[package - 121amd64-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
Sat May 2 05:42:16 UTC 2020
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: yuri at FreeBSD.org
Last committer: zeising at FreeBSD.org
Ident: $FreeBSD: branches/2020Q2/biology/ncbi-cxx-toolkit/Makefile 516742 2019-11-04 21:08:20Z zeising $
Log URL: http://beefy2.nyi.freebsd.org/data/121amd64-quarterly/533598/logs/ncbi-cxx-toolkit-21.0.0_2.log
Build URL: http://beefy2.nyi.freebsd.org/build.html?mastername=121amd64-quarterly&build=533598
Log:
=>> Building biology/ncbi-cxx-toolkit
build started at Sat May 2 03:44:45 UTC 2020
port directory: /usr/ports/biology/ncbi-cxx-toolkit
package name: ncbi-cxx-toolkit-21.0.0_2
building for: FreeBSD 121amd64-quarterly-job-09 12.1-RELEASE-p4 FreeBSD 12.1-RELEASE-p4 amd64
maintained by: yuri at FreeBSD.org
Makefile ident: $FreeBSD: branches/2020Q2/biology/ncbi-cxx-toolkit/Makefile 516742 2019-11-04 21:08:20Z zeising $
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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-1.13.2.txz
[121amd64-quarterly-job-09] Installing pkg-1.13.2...
[121amd64-quarterly-job-09] Extracting pkg-1.13.2: .......... 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
[121amd64-quarterly-job-09] Installing gmake-4.2.1_3...
[121amd64-quarterly-job-09] `-- Installing gettext-runtime-0.20.1...
[121amd64-quarterly-job-09] | `-- Installing indexinfo-0.3.1...
[121amd64-quarterly-job-09] | `-- Extracting indexinfo-0.3.1: .... done
[121amd64-quarterly-job-09] `-- Extracting gettext-runtime-0.20.1: .......... done
[121amd64-quarterly-job-09] 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/python3.7 - not found
===> Installing existing package /packages/All/python37-3.7.7.txz
[121amd64-quarterly-job-09] Installing python37-3.7.7...
[121amd64-quarterly-job-09] `-- Installing libffi-3.2.1_3...
[121amd64-quarterly-job-09] `-- Extracting libffi-3.2.1_3: .......... done
[121amd64-quarterly-job-09] `-- Installing readline-8.0.4...
[121amd64-quarterly-job-09] `-- Extracting readline-8.0.4: .......... done
[121amd64-quarterly-job-09] Extracting python37-3.7.7: .......... done
=====
<snip>
/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/blast/format TMPL=xblastformat -w export-headers
gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/blast/format'
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/blast/format'
/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/blast/format TMPL=xblastformat -w all
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/format/blastxml_format.cpp:501:51: warning: 'CObjectOStreamXml' is deprecated [-Wdeprecated-declarations]
auto_ptr<CObjectOStreamXml> xml_one_hit_os (new CObjectOStreamXml (one_hit_os,false));
^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/serial/objostrxml.hpp:66:5: note: 'CObjectOStreamXml' has been explicitly marked deprecated here
NCBI_DEPRECATED_CTOR(CObjectOStreamXml(CNcbiOstream& out, bool deleteOut));
^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/corelib/ncbimisc.hpp:1118:43: note: expanded from macro 'NCBI_DEPRECATED_CTOR'
# define NCBI_DEPRECATED_CTOR(decl) decl NCBI_DEPRECATED
^
/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__))
^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/format/blastxml_format.cpp:785:50: warning: 'CObjectOStreamXml' is deprecated [-Wdeprecated-declarations]
auto_ptr<CObjectOStreamXml> xml_one_iter_os(new CObjectOStreamXml (one_iter_ss_os,false));
^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/serial/objostrxml.hpp:66:5: note: 'CObjectOStreamXml' has been explicitly marked deprecated here
NCBI_DEPRECATED_CTOR(CObjectOStreamXml(CNcbiOstream& out, bool deleteOut));
^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/corelib/ncbimisc.hpp:1118:43: note: expanded from macro 'NCBI_DEPRECATED_CTOR'
# define NCBI_DEPRECATED_CTOR(decl) decl NCBI_DEPRECATED
^
/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.
