[package - 114i386-quarterly][biology/ncbi-cxx-toolkit] Failed for ncbi-cxx-toolkit-22.0.0 in build
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pkg-fallout at FreeBSD.org
Wed Nov 4 03:22:31 UTC 2020
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 at FreeBSD.org
Last committer: yuri at FreeBSD.org
Ident: $FreeBSD: branches/2020Q4/biology/ncbi-cxx-toolkit/Makefile 549992 2020-09-25 06:57:43Z yuri $
Log URL: http://beefy1.nyi.freebsd.org/data/114i386-quarterly/553708/logs/ncbi-cxx-toolkit-22.0.0.log
Build URL: http://beefy1.nyi.freebsd.org/build.html?mastername=114i386-quarterly&build=553708
Log:
=>> Building biology/ncbi-cxx-toolkit
build started at Sat Oct 31 01:42:10 UTC 2020
port directory: /usr/ports/biology/ncbi-cxx-toolkit
package name: ncbi-cxx-toolkit-22.0.0
building for: FreeBSD 114i386-quarterly-job-10 11.4-RELEASE-p4 FreeBSD 11.4-RELEASE-p4 i386
maintained by: yuri at FreeBSD.org
Makefile ident: $FreeBSD: branches/2020Q4/biology/ncbi-cxx-toolkit/Makefile 549992 2020-09-25 06:57:43Z yuri $
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=======================<phase: check-sanity >============================
===> License PD accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> ncbi-cxx-toolkit-22.0.0 depends on file: /usr/local/sbin/pkg - not found
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[114i386-quarterly-job-10] Installing pkg-1.15.10...
[114i386-quarterly-job-10] Extracting pkg-1.15.10: .......... done
===> ncbi-cxx-toolkit-22.0.0 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of ncbi-cxx-toolkit-22.0.0
===========================================================================
=======================<phase: fetch-depends >============================
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=======================<phase: fetch >============================
===> License PD accepted by the user
===> Fetching all distfiles required by ncbi-cxx-toolkit-22.0.0 for building
===========================================================================
=======================<phase: checksum >============================
===> License PD accepted by the user
===> Fetching all distfiles required by ncbi-cxx-toolkit-22.0.0 for building
=> SHA256 Checksum OK for ncbi_cxx--22_0_0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
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=======================<phase: extract >============================
===> License PD accepted by the user
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===> Extracting for ncbi-cxx-toolkit-22.0.0
=> SHA256 Checksum OK for ncbi_cxx--22_0_0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for ncbi-cxx-toolkit-22.0.0
===> Applying FreeBSD patches for ncbi-cxx-toolkit-22.0.0 from /usr/ports/biology/ncbi-cxx-toolkit/files
===========================================================================
=======================<phase: build-depends >============================
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===> ncbi-cxx-toolkit-22.0.0 depends on package: gmake>=4.3 - found
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[114i386-quarterly-job-10] `-- Extracting libffi-3.3_1: .......... done
<snip>
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/objtools/validator/valid_pub.cpp:36:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objtools/validator/validerror_desc.hpp:40:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objmgr/scope.hpp:51:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objmgr/seq_feat_handle.hpp:43:
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objmgr/impl/annot_collector.hpp:513:5: warning: 'auto_ptr<ncbi::objects::CAnnotMappingCollector>' is deprecated [-Wdeprecated-declarations]
auto_ptr<CAnnotMappingCollector> m_MappingCollector;
^
/usr/include/c++/v1/memory:2130:28: 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:972:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/usr/include/c++/v1/__config:961:48: 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--22_0_0/src/objtools/validator/valid_pub.cpp:36:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objtools/validator/validerror_desc.hpp:40:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objmgr/scope.hpp:51:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objmgr/seq_feat_handle.hpp:43:
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objmgr/impl/annot_collector.hpp:521:5: 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:2130:28: 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:972:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/usr/include/c++/v1/__config:961:48: 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--22_0_0/src/objtools/validator/valid_pub.cpp:36:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objtools/validator/validerror_desc.hpp:40:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objmgr/scope.hpp:51:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objmgr/seq_feat_handle.hpp:43:
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objmgr/impl/annot_collector.hpp:526:13: 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:2130:28: 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:972:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/usr/include/c++/v1/__config:961:48: 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--22_0_0/src/objtools/validator/valid_pub.cpp:36:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objtools/validator/validerror_desc.hpp:43:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objtools/validator/validator.hpp:44:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objects/taxon3/itaxon3.hpp:45:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objects/seqfeat/seqfeat__.hpp:2:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objects/seqfeat/BioSource.hpp:43:
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objects/seqfeat/SubSource.hpp:244:12: warning: 'auto_ptr<ncbi::objects::CLatLonCountryMap>' is deprecated [-Wdeprecated-declarations]
static auto_ptr<CLatLonCountryMap> m_LatLonCountryMap;
^
/usr/include/c++/v1/memory:2130:28: 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:972:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/usr/include/c++/v1/__config:961:48: 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--22_0_0/src/objtools/validator/valid_pub.cpp:36:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objtools/validator/validerror_desc.hpp:43:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objtools/validator/validator.hpp:44:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objects/taxon3/itaxon3.hpp:45:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objects/seqfeat/seqfeat__.hpp:2:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objects/seqfeat/BioSource.hpp:43:
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objects/seqfeat/SubSource.hpp:245:12: warning: 'auto_ptr<ncbi::objects::CLatLonCountryMap>' is deprecated [-Wdeprecated-declarations]
static auto_ptr<CLatLonCountryMap> m_LatLonWaterMap;
^
/usr/include/c++/v1/memory:2130:28: 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:972:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/usr/include/c++/v1/__config:961:48: 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--22_0_0/src/objtools/validator/valid_pub.cpp:36:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objtools/validator/validerror_desc.hpp:43:
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objtools/validator/validator.hpp:121:9: warning: 'auto_ptr<ncbi::objects::validator::CValidator::CCacheImpl>' is deprecated [-Wdeprecated-declarations]
auto_ptr<CCacheImpl> m_impl;
^
