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Maintainer: [email protected] Log URL: https://pkg-status.freebsd.org/ampere5/data/150arm64-default/41b0a5a50014/logs/canu-2.2_10.log Build URL: https://pkg-status.freebsd.org/ampere5/build.html?mastername=150arm64-default&build=41b0a5a50014 Log: =>> Building biology/canu build started at Wed Aug 12 17:47:24 UTC 2026 port directory: /usr/ports/biology/canu package name: canu-2.2_10 building for: FreeBSD 150arm64-default-job-20 15.0-RELEASE-p12 FreeBSD 15.0-RELEASE-p12 arm64 maintained by: [email protected] Makefile datestamp: -rw-r--r-- 1 root wheel 2153 May 12 01:01 /usr/ports/biology/canu/Makefile Ports top last git commit: 41b0a5a5001410dfc9b3315d76b188f59a3f0236 Ports top unclean checkout: no Port dir last git commit: 2a7c0561200c6cf9d0c0252cd4a7ab446eca8e4a Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.8 Host OSVERSION: 1600019 Jail OSVERSION: 1500068 Job Id: 20 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500068 UNAME_v=FreeBSD 15.0-RELEASE-p12 UNAME_r=15.0-RELEASE-p12 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=3.4.8 MASTERMNT=/usr/local/poudriere/data/.m/150arm64-default/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/150arm64-default/20/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=150arm64-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/150arm64-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.8 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- [email protected] --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/canu/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/canu/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/canu/work/.cache HOME=/wrkdirs/usr/ports/biology/canu/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/canu/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/canu/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" --End CONFIGURE_ENV-- --MAKE_ENV-- DESTDIR=/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src CANU_BUILD_ENV=ports PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/canu/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/canu/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/canu/work/.cache HOME=/wrkdirs/usr/ports/biology/canu/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/canu/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/canu/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 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=" " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 " CXXSTD=c++14 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-- JAVASHAREDIR="share/java" JAVAJARDIR="share/java/classes" OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.42.3 PERL_VER=5.42 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.42 DOCSDIR="share/doc/canu" EXAMPLESDIR="share/examples/canu" DATADIR="share/canu" WWWDIR="www/canu" ETCDIR="etc/canu" --End PLIST_SUB-- --SUB_LIST-- JAVASHAREDIR="/usr/local/share/java" JAVAJARDIR="/usr/local/share/java/classes" JAVALIBDIR="/usr/local/share/java/classes" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/canu DOCSDIR=/usr/local/share/doc/canu EXAMPLESDIR=/usr/local/share/examples/canu WWWDIR=/usr/local/www/canu ETCDIR=/usr/local/etc/canu --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 #### #### # 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 3 jobs MAKE_JOBS_NUMBER=3 #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 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) 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-- =======================<phase: check-sanity >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv2 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> canu-2.2_10 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.8.2.pkg [150arm64-default-job-20] Installing pkg-2.8.2... [150arm64-default-job-20] Extracting pkg-2.8.2: .......... done ===> canu-2.2_10 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of canu-2.2_10 =========================================================================== =======================<phase: fetch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: fetch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by canu-2.2_10 for building =========================================================================== =======================<phase: checksum >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by canu-2.2_10 for building => SHA256 Checksum OK for canu-2.2.tar.xz. =========================================================================== =======================<phase: extract-depends>============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: extract >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by canu-2.2_10 for building ===> Extracting for canu-2.2_10 => SHA256 Checksum OK for canu-2.2.tar.xz. cp -f /usr/ports/biology/canu/files/cpuid_arm.c /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src/utility/src/parasail/cpuid.c =========================================================================== =======================<phase: patch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: patch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for canu-2.2_10 ===> Applying FreeBSD patches for canu-2.2_10 from /usr/ports/biology/canu/files =========================================================================== =======================<phase: build-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> canu-2.2_10 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [150arm64-default-job-20] Installing gmake-4.4.1... [150arm64-default-job-20] `-- Installing gettext-runtime-1.0_1... [150arm64-default-job-20] | `-- Installing indexinfo-0.3.1_1... [150arm64-default-job-20] | `-- Extracting