[package - 120armv7-quarterly][biology/ncbi-cxx-toolkit] Failed for ncbi-cxx-toolkit-21.0.0_2 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Thu Oct 31 14:42:18 UTC 2019
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: gerald at 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/516120/logs/ncbi-cxx-toolkit-21.0.0_2.log
Build URL: http://beefy13.nyi.freebsd.org/build.html?mastername=120armv7-quarterly&build=516120
Log:
=>> Building biology/ncbi-cxx-toolkit
build started at Thu Oct 31 12:59:15 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-15 12.0-RELEASE-p11 FreeBSD 12.0-RELEASE-p11 1200086 arm
maintained by: yuri at 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-15] Installing pkg-1.12.0...
[120armv7-quarterly-job-15] 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 -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/splign/splign.cpp -o splign.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 -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/splign/splign_util.cpp -o splign_util.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 -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/splign/splign_exon_trim.cpp -o splign_exon_trim.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 -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/splign/splign_formatter.cpp -o splign_formatter.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 -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/splign/splign_simple.cpp -o splign_simple.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 -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/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 -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/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
/bin/ln -f libxalgoalignsplign.so /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/lib/libxalgoalignsplign.so
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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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