/usr/include/c++/v1/memory:2130:28: note: 'auto_ptr<ncbi::objects::validator::CValidator::CCacheImpl>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/usr/include/c++/v1/__config:972:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/usr/include/c++/v1/__config:961:48: 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--22_0_0/src/objtools/validator/valid_pub.cpp:36:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objtools/validator/validerror_desc.hpp:44:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objtools/validator/validerror_imp.hpp:60:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objtools/validator/gene_cache.hpp:63:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objmgr/util/create_defline.hpp:42:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objmgr/util/indexer.hpp:43:
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_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:2130:28: 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:972:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/usr/include/c++/v1/__config:961:48: 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--22_0_0/src/objtools/validator/valid_pub.cpp:36:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objtools/validator/validerror_desc.hpp:44:
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include/objtools/validator/validerror_imp.hpp:591:12: warning: 'auto_ptr<ncbi::CTextFsa>' is deprecated [-Wdeprecated-declarations]
static auto_ptr<CTextFsa> m_SourceQualTags;
^
/usr/include/c++/v1/memory:2130:28: note: 'auto_ptr<ncbi::CTextFsa>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/usr/include/c++/v1/__config:972:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/usr/include/c++/v1/__config:961:48: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/objtools/validator/valid_pub.cpp:944:13: warning: unused function 's_IsPDBInSep' [-Wunused-function]
static bool s_IsPDBInSep(const CSeq_entry& se, CScope& scope)
^
c++: error: unable to execute command: Killed
c++: error: clang frontend command failed due to signal (use -v to see invocation)
FreeBSD clang version 10.0.0 (git at github.com:llvm/llvm-project.git llvmorg-10.0.0-0-gd32170dbd5b)
Target: i386-unknown-freebsd11.4
Thread model: posix
InstalledDir: /usr/bin
c++: note: diagnostic msg: PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace, preprocessed source, and associated run script.
c++: note: diagnostic msg:
********************
PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT:
Preprocessed source(s) and associated run script(s) are located at:
c++: note: diagnostic msg: /tmp/valid_pub-855467.cpp
c++: note: diagnostic msg: /tmp/valid_pub-855467.sh
c++: note: diagnostic msg:
********************
gmake[5]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/Clang-ReleaseMTDLL/build/Makefile.rules:88: valid_pub.o] Error 254
gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/Clang-ReleaseMTDLL/build/objtools/validator'
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/objtools/validator/dup_feats.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/objtools/validator/go_term_validation_and_cleanup.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/objtools/validator/gene_validator.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/objtools/validator/cdregion_validator.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/objtools/validator/single_feat_validator.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/objtools/validator/splice_problems.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/objtools/validator/translation_problems.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/objtools/validator/gene_cache.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/objtools/validator/tax_validation_and_cleanup.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/objtools/validator/feature_match.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/objtools/validator/validator_barcode.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/objtools/validator/validerror_format.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/objtools/validator/valid_cmdargs.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/objtools/validator/utilities.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/objtools/validator/validerror_graph.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/objtools/validator/validerror_feat.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/objtools/validator/validerror_descr.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/objtools/validator/validerror_desc.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/objtools/validator/validerror_bioseqset.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/objtools/validator/validerror_bioseq.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/objtools/validator/validerror_annot.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/objtools/validator/validerror_align.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/objtools/validator/valid_pub.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/objtools/validator/valid_biosource.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/objtools/validator/validatorp.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/objtools/validator/validator.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_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/Clang-ReleaseMTDLL/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/objtools/validator/validator.cpp -o validator.o
/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_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/Clang-ReleaseMTDLL/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/objtools/validator/validatorp.cpp -o validatorp.o
/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_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/Clang-ReleaseMTDLL/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/objtools/validator/valid_biosource.cpp -o valid_biosource.o
/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_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/Clang-ReleaseMTDLL/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/include /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/objtools/validator/valid_pub.cpp -o valid_pub.o
gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/Clang-ReleaseMTDLL/build/objtools/validator'
FAILED: src/objtools/validator/Makefile.validator.lib
gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/Clang-ReleaseMTDLL/build/objtools/validator'
/bin/rm -f libxvalidate.so libxvalidate.so .xvalidate.dep .libxvalidate.so.stamp
/bin/rm -f /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/Clang-ReleaseMTDLL/lib/libxvalidate.so /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/Clang-ReleaseMTDLL/status/.xvalidate.dep
gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/Clang-ReleaseMTDLL/build/objtools/validator'
gmake[4]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/src/build-system/Makefile.meta_l:318: all.nonusr] Error 2
gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0/Clang-ReleaseMTDLL/build/objtools/validator'
gmake[3]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_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--22_0_0/Clang-ReleaseMTDLL/build/objtools'
gmake[2]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_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--22_0_0/Clang-ReleaseMTDLL/build'
gmake[1]: *** [Makefile:24: all] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--22_0_0'
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/ncbi-cxx-toolkit
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