Date: Fri, 27 Dec 2019 12:32:39 GMT From: pkg-fallout@FreeBSD.org To: yuri@FreeBSD.org Cc: pkg-fallout@FreeBSD.org Subject: [package - head-amd64-default][biology/ncbi-cxx-toolkit] Failed for ncbi-cxx-toolkit-21.0.0_2 in build Message-ID: <201912271232.xBRCWdpD013188@beefy18.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: yuri@FreeBSD.org Last committer: zeising@FreeBSD.org Ident: $FreeBSD: head/biology/ncbi-cxx-toolkit/Makefile 516742 2019-11-04 21:08:20Z zeising $ Log URL: http://beefy18.nyi.freebsd.org/data/head-amd64-default/p520889_s356085/logs/ncbi-cxx-toolkit-21.0.0_2.log Build URL: http://beefy18.nyi.freebsd.org/build.html?mastername=head-amd64-default&build=p520889_s356085 Log: =>> Building biology/ncbi-cxx-toolkit build started at Fri Dec 27 11:13:22 UTC 2019 port directory: /usr/ports/biology/ncbi-cxx-toolkit package name: ncbi-cxx-toolkit-21.0.0_2 building for: FreeBSD head-amd64-default-job-17 13.0-CURRENT FreeBSD 13.0-CURRENT 1300069 amd64 maintained by: yuri@FreeBSD.org Makefile ident: $FreeBSD: head/biology/ncbi-cxx-toolkit/Makefile 516742 2019-11-04 21:08:20Z zeising $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300062 Jail OSVERSION: 1300069 Job Id: 17 !!! Jail is newer than host. (Jail: 1300069, Host: 1300062) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh OSVERSION=1300069 UNAME_v=FreeBSD 13.0-CURRENT 1300069 UNAME_r=13.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root 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=3.2.8-5-gc81843e5 MASTERMNT=/usr/local/poudriere/data/.m/head-amd64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-amd64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-amd64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-amd64-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--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --without-debug --with-dll --without-static --x-libraries=/usr/local/lib --x-includes=/usr/local/include --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PYTHON="/usr/local/bin/python3.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work HOME=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=262144 --End CONFIGURE_ENV-- --MAKE_ENV-- PERL_USE_UNSAFE_INC=1 OPENSSLBASE=/usr OPENSSLDIR=/etc/ssl OPENSSLINC=/usr/include OPENSSLLIB=/usr/lib XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work HOME=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes 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 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " 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-- PYTHON_INCLUDEDIR=include/python3.7m PYTHON_LIBDIR=lib/python3.7 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=lib/python3.7/site-packages PYTHON_SUFFIX=37 PYTHON_VER=3.7 PYTHON_VERSION=python3.7 PYTHON2="@comment " PYTHON3="" OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.30.1 PERL_VER=5.30 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/5.30 DOCSDIR="share/doc/ncbi-cxx-toolkit" EXAMPLESDIR="share/examples/ncbi-cxx-toolkit" DATADIR="share/ncbi-cxx-toolkit" WWWDIR="www/ncbi-cxx-toolkit" ETCDIR="etc/ncbi-cxx-toolkit" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/ncbi-cxx-toolkit DOCSDIR=/usr/local/share/doc/ncbi-cxx-toolkit EXAMPLESDIR=/usr/local/share/examples/ncbi-cxx-toolkit WWWDIR=/usr/local/www/ncbi-cxx-toolkit ETCDIR=/usr/local/etc/ncbi-cxx-toolkit --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 9.0.1 (git@github.com:llvm/llvm-project.git c1a0a213378a458fbea1a5c77b315c7dce08fd05) (based on LLVM 9.0.1) Target: x86_64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 9.0.1 (git@github.com:llvm/llvm-project.git c1a0a213378a458fbea1a5c77b315c7dce08fd05) (based on LLVM 9.0.1) Target: x86_64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--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_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 9.0.1 (git@github.com:llvm/llvm-project.git c1a0a213378a458fbea1a5c77b315c7dce08fd05) (based on LLVM 9.0.1) Target: x86_64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=amd64 OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300069 PYTHONBASE=/usr/local HAVE_COMPAT_IA32_KERN=YES CONFIGURE_MAX_CMD_LEN=262144 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) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 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-- =======================<phase: check-sanity >============================ ===> License PD accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> ncbi-cxx-toolkit-21.0.0_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.12.0.txz [head-amd64-default-job-17] Installing pkg-1.12.0... [head-amd64-default-job-17] Extracting pkg-1.12.0: .......... done ===> ncbi-cxx-toolkit-21.0.0_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of ncbi-cxx-toolkit-21.0.0_2 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License PD accepted by the user ===> Fetching all distfiles required by ncbi-cxx-toolkit-21.0.0_2 for building =========================================================================== =======================<phase: checksum >============================ ===> License PD accepted by the user ===> Fetching all distfiles required by ncbi-cxx-toolkit-21.0.0_2 for building => SHA256 Checksum OK for ncbi_cxx--21_0_0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License PD accepted by the user ===> Fetching all distfiles required by ncbi-cxx-toolkit-21.0.0_2 for building ===> Extracting for ncbi-cxx-toolkit-21.0.0_2 => SHA256 Checksum OK for ncbi_cxx--21_0_0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for ncbi-cxx-toolkit-21.0.0_2 ===> Applying FreeBSD patches for ncbi-cxx-toolkit-21.0.0_2 =========================================================================== =======================<phase: build-depends >============================ ===> ncbi-cxx-toolkit-21.0.0_2 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_3.txz [head-amd64-default-job-17] Installing gmake-4.2.1_3... [head-amd64-default-job-17] `-- Installing gettext-runtime-0.20.1... [head-amd64-default-job-17] | `-- Installing indexinfo-0.3.1... [head-amd64-default-job-17] | `-- Extracting indexinfo-0.3.1: .... done [head-amd64-default-job-17] `-- Extracting gettext-runtime-0.20.1: .......... done [head-amd64-default-job-17] Extracting gmake-4.2.1_3: .......... done ===> ncbi-cxx-toolkit-21.0.0_2 depends on executable: gmake - found ===> Returning to build of ncbi-cxx-toolkit-21.0.0_2 <snip> # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/blastinput/demo/blastinput_demo.cpp:36: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/objmgr/util/sequence.hpp:50: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/objmgr/feat_ci.hpp:37: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/objmgr/annot_types_ci.hpp:38: /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/objmgr/impl/annot_collector.hpp:510:5: warning: 'auto_ptr<ncbi::objects::CAnnotMappingCollector>' is deprecated [-Wdeprecated-declarations] auto_ptr<CAnnotMappingCollector> m_MappingCollector; ^ /usr/include/c++/v1/memory:2079:28: note: 'auto_ptr<ncbi::objects::CAnnotMappingCollector>' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /usr/include/c++/v1/__config:945:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:934:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/blastinput/demo/blastinput_demo.cpp:36: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/objmgr/util/sequence.hpp:50: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/objmgr/feat_ci.hpp:37: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/objmgr/annot_types_ci.hpp:38: /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/objmgr/impl/annot_collector.hpp:518:5: warning: 'auto_ptr<std::__1::set<ncbi::CConstRef<ncbi::objects::CSeq_loc, ncbi::CObjectCounterLocker>, std::__1::less<ncbi::CConstRef<ncbi::objects::CSeq_loc, ncbi::CObjectCounterLocker> >, std::__1::allocator<ncbi::CConstRef<ncbi::objects::CSeq_loc, ncbi::CObjectCounterLocker> > > >' is deprecated [-Wdeprecated-declarations] auto_ptr<TAnnotLocsSet> m_AnnotLocsSet; ^ /usr/include/c++/v1/memory:2079:28: note: 'auto_ptr<std::__1::set<ncbi::CConstRef<ncbi::objects::CSeq_loc, ncbi::CObjectCounterLocker>, std::__1::less<ncbi::CConstRef<ncbi::objects::CSeq_loc, ncbi::CObjectCounterLocker> >, std::__1::allocator<ncbi::CConstRef<ncbi::objects::CSeq_loc, ncbi::CObjectCounterLocker> > > >' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /usr/include/c++/v1/__config:945:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:934:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/blastinput/demo/blastinput_demo.cpp:36: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/objmgr/util/sequence.hpp:50: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/objmgr/feat_ci.hpp:37: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/objmgr/annot_types_ci.hpp:38: /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/objmgr/impl/annot_collector.hpp:523:13: warning: 'auto_ptr<std::__1::set<ncbi::objects::CAnnotName, std::__1::less<ncbi::objects::CAnnotName>, std::__1::allocator<ncbi::objects::CAnnotName> > >' is deprecated [-Wdeprecated-declarations] mutable auto_ptr<TAnnotNames> m_AnnotNames; ^ /usr/include/c++/v1/memory:2079:28: note: 