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Date:      Sat, 28 Dec 2019 21:48:34 GMT
From:      pkg-fallout@FreeBSD.org
To:        pkg-fallout@FreeBSD.org
Subject:   [package - 120arm64-quarterly][biology/ncbi-cxx-toolkit] Failed for ncbi-cxx-toolkit-21.0.0_2 in build
Message-ID:  <201912282148.xBSLmYAt033915@thunderx1.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: gerald@FreeBSD.org
Ident:          $FreeBSD: branches/2019Q4/biology/ncbi-cxx-toolkit/Makefile 507372 2019-07-26 20:46:53Z gerald $
Log URL:        http://thunderx1.nyi.freebsd.org/data/120arm64-quarterly/521041/logs/ncbi-cxx-toolkit-21.0.0_2.log
Build URL:      http://thunderx1.nyi.freebsd.org/build.html?mastername=120arm64-quarterly&build=521041
Log:

=>> Building biology/ncbi-cxx-toolkit
build started at Sat Dec 28 16:17:02 UTC 2019
port directory: /usr/ports/biology/ncbi-cxx-toolkit
package name: ncbi-cxx-toolkit-21.0.0_2
building for: FreeBSD 120arm64-quarterly-job-18 12.0-RELEASE-p12 FreeBSD 12.0-RELEASE-p12 1200086 arm64
maintained by: yuri@FreeBSD.org
Makefile ident:      $FreeBSD: branches/2019Q4/biology/ncbi-cxx-toolkit/Makefile 507372 2019-07-26 20:46:53Z gerald $
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=======================<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
[120arm64-quarterly-job-18] Installing pkg-1.12.0...
[120arm64-quarterly-job-18] 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
[120arm64-quarterly-job-18] Installing gmake-4.2.1_3...
[120arm64-quarterly-job-18] `-- Installing gettext-runtime-0.20.1...
[120arm64-quarterly-job-18] |   `-- Installing indexinfo-0.3.1...
[120arm64-quarterly-job-18] |   `-- Extracting indexinfo-0.3.1: .... done
[120arm64-quarterly-job-18] `-- Extracting gettext-runtime-0.20.1: .......... done
[120arm64-quarterly-job-18] 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
===>   ncbi-cxx-toolkit-21.0.0_2 depends on file: /usr/local/bin/python3.6 - not found
===>   Installing existing package /packages/All/python36-3.6.9_1.txz
[120arm64-quarterly-job-18] Installing python36-3.6.9_1...
[120arm64-quarterly-job-18] `-- Installing libffi-3.2.1_3...
[120arm64-quarterly-job-18] `-- Extracting libffi-3.2.1_3: .......... done
[120arm64-quarterly-job-18] `-- Installing readline-8.0.0...
[120arm64-quarterly-job-18] `-- Extracting readline-8.0.0: .......... done
[120arm64-quarterly-job-18] Extracting python36-3.6.9_1: .......... done
=====
Message from python36-3.6.9_1:
<snip>
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/objects/seq/Seq_literal.hpp:68:5: note: 'IsBridgeable' has been explicitly marked deprecated here
    NCBI_DEPRECATED EBridgeableStatus IsBridgeable() const { return GetBridgeability(); }
    ^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/inc/ncbiconf_unix.h:832:40: note: expanded from macro 'NCBI_DEPRECATED'
#define NCBI_DEPRECATED __attribute__((__deprecated__))
                                       ^
2 warnings generated.
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/compart_matching.cpp:75:18: warning: unused variable 'kUI8_MidWord' [-Wunused-const-variable]
    const Uint8  kUI8_MidWord             (kUI8_LoWord << 16);
                 ^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/compart_matching.cpp:88:18: warning: unused variable 'kSeqDbMemBound' [-Wunused-const-variable]
    const Uint8  kSeqDbMemBound           (512 * 1024 * 1024);
                 ^
2 warnings generated.
gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/align/splign'
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/compart_matching.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/splign_cmdargs.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/splign_simple.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/splign_formatter.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/splign_exon_trim.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/splign_util.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/splign.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  /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/splign.cpp -o splign.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_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  /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/splign_util.cpp -o splign_util.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_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  /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/splign_exon_trim.cpp -o splign_exon_trim.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_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  /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/splign_formatter.cpp -o splign_formatter.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_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  /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/splign_simple.cpp -o splign_simple.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_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  /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/splign_cmdargs.cpp -o splign_cmdargs.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_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  /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/compart_matching.cpp -o compart_matching.o 
/bin/rm -f libxalgoalignsplign.so .libxalgoalignsplign.so.stamp
/usr/bin/c++  -stdlib=libc++ -std=gnu++11  -shared -o libxalgoalignsplign.so -Wl,-rpath,/usr/local/lib -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -fstack-protector-strong -O -fPIC splign.o splign_util.o splign_exon_trim.o splign_formatter.o splign_simple.o splign_cmdargs.o compart_matching.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 -lm -pthread 
/bin/sh /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/scripts/common/impl/if_diff.sh /bin/ln -f libxalgoalignsplign.so /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/lib
/bin/ln -f libxalgoalignsplign.so /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/lib/libxalgoalignsplign.so
/bin/ln -f .xalgoalignsplign.dep /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/status/.xalgoalignsplign.dep
gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/align/splign'
/usr/local/bin/gmake -C unit_test -w  all_r  ||  exit 5
gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/align/splign/unit_test'
gmake[7]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/align/splign/unit_test'
gmake[7]: *** No rule to make target '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/status/Boost.Test.Included.enabled', needed by 'requirements'.  Stop.
gmake[7]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/align/splign/unit_test'
NOTE:  skipping project "unit_test_splign" due to unmet requirements
gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/align/splign/unit_test'
gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/align/splign'
/usr/local/bin/gmake -C contig_assembly -w  all_r  ||  exit 5
gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/align/contig_assembly'
/usr/local/bin/gmake -f /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/Makefile.lib.tmpl srcdir=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/contig_assembly TMPL=xalgocontig_assembly -w export-headers
gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/align/contig_assembly'
gmake[6]: Nothing to be done for 'export-headers'.
gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/align/contig_assembly'
/usr/local/bin/gmake -f /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/Makefile.lib.tmpl srcdir=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/contig_assembly TMPL=xalgocontig_assembly -w all
gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/align/contig_assembly'
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/contig_assembly/contig_assembly.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  /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/contig_assembly/contig_assembly.cpp -o contig_assembly.o 
/bin/rm -f libxalgocontig_assembly.so .libxalgocontig_assembly.so.stamp
/usr/bin/c++  -stdlib=libc++ -std=gnu++11  -shared -o libxalgocontig_assembly.so -Wl,-rpath,/usr/local/lib -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -fstack-protector-strong -O -fPIC contig_assembly.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 -lproteinkmer -lxblast -lxalgoblastdbindex -lcomposition_adjustment -lxalgodustmask -lxalgowinmask -lseqmasks_io -lseqdb -lblast_services -lxalnmgr -lxobjutil -lxobjread -lvariation -lcreaders -lsubmit -lxnetblastcli -lxnetblast -lblastdb -lscoremat -ltables -llmdb -lxalnmgr -pthread -lm -pthread 
/bin/sh /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/scripts/common/impl/if_diff.sh /bin/ln -f libxalgocontig_assembly.so /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/lib
/bin/ln -f libxalgocontig_assembly.so /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/lib/libxalgocontig_assembly.so
/bin/ln -f .xalgocontig_assembly.dep /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/status/.xalgocontig_assembly.dep
gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/align/contig_assembly'
/usr/local/bin/gmake -C demo -w  all_r  ||  exit 5
gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/align/contig_assembly/demo'
/usr/local/bin/gmake -f /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/Makefile.app.tmpl srcdir=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/contig_assembly/demo TMPL=demo_contig_assembly -w all
