Date: Sun, 15 Jan 2017 04:56:27 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 110armv6-quarterly][biology/avida] Failed for avida-2.12.4 in build Message-ID: <201701150456.v0F4uRv3004201@beefy15.nyi.freebsd.org>
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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: ports@FreeBSD.org Last committer: marino@FreeBSD.org Ident: $FreeBSD: branches/2017Q1/biology/avida/Makefile 426378 2016-11-19 14:56:46Z marino $ Log URL: http://beefy15.nyi.freebsd.org/data/110armv6-quarterly/431453/logs/avida-2.12.4.log Build URL: http://beefy15.nyi.freebsd.org/build.html?mastername=110armv6-quarterly&build=431453 Log: ====>> Building biology/avida build started at Sun Jan 15 04:56:03 UTC 2017 port directory: /usr/ports/biology/avida building for: FreeBSD 110armv6-quarterly-job-02 11.0-RELEASE-p5 FreeBSD 11.0-RELEASE-p5 r309692 arm maintained by: ports@FreeBSD.org Makefile ident: $FreeBSD: branches/2017Q1/biology/avida/Makefile 426378 2016-11-19 14:56:46Z marino $ Poudriere version: 3.1.14 Host OSVERSION: 1200017 Jail OSVERSION: 1100122 Job Id: 02 ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv6 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o UNAME_v=FreeBSD 11.0-RELEASE-p5 r309692 UNAME_r=11.0-RELEASE-p5 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 OPSYS=FreeBSD ARCH=armv6 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/110armv6-quarterly/ref QEMU_EMULATING=1 UID=0 PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin _JAVA_VERSION_LIST_REGEXP=1.6\|1.7\|1.8\|1.6+\|1.7+\|1.8+ POUDRIERE_BUILD_TYPE=bulk PKGNAME=avida-2.12.4 OSREL=11.0 _OSRELEASE=11.0-RELEASE-p5 PYTHONBASE=/usr/local OLDPWD=/ _SMP_CPUS=28 PWD=/usr/local/poudriere/data/.m/110armv6-quarterly/ref/.p/pool MASTERNAME=110armv6-quarterly SCRIPTPREFIX=/usr/local/share/poudriere _JAVA_VENDOR_LIST_REGEXP=openjdk\|oracle\|sun USER=root HOME=/root POUDRIERE_VERSION=3.1.14 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh CONFIGURE_MAX_CMD_LEN=262144 LIBEXECPREFIX=/usr/local/libexec/poudriere LOCALBASE=/usr/local PACKAGE_BUILDING=yes _JAVA_OS_LIST_REGEXP=native\|linux OSVERSION=1100122 ---End Environment--- ---Begin OPTIONS List--- ===> The following configuration options are available for avida-2.12.4: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/avida/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/avida/work HOME=/wrkdirs/usr/ports/biology/avida/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/avida/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/avida/work HOME=/wrkdirs/usr/ports/biology/avida/work TMPDIR="/tmp" NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -fno-strict-aliasing" CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 444" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- CMAKE_BUILD_TYPE="release" OSREL=11.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib DOCSDIR="share/doc/avida" EXAMPLESDIR="share/examples/avida" DATADIR="share/avida" WWWDIR="www/avida" ETCDIR="etc/avida" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/avida DOCSDIR=/usr/local/share/doc/avida EXAMPLESDIR=/usr/local/share/examples/avida WWWDIR=/usr/local/www/avida ETCDIR=/usr/local/etc/avida --End SUB_LIST-- ---Begin make.conf--- .sinclude "/etc/make.nxb.conf" USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles MACHINE=arm MACHINE_ARCH=armv6 ARCH=${MACHINE_ARCH} #### /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 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ---Begin make.nxb.conf--- CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ AS=/nxb-bin/usr/bin/as NM=/nxb-bin/usr/bin/nm LD=/nxb-bin/usr/bin/ld OBJCOPY=/nxb-bin/usr/bin/objcopy