'auto_ptr<std::__1::set<ncbi::objects::CAnnotName, std::__1::less<ncbi::objects::CAnnotName>, std::__1::allocator<ncbi::objects::CAnnotName> > >' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /usr/include/c++/v1/__config:945:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:934:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/blastinput/demo/blastinput_demo.cpp:36: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/objmgr/util/sequence.hpp:54: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/objmgr/util/create_defline.hpp:39: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/objects/seqfeat/BioSource.hpp:43: /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/objects/seqfeat/SubSource.hpp:233:12: warning: 'auto_ptr<ncbi::objects::CLatLonCountryMap>' is deprecated [-Wdeprecated-declarations] static auto_ptr<CLatLonCountryMap> m_LatLonCountryMap; ^ /usr/include/c++/v1/memory:2079:28: note: 'auto_ptr<ncbi::objects::CLatLonCountryMap>' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /usr/include/c++/v1/__config:945:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:934:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/blastinput/demo/blastinput_demo.cpp:36: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/objmgr/util/sequence.hpp:54: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/objmgr/util/create_defline.hpp:39: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/objects/seqfeat/BioSource.hpp:43: /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/objects/seqfeat/SubSource.hpp:234:12: warning: 'auto_ptr<ncbi::objects::CLatLonCountryMap>' is deprecated [-Wdeprecated-declarations] static auto_ptr<CLatLonCountryMap> m_LatLonWaterMap; ^ /usr/include/c++/v1/memory:2079:28: note: 'auto_ptr<ncbi::objects::CLatLonCountryMap>' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /usr/include/c++/v1/__config:945:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:934:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/blastinput/demo/blastinput_demo.cpp:36: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/objmgr/util/sequence.hpp:54: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/objmgr/util/create_defline.hpp:41: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/objmgr/util/feature.hpp:40: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/objects/seqfeat/Gb_qual.hpp:51: /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/serial/iterator.hpp:467:5: warning: 'auto_ptr<std::__1::set<const void *, std::__1::less<const void *>, std::__1::allocator<const void *> > >' is deprecated [-Wdeprecated-declarations] auto_ptr<TVisitedObjects> m_VisitedObjects; ^ /usr/include/c++/v1/memory:2079:28: note: 'auto_ptr<std::__1::set<const void *, std::__1::less<const void *>, std::__1::allocator<const void *> > >' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /usr/include/c++/v1/__config:945:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:934:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/blastinput/demo/blastinput_demo.cpp:36: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/objmgr/util/sequence.hpp:54: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/objmgr/util/create_defline.hpp:42: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/objmgr/util/indexer.hpp:43: /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/objmgr/object_manager.hpp:276:5: warning: 'auto_ptr<ncbi::CPluginManager<ncbi::objects::CDataLoader> >' is deprecated [-Wdeprecated-declarations] auto_ptr<TPluginManager> m_PluginManager; ^ /usr/include/c++/v1/memory:2079:28: note: 'auto_ptr<ncbi::CPluginManager<ncbi::objects::CDataLoader> >' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /usr/include/c++/v1/__config:945:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:934:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/blastinput/demo/blastinput_demo.cpp:36: /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/objmgr/util/sequence.hpp:364:9: warning: 'auto_ptr<ncbi::objects::CFeat_CI>' is deprecated [-Wdeprecated-declarations] auto_ptr<CFeat_CI> &feat_ci, ^ /usr/include/c++/v1/memory:2079:28: note: 'auto_ptr<ncbi::objects::CFeat_CI>' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /usr/include/c++/v1/__config:945:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:934:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/blastinput/demo/blastinput_demo.cpp:36: /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/objmgr/util/sequence.hpp:862:5: warning: 'auto_ptr<ncbi::objects::sequence::CDeflineGenerator>' is deprecated [-Wdeprecated-declarations] auto_ptr<sequence::CDeflineGenerator> m_Gen; ^ /usr/include/c++/v1/memory:2079:28: note: 'auto_ptr<ncbi::objects::sequence::CDeflineGenerator>' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /usr/include/c++/v1/__config:945:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:934:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/blastinput/demo/blastinput_demo.cpp:40: /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/algo/blast/blastinput/blast_input_aux.hpp:64:5: warning: 'auto_ptr<std::__1::basic_ostream<char> >' is deprecated [-Wdeprecated-declarations] auto_ptr<CNcbiOstream> m_FileStream; ^ /usr/include/c++/v1/memory:2079:28: note: 'auto_ptr<std::__1::basic_ostream<char> >' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /usr/include/c++/v1/__config:945:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:934:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/blastinput/demo/blastinput_demo.cpp:70:5: warning: 'auto_ptr<ncbi::CArgDescriptions>' is deprecated [-Wdeprecated-declarations] auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions); ^ /usr/include/c++/v1/memory:2079:28: note: 'auto_ptr<ncbi::CArgDescriptions>' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /usr/include/c++/v1/__config:945:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:934:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ 18 warnings generated. ld: error: /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/lib/libvalid.so: undefined reference to ncbi::CRegexp::CRegexp(ncbi::CTempStringEx, unsigned int) ld: error: /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/lib/libvalid.so: undefined reference to ncbi::CRegexp::~CRegexp() c++: error: linker command failed with exit code 1 (use -v to see invocation) gmake[7]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/Makefile.app:156: blastinput_demo] Error 1 gmake[7]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/blast/blastinput/demo' Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/blastinput/demo/blastinput_demo.cpp. /usr/bin/c++ -stdlib=libc++ -std=gnu++11 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/util/lmdb -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/util/lmdb /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/blastinput/demo/blastinput_demo.cpp -o blastinput_demo.o /usr/bin/c++ -stdlib=libc++ -std=gnu++11 -Wl,-rpath,/usr/local/lib -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -fstack-protector-strong -O blastinput_demo.o -Wl,-rpath-link,/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/lib -L/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/lib -lblastinput -lncbi_xloader_blastdb_rmt -lncbi_xloader_blastdb -lxblastformat -lalign_format -ltaxon1 -lblastdb_format -lgene_info -lxformat -lxcleanup -lgbseq -lmlacli -lmla -lmedlars -lpubmed -lvalid -ltaxon3 -lxalnmgr -lblastxml -lblastxml2 -lxcgi -lxhtml -lentrez2cli -lentrez2 -lproteinkmer -lxblast -lxalgoblastdbindex -lcomposition_adjustment -lxalgodustmask -lxalgowinmask -lseqmasks_io -lseqdb -lblast_services -lxalnmgr -lxobjutil -lxobjread -lvariation -lcreaders -lsubmit -lxnetblastcli -lxnetblast -lblastdb -lscoremat -ltables -llmdb -lncbi_xloader_genbank -lncbi_xreader_id1 -lncbi_xreader_id2 -lncbi_xreader_cache -ld bapi_driver -lncbi_xreader -lxconnect -lid1 -lid2 -lxobjmgr -lgenome_collection -lseqedit -lseqsplit -lsubmit -lseqset -lseq -lseqcode -lsequtil -lpub -lmedline -lbiblio -lgeneral -lxser -lxutil -lxncbi -lxcompress -pthread -lz -lz -lbz2 -lm -pthread -o blastinput_demo gmake[7]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/blast/blastinput/demo' FAILED: src/algo/blast/blastinput/demo/Makefile.blastinput_demo.app gmake[7]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/blast/blastinput/demo' gmake[7]: warning: -jN forced in submake: disabling jobserver mode. /bin/rm -f blastinput_demo .blastinput_demo.stamp gmake[7]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/blast/blastinput/demo' gmake[6]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/build-system/Makefile.meta_l:304: all.nonusr] Error 2 gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/blast/blastinput/demo' gmake[5]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/build-system/Makefile.meta_r:41: all_r.real] Error 5 gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/blast/blastinput' gmake[4]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/build-system/Makefile.meta_r:41: all_r.real] Error 5 gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/blast' gmake[3]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/build-system/Makefile.meta_r:41: all_r.real] Error 5 gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo' gmake[2]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/build-system/Makefile.meta_r:41: all_r.real] Error 5 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build' gmake[1]: *** [Makefile:24: all] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0' ===> 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/ncbi-cxx-toolkit
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