gmake[7]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/align/contig_assembly/demo'
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/contig_assembly/demo/demo_contig_assembly.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  /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/contig_assembly/demo/demo_contig_assembly.cpp -o demo_contig_assembly.o 
/usr/bin/c++ -stdlib=libc++ -std=gnu++11 -Wl,-rpath,/usr/local/lib -Wl,-rpath,/usr/local/lib -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -fstack-protector-strong -O demo_contig_assembly.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 -lxalgocontig_assembly -lxalgoalignnw -lxalgoseq -lxregexp -lproteinkmer -lxblast -lxalgoblastdbindex -lcomposition_adjustment -lxalgodustmask -lxalgowinmask -lseqmasks_io -lseqdb -lblast_services -lxalnmgr -lxobjutil -lxobjread -lvariation -lcreaders -lsubmit -lxnetblastcli -lxnetblast -lblastdb -lscoremat -ltables -llmdb -ltaxon1 -lncbi_xloader_genbank -lncbi_xreader_id1 -lncbi_xreader_id2 -lncbi_xreader_cache -ldbapi_driver -lncbi_xreader -lxconnect -lid1 -lid2 -lxobjmgr -lgenome_collection -lseqedit -lseqsplit -lsubmit -lseqset -lseq -lseqcode -lsequtil -lpub -lmedline -lbiblio -lgeneral -lx
 ser -lxutil -lxncbi -lxcompress -L/usr/local/lib -lpcre -lz -lbz2 -lz -pthread -lm -pthread -o demo_contig_assembly
/bin/sh /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/scripts/common/impl/if_diff.sh /bin/ln -f demo_contig_assembly /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/bin
/bin/ln -f demo_contig_assembly /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/bin/demo_contig_assembly
gmake[7]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/align/contig_assembly/demo'
gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/align/contig_assembly/demo'
gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/align/contig_assembly'
/usr/local/bin/gmake -C prosplign -w  all_r  ||  exit 5
gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/align/prosplign'
/usr/local/bin/gmake -f /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/Makefile.lib.tmpl srcdir=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign TMPL=prosplign -w export-headers
gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/align/prosplign'
gmake[6]: Nothing to be done for 'export-headers'.
gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/align/prosplign'
/usr/local/bin/gmake -f /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/Makefile.lib.tmpl srcdir=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign TMPL=prosplign -w all
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:839:45: error: call to implicitly-deleted copy constructor of 'ncbi::COneStage'
    virtual COneStage* clone() { return new COneStage(*this); }
                                            ^         ~~~~~
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:836:19: note: copy constructor of 'COneStage' is implicitly deleted because base class 'CProSplign::CImplementation' has a deleted copy constructor
class COneStage : public CProSplign::CImplementation {
                  ^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:832:25: note: copy constructor of 'CImplementation' is implicitly deleted because field 'm_Interrupt' has a deleted copy constructor
    CProSplignInterrupt m_Interrupt;
                        ^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/nucprot.hpp:206:20: note: copy constructor of 'CProSplignInterrupt' is implicitly deleted because field 'm_Interrupt' has a deleted copy constructor
    CAtomicCounter m_Interrupt;
                   ^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/corelib/ncbicntr.hpp:94:20: note: copy constructor of 'CAtomicCounter' is implicitly deleted because field 'm_Value' has no copy constructor
    volatile TData m_Value;  ///< Internal counter value
                   ^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:893:48: error: call to implicitly-deleted copy constructor of 'ncbi::CTwoStageOld'
    virtual CTwoStageOld* clone() { return new CTwoStageOld(*this); }
                                               ^            ~~~~~
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:890:22: note: copy constructor of 'CTwoStageOld' is implicitly deleted because base class 'ncbi::CTwoStage' has a deleted copy constructor
class CTwoStageOld : public CTwoStage {
                     ^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:859:19: note: copy constructor of 'CTwoStage' is implicitly deleted because base class 'CProSplign::CImplementation' has a deleted copy constructor
class CTwoStage : public CProSplign::CImplementation {
                  ^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:832:25: note: copy constructor of 'CImplementation' is implicitly deleted because field 'm_Interrupt' has a deleted copy constructor
    CProSplignInterrupt m_Interrupt;
                        ^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/nucprot.hpp:206:20: note: copy constructor of 'CProSplignInterrupt' is implicitly deleted because field 'm_Interrupt' has a deleted copy constructor
    CAtomicCounter m_Interrupt;
                   ^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/corelib/ncbicntr.hpp:94:20: note: copy constructor of 'CAtomicCounter' is implicitly deleted because field 'm_Value' has no copy constructor
    volatile TData m_Value;  ///< Internal counter value
                   ^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:902:48: error: call to implicitly-deleted copy constructor of 'ncbi::CTwoStageNew'
    virtual CTwoStageNew* clone() { return new CTwoStageNew(*this); }
                                               ^            ~~~~~
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:899:22: note: copy constructor of 'CTwoStageNew' is implicitly deleted because base class 'ncbi::CTwoStage' has a deleted copy constructor
class CTwoStageNew : public CTwoStage {
                     ^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:859:19: note: copy constructor of 'CTwoStage' is implicitly deleted because base class 'CProSplign::CImplementation' has a deleted copy constructor