SIZE=/nxb-bin/usr/bin/size STRIPBIN=/nxb-bin/usr/bin/strip SED=/nxb-bin/usr/bin/sed READELF=/nxb-bin/usr/bin/readelf RANLIB=/nxb-bin/usr/bin/ranlib YACC=/nxb-bin/usr/bin/yacc MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex ---End make.nxb.conf--- =======================<phase: check-sanity >============================ ===> NOTICE: The avida port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> License GPLv3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> avida-2.12.4 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.9.4_1.txz pkg-static: Warning: Major OS version upgrade detected. Running "pkg-static install -f pkg" recommended [110armv6-quarterly-job-02] Installing pkg-1.9.4_1... [110armv6-quarterly-job-02] Extracting pkg-1.9.4_1: .......... done ===> avida-2.12.4 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of avida-2.12.4 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> NOTICE: The avida port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by avida-2.12.4 for building =========================================================================== =======================<phase: checksum >============================ ===> NOTICE: The avida port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by avida-2.12.4 for building => SHA256 Checksum OK for avida-2.12.4-src.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> NOTICE: The avida port currently does not have a maintainer. As a result, it is <snip> https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by avida-2.12.4 for building ===> Extracting for avida-2.12.4 => SHA256 Checksum OK for avida-2.12.4-src.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for avida-2.12.4 ===> Applying FreeBSD patches for avida-2.12.4 =========================================================================== =======================<phase: build-depends >============================ ===> avida-2.12.4 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-3.7.1.txz pkg-static: Warning: Major OS version upgrade detected. Running "pkg-static install -f pkg" recommended [110armv6-quarterly-job-02] Installing cmake-3.7.1... [110armv6-quarterly-job-02] `-- Installing expat-2.2.0_1... [110armv6-quarterly-job-02] `-- Extracting expat-2.2.0_1: .......... done [110armv6-quarterly-job-02] `-- Installing cmake-modules-3.7.1... [110armv6-quarterly-job-02] `-- Extracting cmake-modules-3.7.1: .......... done [110armv6-quarterly-job-02] `-- Installing curl-7.52.1_1... [110armv6-quarterly-job-02] | `-- Installing libnghttp2-1.18.0... [110armv6-quarterly-job-02] | `-- Extracting libnghttp2-1.18.0: .......... done [110armv6-quarterly-job-02] | `-- Installing ca_root_nss-3.28.1... [110armv6-quarterly-job-02] | `-- Extracting ca_root_nss-3.28.1: ........ done [110armv6-quarterly-job-02] `-- Extracting curl-7.52.1_1: .......... done [110armv6-quarterly-job-02] `-- Installing libarchive-3.2.2,1... [110armv6-quarterly-job-02] | `-- Installing liblz4-131... [110armv6-quarterly-job-02] | `-- Extracting liblz4-131: .......... done [110armv6-quarterly-job-02] | `-- Installing lzo2-2.09... [110armv6-quarterly-job-02] | `-- Extracting lzo2-2.09: .......... done [110armv6-quarterly-job-02] `-- Extracting libarchive-3.2.2,1: .......... done [110armv6-quarterly-job-02] `-- Installing jsoncpp-1.8.0_1... [110armv6-quarterly-job-02] `-- Extracting jsoncpp-1.8.0_1: .......... done [110armv6-quarterly-job-02] `-- Installing libuv-1.10.1... [110armv6-quarterly-job-02] `-- Extracting libuv-1.10.1: .......... done [110armv6-quarterly-job-02] Extracting cmake-3.7.1: .......... done Message from ca_root_nss-3.28.1: ********************************* WARNING ********************************* FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. *********************************** NOTE ********************************** This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem *************************************************************************** ===> avida-2.12.4 depends on file: /usr/local/bin/cmake - found ===> Returning to build of avida-2.12.4 =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for avida-2.12.4 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/avida/work/.build -- The C compiler identification is Clang 3.8.0 -- The CXX compiler identification is Clang 3.8.0 -- Check for working C compiler: /nxb-bin/usr/bin/cc -- Check for working C compiler: /nxb-bin/usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /nxb-bin/usr/bin/c++ -- Check for working CXX compiler: /nxb-bin/usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test HAVE_FUSED_MADD -- Performing Test HAVE_FUSED_MADD - Failed -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE CMAKE_MODULE_LINKER_FLAGS THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /wrkdirs/usr/ports/biology/avida/work/.build =========================================================================== =======================<phase: build >============================ ===> Building for avida-2.12.4 /usr/local/bin/cmake -H/wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src -B/wrkdirs/usr/ports/biology/avida/work/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /wrkdirs/usr/ports/biology/avida/work/.build/CMakeFiles /wrkdirs/usr/ports/biology/avida/work/.build/CMakeFiles/progress.marks /nxb-bin/usr/bin/make -f CMakeFiles/Makefile2 all /nxb-bin/usr/bin/make -f libs/apto/src/CMakeFiles/aptostatic.dir/build.make libs/apto/src/CMakeFiles/aptostatic.dir/depend cd /wrkdirs/usr/ports/biology/avida/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src /wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/apto/src /wrkdirs/usr/ports/biology/avida/work/.build /wrkdirs/usr/ports/biology/avida/work/.build/libs/apto/src /wrkdirs/usr/ports/biology/avida/work/.build/libs/apto/src/CMakeFiles/aptostatic.dir/DependInfo.cmake Scanning dependencies of target aptostatic /nxb-bin/usr/bin/make -f libs/apto/src/CMakeFiles/aptostatic.dir/build.make libs/apto/src/CMakeFiles/aptostatic.dir/build [ 1%] Building CXX object libs/apto/src/CMakeFiles/aptostatic.dir/core/FileSystem.cc.o cd /wrkdirs/usr/ports/biology/avida/work/.build/libs/apto/src && /nxb-bin/usr/bin/c++ -I/wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/apto/src/../include -O2 -pipe -fno-strict-aliasing -funroll-loops -fstrict-aliasing -ftree-vectorize -fvisibility-inlines-hidden -Wextra -Wno-unknown-pragmas -Wno-trigraphs -DNDEBUG -o CMakeFiles/aptostatic.dir/core/FileSystem.cc.o -c /wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/apto/src/core/FileSystem.cc [ 1%] Building CXX object libs/apto/src/CMakeFiles/aptostatic.dir/core/RefCount.cc.o cd /wrkdirs/usr/ports/biology/avida/work/.build/libs/apto/src && /nxb-bin/usr/bin/c++ -I/wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/apto/src/../include -O2 -pipe -fno-strict-aliasing -funroll-loops -fstrict-aliasing -ftree-vectorize -fvisibility-inlines-hidden -Wextra -Wno-unknown-pragmas -Wno-trigraphs -DNDEBUG -o CMakeFiles/aptostatic.dir/core/RefCount.cc.o -c /wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/apto/src/core/RefCount.cc [ 2%] Building CXX object libs/apto/src/CMakeFiles/aptostatic.dir/core/Thread.cc.o cd /wrkdirs/usr/ports/biology/avida/work/.build/libs/apto/src && /nxb-bin/usr/bin/c++ -I/wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/apto/src/../include -O2 -pipe -fno-strict-aliasing -funroll-loops -fstrict-aliasing -ftree-vectorize -fvisibility-inlines-hidden -Wextra -Wno-unknown-pragmas -Wno-trigraphs -DNDEBUG -o CMakeFiles/aptostatic.dir/core/Thread.cc.o -c /wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/apto/src/core/Thread.cc [ 3%] Building CXX object libs/apto/src/CMakeFiles/aptostatic.dir/platform/Platform.cc.o cd /wrkdirs/usr/ports/biology/avida/work/.build/libs/apto/src && /nxb-bin/usr/bin/c++ -I/wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/apto/src/../include -O2 -pipe -fno-strict-aliasing -funroll-loops -fstrict-aliasing -ftree-vectorize -fvisibility-inlines-hidden -Wextra -Wno-unknown-pragmas -Wno-trigraphs -DNDEBUG -o CMakeFiles/aptostatic.dir/platform/Platform.cc.o -c /wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/apto/src/platform/Platform.cc [ 3%] Building CXX object libs/apto/src/CMakeFiles/aptostatic.dir/stat/ContingencyTable.cc.o cd /wrkdirs/usr/ports/biology/avida/work/.build/libs/apto/src && /nxb-bin/usr/bin/c++ -I/wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/apto/src/../include -O2 -pipe -fno-strict-aliasing -funroll-loops -fstrict-aliasing -ftree-vectorize -fvisibility-inlines-hidden -Wextra -Wno-unknown-pragmas -Wno-trigraphs -DNDEBUG -o CMakeFiles/aptostatic.dir/stat/ContingencyTable.cc.o -c /wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/apto/src/stat/ContingencyTable.cc [ 4%] Building CXX object libs/apto/src/CMakeFiles/aptostatic.dir/stat/FishersExact.cc.o cd /wrkdirs/usr/ports/biology/avida/work/.build/libs/apto/src && /nxb-bin/usr/bin/c++ -I/wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/apto/src/../include -O2 -pipe -fno-strict-aliasing -funroll-loops -fstrict-aliasing -ftree-vectorize -fvisibility-inlines-hidden -Wextra -Wno-unknown-pragmas -Wno-trigraphs -DNDEBUG -o CMakeFiles/aptostatic.dir/stat/FishersExact.cc.o -c /wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/apto/src/stat/FishersExact.cc /wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/apto/src/stat/FishersExact.cc:1052:21: warning: unsequenced modification and access to 'idx_inc' [-Wunsequenced] while (row_diff[++idx_inc] == row_marginals[idx_inc]) ; ^ ~~~~~~~ 1 warning generated. [ 4%] Linking CXX static library ../../../lib/libapto.a cd /wrkdirs/usr/ports/biology/avida/work/.build/libs/apto/src && /usr/local/bin/cmake -P CMakeFiles/aptostatic.dir/cmake_clean_target.cmake cd /wrkdirs/usr/ports/biology/avida/work/.build/libs/apto/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/aptostatic.dir/link.txt --verbose=1 /nxb-bin/usr/bin/ar qc ../../../lib/libapto.a CMakeFiles/aptostatic.dir/core/FileSystem.cc.o CMakeFiles/aptostatic.dir/core/RefCount.cc.o CMakeFiles/aptostatic.dir/core/Thread.cc.o CMakeFiles/aptostatic.dir/platform/Platform.cc.o CMakeFiles/aptostatic.dir/stat/ContingencyTable.cc.o CMakeFiles/aptostatic.dir/stat/FishersExact.cc.o /nxb-bin/usr/bin/ranlib ../../../lib/libapto.a [ 4%] Built target aptostatic /nxb-bin/usr/bin/make -f libs/apto/src/CMakeFiles/aptoshared.dir/build.make libs/apto/src/CMakeFiles/aptoshared.dir/depend cd /wrkdirs/usr/ports/biology/avida/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src /wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/apto/src /wrkdirs/usr/ports/biology/avida/work/.build /wrkdirs/usr/ports/biology/avida/work/.build/libs/apto/src /wrkdirs/usr/ports/biology/avida/work/.build/libs/apto/src/CMakeFiles/aptoshared.dir/DependInfo.cmake Scanning dependencies of target aptoshared /nxb-bin/usr/bin/make -f libs/apto/src/CMakeFiles/aptoshared.dir/build.make libs/apto/src/CMakeFiles/aptoshared.dir/build [ 4%] Building CXX object