indexinfo-0.3.1_1: .... done [150arm64-default-job-20] `-- Extracting gettext-runtime-1.0_1: .......... done [150arm64-default-job-20] Extracting gmake-4.4.1: .......... done ===> canu-2.2_10 depends on package: gmake>=4.4.1 - found ===> Returning to build of canu-2.2_10 ===> canu-2.2_10 depends on file: /usr/local/openjdk25/bin/java - not found ===> Installing existing package /packages/All/openjdk25-25.0.4+7.f.1.pkg [150arm64-default-job-20] Installing openjdk25-25.0.4+7.f.1... [150arm64-default-job-20] `-- Installing alsa-lib-1.2.16.1... [150arm64-default-job-20] `-- Extracting alsa-lib-1.2.16.1: .......... done [150arm64-default-job-20] `-- Installing fontconfig-2.17.1,1... [150arm64-default-job-20] | `-- Installing expat-2.8.2... [150arm64-default-job-20] | `-- Extracting expat-2.8.2: .......... done [150arm64-default-job-20] | `-- Installing freetype2-2.14.3... [150arm64-default-job-20] | | `-- Installing brotli-1.2.0,1... [150arm64-default-job-20] | | `-- Extracting brotli-1.2.0,1: .......... done [150arm64-default-job-20] | | `-- Installing png-1.6.58... [150arm64-default-job-20] | | `-- Extracting png-1.6.58: .......... done [150arm64-default-job-20] | `-- Extracting freetype2-2.14.3: .......... done <snip> In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:453:5: warning: 'unary_function<double, unsigned long>' is deprecated [-Wdeprecated-declarations] 453 | BOOST_HASH_SPECIALIZE(double) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function<type, std::size_t> \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function<double, unsigned long>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:454:5: warning: 'unary_function<long double, unsigned long>' is deprecated [-Wdeprecated-declarations] 454 | BOOST_HASH_SPECIALIZE(long double) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function<type, std::size_t> \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function<long double, unsigned long>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:456:5: warning: 'unary_function<std::string, unsigned long>' is deprecated [-Wdeprecated-declarations] 456 | BOOST_HASH_SPECIALIZE_REF(std::string) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:430:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE_REF' 430 | : public std::unary_function<type, std::size_t> \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function<std::string, unsigned long>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:458:5: warning: 'unary_function<std::wstring, unsigned long>' is deprecated [-Wdeprecated-declarations] 458 | BOOST_HASH_SPECIALIZE_REF(std::wstring) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:430:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE_REF' 430 | : public std::unary_function<type, std::size_t> \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function<std::wstring, unsigned long>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:462:5: warning: 'unary_function<long long, unsigned long>' is deprecated [-Wdeprecated-declarations] 462 | BOOST_HASH_SPECIALIZE(boost::long_long_type) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function<type, std::size_t> \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function<long long, unsigned long>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:463:5: warning: 'unary_function<unsigned long long, unsigned long>' is deprecated [-Wdeprecated-declarations] 463 | BOOST_HASH_SPECIALIZE(boost::ulong_long_type) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function<type, std::size_t> \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function<unsigned long long, unsigned long>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:467:5: warning: 'unary_function<__int128, unsigned long>' is deprecated [-Wdeprecated-declarations] 467 | BOOST_HASH_SPECIALIZE(boost::int128_type) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function<type, std::size_t> \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function<__int128, unsigned long>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:468:5: warning: 'unary_function<unsigned __int128, unsigned long>' is deprecated [-Wdeprecated-declarations] 468 | BOOST_HASH_SPECIALIZE(boost::uint128_type) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function<type, std::size_t> \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function<unsigned __int128, unsigned long>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:472:5: warning: 'unary_function<std::type_index, unsigned long>' is deprecated [-Wdeprecated-declarations] 472 | BOOST_HASH_SPECIALIZE(std::type_index) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function<type, std::size_t> \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function<std::type_index, unsigned long>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:36: In file included from utgcns/libboost/boost/property_map/property_map.hpp:600: In file included from utgcns/libboost/boost/property_map/vector_property_map.hpp:14: In file included from utgcns/libboost/boost/shared_ptr.hpp:17: In file included from utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:28: In file included from utgcns/libboost/boost/smart_ptr/detail/shared_count.hpp:30: utgcns/libboost/boost/smart_ptr/detail/sp_counted_base.hpp:63:11: fatal error: 'boost/smart_ptr/detail/sp_counted_base_sync.hpp' file not found 63 | # include <boost/smart_ptr/detail/sp_counted_base_sync.hpp> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 28 warnings and 1 error generated. gmake: *** [Makefile:725: /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o] Error 1 gmake: *** Waiting for unfinished jobs.... ===> 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 making "build" in /usr/ports/biology/canu