class CTwoStage : public CProSplign::CImplementation {
                  ^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:832:25: note: copy constructor of 'CImplementation' is implicitly deleted because field 'm_Interrupt' has a deleted copy constructor
    CProSplignInterrupt m_Interrupt;
                        ^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/nucprot.hpp:206:20: note: copy constructor of 'CProSplignInterrupt' is implicitly deleted because field 'm_Interrupt' has a deleted copy constructor
    CAtomicCounter m_Interrupt;
                   ^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/corelib/ncbicntr.hpp:94:20: note: copy constructor of 'CAtomicCounter' is implicitly deleted because field 'm_Value' has no copy constructor
    volatile TData m_Value;  ///< Internal counter value
                   ^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:973:50: error: call to implicitly-deleted copy constructor of 'ncbi::CIntronlessOld'
    virtual CIntronlessOld* clone() { return new CIntronlessOld(*this); }
                                                 ^              ~~~~~
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:970:24: note: copy constructor of 'CIntronlessOld' is implicitly deleted because base class 'ncbi::CIntronless' has a deleted copy constructor
class CIntronlessOld : public CIntronless {
                       ^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:961:21: note: copy constructor of 'CIntronless' is implicitly deleted because base class 'CProSplign::CImplementation' has a deleted copy constructor
class CIntronless : public CProSplign::CImplementation {
                    ^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:832:25: note: copy constructor of 'CImplementation' is implicitly deleted because field 'm_Interrupt' has a deleted copy constructor
    CProSplignInterrupt m_Interrupt;
                        ^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/nucprot.hpp:206:20: note: copy constructor of 'CProSplignInterrupt' is implicitly deleted because field 'm_Interrupt' has a deleted copy constructor
    CAtomicCounter m_Interrupt;
                   ^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/corelib/ncbicntr.hpp:94:20: note: copy constructor of 'CAtomicCounter' is implicitly deleted because field 'm_Value' has no copy constructor
    volatile TData m_Value;  ///< Internal counter value
                   ^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:981:50: error: call to implicitly-deleted copy constructor of 'ncbi::CIntronlessNew'
    virtual CIntronlessNew* clone() { return new CIntronlessNew(*this); }
                                                 ^              ~~~~~
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:978:24: note: copy constructor of 'CIntronlessNew' is implicitly deleted because base class 'ncbi::CIntronless' has a deleted copy constructor
class CIntronlessNew : public CIntronless {
                       ^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:961:21: note: copy constructor of 'CIntronless' is implicitly deleted because base class 'CProSplign::CImplementation' has a deleted copy constructor
class CIntronless : public CProSplign::CImplementation {
                    ^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:832:25: note: copy constructor of 'CImplementation' is implicitly deleted because field 'm_Interrupt' has a deleted copy constructor
    CProSplignInterrupt m_Interrupt;
                        ^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/nucprot.hpp:206:20: note: copy constructor of 'CProSplignInterrupt' is implicitly deleted because field 'm_Interrupt' has a deleted copy constructor
    CAtomicCounter m_Interrupt;
                   ^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/corelib/ncbicntr.hpp:94:20: note: copy constructor of 'CAtomicCounter' is implicitly deleted because field 'm_Value' has no copy constructor
    volatile TData m_Value;  ///< Internal counter value
                   ^
5 errors generated.
gmake[6]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/Makefile.rules:80: prosplign.o] Error 1
gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/align/prosplign'
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/compartments.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/AlignInfo.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/intron.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/nucprot.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/Info.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/AliSeqAlign.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/Ali.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/NSeq.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/PSeq.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/scoring.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.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  /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp -o prosplign.o 
gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/align/prosplign'
FAILED: src/algo/align/prosplign/Makefile.prosplign.lib
gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/align/prosplign'
/bin/rm -f libprosplign.so libprosplign.so .prosplign.dep .libprosplign.so.stamp
/bin/rm -f /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/lib/libprosplign.so /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/status/.prosplign.dep
gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/align/prosplign'
gmake[5]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/build-system/Makefile.meta_l:303: all.nonusr] Error 2
gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/align/prosplign'
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/align'
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'
*** Error code 1

Stop.
make: stopped in /usr/ports/biology/ncbi-cxx-toolkit



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