libs/apto/src/CMakeFiles/aptoshared.dir/core/FileSystem.cc.o cd /wrkdirs/usr/ports/biology/avida/work/.build/libs/apto/src && /nxb-bin/usr/bin/c++ -Daptoshared_EXPORTS -I/wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/apto/src/../include -O2 -pipe -fno-strict-aliasing -funroll-loops -fstrict-aliasing -ftree-vectorize -fvisibility-inlines-hidden -Wextra -Wno-unknown-pragmas -Wno-trigraphs -DNDEBUG -fPIC -o CMakeFiles/aptoshared.dir/core/FileSystem.cc.o -c /wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/apto/src/core/FileSystem.cc [ 5%] Building CXX object libs/apto/src/CMakeFiles/aptoshared.dir/core/RefCount.cc.o cd /wrkdirs/usr/ports/biology/avida/work/.build/libs/apto/src && /nxb-bin/usr/bin/c++ -Daptoshared_EXPORTS -I/wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/apto/src/../include -O2 -pipe -fno-strict-aliasing -funroll-loops -fstrict-aliasing -ftree-vectorize -fvisibility-inlines-hidden -Wextra -Wno-unknown-pragmas -Wno-trigraphs -DNDEBUG -fPIC -o CMakeFiles/aptoshared.dir/core/RefCount.cc.o -c /wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/apto/src/core/RefCount.cc [ 5%] Building CXX object libs/apto/src/CMakeFiles/aptoshared.dir/core/Thread.cc.o cd /wrkdirs/usr/ports/biology/avida/work/.build/libs/apto/src && /nxb-bin/usr/bin/c++ -Daptoshared_EXPORTS -I/wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/apto/src/../include -O2 -pipe -fno-strict-aliasing -funroll-loops -fstrict-aliasing -ftree-vectorize -fvisibility-inlines-hidden -Wextra -Wno-unknown-pragmas -Wno-trigraphs -DNDEBUG -fPIC -o CMakeFiles/aptoshared.dir/core/Thread.cc.o -c /wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/apto/src/core/Thread.cc [ 6%] Building CXX object libs/apto/src/CMakeFiles/aptoshared.dir/platform/Platform.cc.o cd /wrkdirs/usr/ports/biology/avida/work/.build/libs/apto/src && /nxb-bin/usr/bin/c++ -Daptoshared_EXPORTS -I/wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/apto/src/../include -O2 -pipe -fno-strict-aliasing -funroll-loops -fstrict-aliasing -ftree-vectorize -fvisibility-inlines-hidden -Wextra -Wno-unknown-pragmas -Wno-trigraphs -DNDEBUG -fPIC -o CMakeFiles/aptoshared.dir/platform/Platform.cc.o -c /wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/apto/src/platform/Platform.cc [ 6%] Building CXX object libs/apto/src/CMakeFiles/aptoshared.dir/stat/ContingencyTable.cc.o cd /wrkdirs/usr/ports/biology/avida/work/.build/libs/apto/src && /nxb-bin/usr/bin/c++ -Daptoshared_EXPORTS -I/wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/apto/src/../include -O2 -pipe -fno-strict-aliasing -funroll-loops -fstrict-aliasing -ftree-vectorize -fvisibility-inlines-hidden -Wextra -Wno-unknown-pragmas -Wno-trigraphs -DNDEBUG -fPIC -o CMakeFiles/aptoshared.dir/stat/ContingencyTable.cc.o -c /wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/apto/src/stat/ContingencyTable.cc [ 7%] Building CXX object libs/apto/src/CMakeFiles/aptoshared.dir/stat/FishersExact.cc.o cd /wrkdirs/usr/ports/biology/avida/work/.build/libs/apto/src && /nxb-bin/usr/bin/c++ -Daptoshared_EXPORTS -I/wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/apto/src/../include -O2 -pipe -fno-strict-aliasing -funroll-loops -fstrict-aliasing -ftree-vectorize -fvisibility-inlines-hidden -Wextra -Wno-unknown-pragmas -Wno-trigraphs -DNDEBUG -fPIC -o CMakeFiles/aptoshared.dir/stat/FishersExact.cc.o -c /wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/apto/src/stat/FishersExact.cc /wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/apto/src/stat/FishersExact.cc:1052:21: warning: unsequenced modification and access to 'idx_inc' [-Wunsequenced] while (row_diff[++idx_inc] == row_marginals[idx_inc]) ; ^ ~~~~~~~ 1 warning