From nobody Sat Feb 25 10:15:54 2023 X-Original-To: pkg-fallout@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4PP2hq2rxCz3syTx for ; Sat, 25 Feb 2023 10:15:55 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4PP2hp6SlFz4GNF; Sat, 25 Feb 2023 10:15:54 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1677320154; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc; bh=pkaxBoapQjzCb15sJlF3qujlI6aj8RcHUZzqjE/CBqY=; b=w6ewfBP0e7R/SclwkiLC2E8J3/pioVptSbVBkB3M27gznjkf56zrNHsmNbEBAj9MBE+Llq BUav4lkju3ajEFU19jOSL+WDzTWglXhluZDuuDZ9HawssN4aRj2V8iEzGOm1wms8vMdtUC WqlmWKnk2nEVGDgQXDKxf8QuCA6ADFjU4zsRmKPRuEQb+ot/fd2CfIn0oBFoxZ5J7UTp6u s5dD1D+JHUkr7aSdJ+YtQXtfnTnhZBGPpv7LLZeBBdRh48j2StollopHmnRWUgYNq9dJq9 R7HUVH6oYlSO2EaHtUp2R5ldevDM+8NxxX8iYczbBHeUd4n2SJQAYSau2PfWgg== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1677320154; a=rsa-sha256; cv=none; b=ZOVfaysrFhoAgRY3gA6ilH2PT5NHj3lG8AaEZ3hlMvVRcureVdMu8lbzCzkTSOTkISQ7cU MRni+U0y2I+CF/rJTGRTurXoF5zFLCyGAjfN1hgUNi2CWMVXtsu/NfvFKWpfZ35rxrOxt1 B4f5YP5Yca7ExSJ03DXP9eACnHN5XQ3nph5ug1JF9TQJU37dyfZZjKXCov4BmRsQDkKb/5 m4KnMis0kf223KL4MVcwiMqFmSMOpUGv+YHkbI53lbuOL1jwTVQowS/MYEm/ShDD4b6/vf k6rfBqFwglh/ahqKQMbFXKmFIPzE379kEts7Yj3YSXw7ep0mQQ0yMfRLlZsyfQ== Received: from ampere2.nyi.freebsd.org (ampere2.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:24]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4PP2hp5Vx9z119P; Sat, 25 Feb 2023 10:15:54 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from ampere2.nyi.freebsd.org (localhost [127.0.0.1]) by ampere2.nyi.freebsd.org (8.16.1/8.16.1) with ESMTP id 31PAFsKC015370; Sat, 25 Feb 2023 10:15:54 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by ampere2.nyi.freebsd.org (8.16.1/8.16.1/Submit) id 31PAFslU015367; Sat, 25 Feb 2023 10:15:54 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Sat, 25 Feb 2023 10:15:54 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202302251015.31PAFslU015367@ampere2.nyi.freebsd.org> To: yuri@FreeBSD.org Subject: [package - main-arm64-default][biology/abyss] Failed for abyss-2.3.5_1 in build Cc: pkg-fallout@FreeBSD.org X-ThisMailContainsUnwantedMimeParts: N List-Id: Fallout logs from package building List-Archive: https://lists.freebsd.org/archives/freebsd-pkg-fallout List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-freebsd-pkg-fallout@freebsd.org You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: yuri@FreeBSD.org Log URL: https://pkg-status.freebsd.org/ampere2/data/main-arm64-default/p1b4f77b589d3_s357492c995/logs/abyss-2.3.5_1.log Build URL: https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-arm64-default&build=p1b4f77b589d3_s357492c995 Log: =>> Building biology/abyss build started at Sat Feb 25 10:09:53 UTC 2023 port directory: /usr/ports/biology/abyss package name: abyss-2.3.5_1 building for: FreeBSD main-arm64-default-job-04 14.0-CURRENT FreeBSD 14.0-CURRENT 1400081 arm64 maintained by: yuri@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1400073 Jail OSVERSION: 1400081 Job Id: 04 !!! Jail is newer than host. (Jail: 1400081, Host: 1400073) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh OSVERSION=1400081 UNAME_v=FreeBSD 14.0-CURRENT 1400081 UNAME_r=14.0-CURRENT 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 LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-23-ga7f8d188 MASTERMNT=/usr/local/poudriere/data/.m/main-arm64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/main-arm64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=main-arm64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/main-arm64-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for abyss-2.3.5_1: 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=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=2.71 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=2.71 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " MANPREFIX="/usr/local" 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=14.0 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 PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 15.0.7 (https://github.com/llvm/llvm-project.git llvmorg-15.0.7-0-g8dfdcc7b7bf6) Target: aarch64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 15.0.7 (https://github.com/llvm/llvm-project.git llvmorg-15.0.7-0-g8dfdcc7b7bf6) Target: aarch64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_53255a77=yes CC_OUTPUT_921dbbb2_911cfe02=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes CC_OUTPUT_921dbbb2_af59ad06=yes CC_OUTPUT_921dbbb2_a15f3fcf=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 15.0.7 (https://github.com/llvm/llvm-project.git llvmorg-15.0.7-0-g8dfdcc7b7bf6) Target: aarch64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=aarch64 OPSYS=FreeBSD _OSRELEASE=14.0-CURRENT OSREL=14.0 OSVERSION=1400081 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 1048576 stack size (kbytes, -s) 1048576 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) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===> License GPLv3 accepted by the user =========================================================================== =================================================== ===> abyss-2.3.5_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.19.1_1.pkg [main-arm64-default-job-04] Installing pkg-1.19.1_1... [main-arm64-default-job-04] Extracting pkg-1.19.1_1: .......... done ===> abyss-2.3.5_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of abyss-2.3.5_1 =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by abyss-2.3.5_1 for building =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by abyss-2.3.5_1 for building => SHA256 Checksum OK for bcgsc-abyss-2.3.5_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by abyss-2.3.5_1 for building ===> Extracting for abyss-2.3.5_1 => SHA256 Checksum OK for bcgsc-abyss-2.3.5_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for abyss-2.3.5_1 ===> Applying FreeBSD patches for abyss-2.3.5_1 from /usr/ports/biology/abyss/files =========================================================================== =================================================== ===> abyss-2.3.5_1 depends on file: /usr/local/include/boost/version.hpp - not found ===> Installing existing package /packages/All/boost-libs-1.81.0.pkg rm -f libdatalayer.a ar cru libdatalayer.a libdatalayer_a-FastaReader.o libdatalayer_a-FastaWriter.o ranlib libdatalayer.a c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -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 mv -f .deps/abyss_tofastq-abyss-tofastq.Tpo .deps/abyss_tofastq-abyss-tofastq.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -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[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/DataLayer' Making all in DataBase gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/DataBase' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -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 c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -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 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -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/abyss_db_csv-DB.Tpo .deps/abyss_db_csv-DB.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -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 mv -f .deps/libdb_a-DB.Tpo .deps/libdb_a-DB.Po rm -f libdb.a ar cru libdb.a libdb_a-DB.o ../Common/libcommon.a ranlib libdb.a gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/DataBase' Making all in FMIndex gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/FMIndex' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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_count-count.Tpo .deps/abyss_count-count.Po rm -f libfmindex.a ar cru libfmindex.a libfmindex_a-bit_array.o ranlib libfmindex.a c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-count abyss_count-count.o libfmindex.a ../Common/libcommon.a -ldl -lm mv -f .deps/abyss_dawg-abyss-dawg.Tpo .deps/abyss_dawg-abyss-dawg.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-dawg abyss_dawg-abyss-dawg.o libfmindex.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/FMIndex' Making all in Assembly gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/Assembly' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -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 c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -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 mv -f .deps/libassembly_a-AssemblyAlgorithms.Tpo .deps/libassembly_a-AssemblyAlgorithms.Po rm -f libassembly.a ar cru libassembly.a libassembly_a-AssemblyAlgorithms.o libassembly_a-Options.o ../Common/libcommon.a ranlib libassembly.a gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/Assembly' Making all in dialign gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/dialign' depbase=`echo museq.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -O2 -pipe -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-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -O2 -pipe -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-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -O2 -pipe -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 $depbase.Po assemble.c:37:32: warning: inline function 'find_eqc' is not defined [-Wundefined-inline] extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos); ^ assemble.c:115:9: note: used here tap = find_eqc(ap, s1, sp1); ^ assemble.c:13:20: warning: inline function 'calc_weight' is not defined [-Wundefined-inline] extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, ^ assemble.c:459:4: note: used here calc_weight(dg, smatrix, pdist); ^ assemble.c:40:20: warning: inline function 'align_diag' is not defined [-Wundefined-inline] extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); ^ assemble.c:532:24: note: used here alignedSomething = align_diag(algn, smatrix, dg) || alignedSomething; ^ depbase=`echo diag.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -O2 -pipe -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 $depbase.Po diag.c:739:9: warning: equality comparison result unused [-Wunused-comparison] sdg == NULL; ~~~~^~~~~~~ diag.c:739:9: note: use '=' to turn this equality comparison into an assignment sdg == NULL; ^~ = 3 warnings generated. depbase=`echo io.