gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Sealer' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Sealer' /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' install -s -m 555 abyss-sealer '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/share/man/man1' install -m 0644 abyss-sealer.1 '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/share/man/man1' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Sealer' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Sealer' Making install in RResolver gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/RResolver' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/RResolver' /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' install -s -m 555 abyss-rresolver-short '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/RResolver' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/RResolver' Making install in AdjList gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/AdjList' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/AdjList' /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' install -s -m 555 AdjList '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/bin' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/AdjList' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/AdjList' Making install in vendor gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/vendor' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/vendor' gmake[2]: Nothing to be done for 'install-exec-am'. gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/vendor' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/vendor' Making install in vendor/gtest-1.7.0 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/vendor/gtest-1.7.0' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/vendor/gtest-1.7.0' gmake[2]: Nothing to be done for 'install-exec-am'. gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/vendor/gtest-1.7.0' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/vendor/gtest-1.7.0' Making install in Unittest gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Unittest' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Unittest' gmake[2]: Nothing to be done for 'install-exec-am'. gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Unittest' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10/Unittest' gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10' gmake[2]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/share/doc/abyss' install -m 0644 ChangeLog CITATION.bib CITATION.md COPYRIGHT LICENSE README.md README.html '/wrkdirs/usr/ports/biology/abyss/work/stage/usr/local/share/doc/abyss' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.10' ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2025-05-04T14:28:56+0000' 'PKG_NOTE_ports_top_git_hash=5529c5919b' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=1a35b19e6d' '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 abyss-2.3.10 ===> Building abyss-2.3.10 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for abyss-2.3.10 build of biology/abyss | abyss-2.3.10 ended at Sun May 4 15:38:58 BST 2025 build time: 00:10:02