generated. [ 7%] Linking CXX shared library ../../../lib/libapto.so cd /wrkdirs/usr/ports/biology/avida/work/.build/libs/apto/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/aptoshared.dir/link.txt --verbose=1 /nxb-bin/usr/bin/c++ -fPIC -O2 -pipe -fno-strict-aliasing -funroll-loops -fstrict-aliasing -ftree-vectorize -fvisibility-inlines-hidden -Wextra -Wno-unknown-pragmas -Wno-trigraphs -DNDEBUG -shared -Wl,-soname,libapto.so -o ../../../lib/libapto.so CMakeFiles/aptoshared.dir/core/FileSystem.cc.o CMakeFiles/aptoshared.dir/core/RefCount.cc.o CMakeFiles/aptoshared.dir/core/Thread.cc.o CMakeFiles/aptoshared.dir/platform/Platform.cc.o CMakeFiles/aptoshared.dir/stat/ContingencyTable.cc.o CMakeFiles/aptoshared.dir/stat/FishersExact.cc.o -pthread -pthread [ 7%] Built target aptoshared /nxb-bin/usr/bin/make -f libs/tcmalloc-1.4/CMakeFiles/tcmalloc-1.4.dir/build.make libs/tcmalloc-1.4/CMakeFiles/tcmalloc-1.4.dir/depend cd /wrkdirs/usr/ports/biology/avida/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src /wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/tcmalloc-1.4 /wrkdirs/usr/ports/biology/avida/work/.build /wrkdirs/usr/ports/biology/avida/work/.build/libs/tcmalloc-1.4 /wrkdirs/usr/ports/biology/avida/work/.build/libs/tcmalloc-1.4/CMakeFiles/tcmalloc-1.4.dir/DependInfo.cmake Scanning dependencies of target tcmalloc-1.4 /nxb-bin/usr/bin/make -f libs/tcmalloc-1.4/CMakeFiles/tcmalloc-1.4.dir/build.make libs/tcmalloc-1.4/CMakeFiles/tcmalloc-1.4.dir/build [ 7%] Building CXX object libs/tcmalloc-1.4/CMakeFiles/tcmalloc-1.4.dir/src/atomicops-internals-x86.cc.o cd /wrkdirs/usr/ports/biology/avida/work/.build/libs/tcmalloc-1.4 && /nxb-bin/usr/bin/c++ -I/wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/tcmalloc-1.4/src -O2 -pipe -fno-strict-aliasing -funroll-loops -fstrict-aliasing -ftree-vectorize -fvisibility-inlines-hidden -Wextra -Wno-unknown-pragmas -Wno-trigraphs -DNDEBUG -o CMakeFiles/tcmalloc-1.4.dir/src/atomicops-internals-x86.cc.o -c /wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/tcmalloc-1.4/src/atomicops-internals-x86.cc In file included from /wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/tcmalloc-1.4/src/atomicops-internals-x86.cc:56: In file included from /wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/tcmalloc-1.4/src/atomicops.h:126: /wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/tcmalloc-1.4/src/atomicops-internals-x86.h:98:26: error: invalid output constraint '=a' in asm : "=a" (prev) ^ /wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/tcmalloc-1.4/src/atomicops-internals-x86.h:386:5: error: unknown register name 'st' in asm "st", "st(1)", "st(2)", "st(3)", "st(4)", ^ /wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/tcmalloc-1.4/src/atomicops-internals-x86.h:409:26: error: unknown register name 'st' in asm "st", "st(1)", "st(2)", "st(3)", "st(4)", ^ In file included from /wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/tcmalloc-1.4/src/atomicops-internals-x86.cc:57: /wrkdirs/usr/ports/biology/avida/work/avida-2.12.4-src/libs/tcmalloc-1.4/src/basictypes.h:105:51: warning: shifting a negative signed value is undefined [-Wshift-negative-value] const int64 kint64min = ( ((( int64) kint32min) << 32) | 0 ); ~~~~~~~~~~~~~~~~~~~~ ^ 1 warning and 3 errors generated. *** Error code 1 Stop. make[3]: stopped in /wrkdirs/usr/ports/biology/avida/work/.build *** Error code 1 Stop. make[2]: stopped in /wrkdirs/usr/ports/biology/avida/work/.build *** Error code 1 Stop. make[1]: stopped in /wrkdirs/usr/ports/biology/avida/work/.build *** Error code 1 Stop. make: stopped in /usr/ports/biology/avida
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