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -O2 -pipe -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 $depbase.Po 1 warning generated. depbase=`echo orf.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -O2 -pipe -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-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -O2 -pipe -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-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -O2 -pipe -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-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -O2 -pipe -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 cru libdialign.a alig.o assemble.o diag.o io.o orf.o parameters.o prob.o translate.o ranlib libdialign.a cc -O2 -pipe -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[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/dialign' Making all in Align gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/Align' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -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 c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -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-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -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/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-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -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-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -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-dialign.Tpo .deps/libalign_a-dialign.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -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/libalign_a-smith_waterman.Tpo .deps/libalign_a-smith_waterman.Po rm -f libalign.a ar cru 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 -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 mv -f .deps/abyss_mergepairs-mergepairs.Tpo .deps/abyss_mergepairs-mergepairs.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -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[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/Align' Making all in ABYSS gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/ABYSS' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 ld: warning: ../DataBase/libdb.a: archive member 'libcommon.a' is neither ET_REL nor LLVM bitcode ld: warning: ../Assembly/libassembly.a: archive member 'libcommon.a' is neither ET_REL nor LLVM bitcode gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/ABYSS' Making all in Parallel gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/Parallel' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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-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-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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_P-NetworkSequenceCollection.Tpo .deps/ABYSS_P-NetworkSequenceCollection.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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-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-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 ld: warning: ../Assembly/libassembly.a: archive member 'libcommon.a' is neither ET_REL nor LLVM bitcode ld: warning: ../DataBase/libdb.a: archive member 'libcommon.a' is neither ET_REL nor LLVM bitcode mv -f .deps/abyss_paired_dbg_mpi-NetworkSequenceCollection.Tpo .deps/abyss_paired_dbg_mpi-NetworkSequenceCollection.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 ld: warning: ../Assembly/libassembly.a: archive member 'libcommon.a' is neither ET_REL nor LLVM bitcode ld: warning: ../DataBase/libdb.a: archive member 'libcommon.a' is neither ET_REL nor LLVM bitcode gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/Parallel' Making all in Bloom gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/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-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/Bloom' Making all in BloomDBG gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/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-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/BloomDBG' Making all in Konnector gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/Konnector' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o konnector konnector-konnector.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/Konnector' Making all in Consensus gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/Consensus' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -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: error: variable 'numIgnored' set but not used [-Werror,-Wunused-but-set-variable] unsigned numIgnored = 0; ^ 1 error generated. gmake[3]: *** [Makefile:407: Consensus-Consensus.o] Error 1 gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5/Consensus' gmake[2]: *** [Makefile:488: all-recursive] Error 1 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5' gmake[1]: *** [Makefile:408: all] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.5' ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped in /usr/ports/biology/abyss