You are receiving this mail as a port that you maintain
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Please investigate the failure and submit a PR to fix
build.

Maintainer:     y...@freebsd.org
Last committer: ger...@freebsd.org
Ident:          $FreeBSD: branches/2019Q4/biology/ncbi-cxx-toolkit/Makefile 
507372 2019-07-26 20:46:53Z gerald $
Log URL:        
http://beefy13.nyi.freebsd.org/data/120armv7-quarterly/514178/logs/ncbi-cxx-toolkit-21.0.0_2.log
Build URL:      
http://beefy13.nyi.freebsd.org/build.html?mastername=120armv7-quarterly&build=514178
Log:

=>> Building biology/ncbi-cxx-toolkit
build started at Thu Oct 10 11:19:07 UTC 2019
port directory: /usr/ports/biology/ncbi-cxx-toolkit
package name: ncbi-cxx-toolkit-21.0.0_2
building for: FreeBSD 120armv7-quarterly-job-03 12.0-RELEASE-p10 FreeBSD 
12.0-RELEASE-p10 1200086 arm
maintained by: y...@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
[120armv7-quarterly-job-03] Installing pkg-1.12.0...
[120armv7-quarterly-job-03] 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  >============================
<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-ReleaseMTDLL/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-ReleaseMTDLL/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.
/nxb-bin/usr/bin/c++  -stdlib=libc++ -std=gnu++11 -c -Wall -Wno-format-y2k  
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 -o splign_util.o 
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/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/splign_exon_trim.cpp
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 -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include  
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 -o splign_simple.o 
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 -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 
/nxb-bin/usr/bin/c++  -stdlib=libc++ -std=gnu++11 -c -Wall -Wno-format-y2k  
-pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing   
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-I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/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
/nxb-bin/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-ReleaseMTDLL/lib
 
-L/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/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-ReleaseMTDLL/lib
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/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/status/.xalgoalignsplign.dep
gmake[6]: Leaving directory 
'/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/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-ReleaseMTDLL/build/algo/align/splign/unit_test'
gmake[7]: Entering directory 
'/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/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-ReleaseMTDLL/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-ReleaseMTDLL/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-ReleaseMTDLL/build/algo/align/splign/unit_test'
gmake[5]: Leaving directory 
'/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/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-ReleaseMTDLL/build/algo/align/contig_assembly'
/usr/local/bin/gmake -f 
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/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-ReleaseMTDLL/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-ReleaseMTDLL/build/algo/align/contig_assembly'
/usr/local/bin/gmake -f 
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/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-ReleaseMTDLL/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.
/nxb-bin/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-ReleaseMTDLL/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
/nxb-bin/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-ReleaseMTDLL/lib
 
-L/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/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-ReleaseMTDLL/lib
/bin/ln -f libxalgocontig_assembly.so 
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/lib/libxalgocontig_assembly.so
/bin/ln -f .xalgocontig_assembly.dep 
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/status/.xalgocontig_assembly.dep
gmake[6]: Leaving directory 
'/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/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-ReleaseMTDLL/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-ReleaseMTDLL/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-ReleaseMTDLL/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.
/nxb-bin/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-ReleaseMTDLL/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 
/nxb-bin/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-ReleaseMTDLL/lib
 
-L/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/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
  -lxser -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-ReleaseMTDLL/bin
/bin/ln -f demo_contig_assembly 
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/bin/demo_contig_assembly
gmake[7]: Leaving directory 
'/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/algo/align/contig_assembly/demo'
gmake[6]: Leaving directory 
'/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/algo/align/contig_assembly/demo'
gmake[5]: Leaving directory 
'/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/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-ReleaseMTDLL/build/algo/align/prosplign'
/usr/local/bin/gmake -f 
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/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-ReleaseMTDLL/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-ReleaseMTDLL/build/algo/align/prosplign'
/usr/local/bin/gmake -f 
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/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-ReleaseMTDLL/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-ReleaseMTDLL/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.
/nxb-bin/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-ReleaseMTDLL/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-ReleaseMTDLL/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-ReleaseMTDLL/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-ReleaseMTDLL/lib/libprosplign.so
 
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/status/.prosplign.dep
gmake[6]: Leaving directory 
'/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/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-ReleaseMTDLL/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-ReleaseMTDLL/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-ReleaseMTDLL/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-ReleaseMTDLL/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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