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/format/blast_format.cpp:49:
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/algo/blast/format/data4xmlformat.hpp:155:23: warning: 'GetFilterString' is deprecated [-Wdeprecated-declarations]
m_Options.GetFilterString(); /* NCBI_FAKE_WARNING */
^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/algo/blast/api/blast_options.hpp:171:5: note: 'GetFilterString' has been explicitly marked deprecated here
NCBI_DEPRECATED char* GetFilterString() const;
^
/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__))
^
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/format/blast_format.cpp:51:
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/algo/blast/format/data4xml2format.hpp:140:24: warning: 'GetFilterString' is deprecated [-Wdeprecated-declarations]
m_Options->GetFilterString(); /* NCBI_FAKE_WARNING */
^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/algo/blast/api/blast_options.hpp:171:5: note: 'GetFilterString' has been explicitly marked deprecated here
NCBI_DEPRECATED char* GetFilterString() const;
^
/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.
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/format/data4xmlformat.cpp:37:
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/algo/blast/format/data4xmlformat.hpp:155:23: warning: 'GetFilterString' is deprecated [-Wdeprecated-declarations]
m_Options.GetFilterString(); /* NCBI_FAKE_WARNING */
^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/algo/blast/api/blast_options.hpp:171:5: note: 'GetFilterString' has been explicitly marked deprecated here
NCBI_DEPRECATED char* GetFilterString() const;
^
/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__))
^
1 warning generated.
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/format/data4xml2format.cpp:36:
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/algo/blast/format/data4xml2format.hpp:140:24: warning: 'GetFilterString' is deprecated [-Wdeprecated-declarations]
m_Options->GetFilterString(); /* NCBI_FAKE_WARNING */
^
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/algo/blast/api/blast_options.hpp:171:5: note: 'GetFilterString' has been explicitly marked deprecated here
NCBI_DEPRECATED char* GetFilterString() const;
^
/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__))
^
1 warning generated.
gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/blast/format'
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/format/blast_async_format.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/format/sam.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/format/vecscreen_run.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/format/build_archive.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/format/data4xml2format.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/format/data4xmlformat.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/format/blast_format.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/format/blastxml2_format.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/format/blastxml_format.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/format/blastfmtutil.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 -DNCBI_MODULE=BLASTFORMAT -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/blast/format/blastfmtutil.cpp -o blastfmtutil.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 -DNCBI_MODULE=BLASTFORMAT -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/blast/format/blastxml_format.cpp -o blastxml_format.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 -DNCBI_MODULE=BLASTFORMAT -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/blast/format/blastxml2_format.cpp -o blastxml2_format.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 -DNCBI_MODULE=BLASTFORMAT -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/blast/format/blast_format.cpp -o blast_format.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 -DNCBI_MODULE=BLASTFORMAT -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/blast/format/data4xmlformat.cpp -o data4xmlformat.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 -DNCBI_MODULE=BLASTFORMAT -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/blast/format/data4xml2format.cpp -o data4xml2format.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 -DNCBI_MODULE=BLASTFORMAT -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/blast/format/build_archive.cpp -o build_archive.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 -DNCBI_MODULE=BLASTFORMAT -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/blast/format/vecscreen_run.cpp -o vecscreen_run.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 -DNCBI_MODULE=BLASTFORMAT -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/blast/format/sam.cpp -o sam.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 -DNCBI_MODULE=BLASTFORMAT -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/blast/format/blast_async_format.cpp -o blast_async_format.o
/bin/rm -f libxblastformat.so .libxblastformat.so.stamp
/usr/bin/c++ -stdlib=libc++ -std=gnu++11 -shared -o libxblastformat.so -Wl,-rpath,/usr/local/lib -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -fstack-protector-strong -O -fPIC blastfmtutil.o blastxml_format.o blastxml2_format.o blast_format.o data4xmlformat.o data4xml2format.o build_archive.o vecscreen_run.o sam.o blast_async_format.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 -lalign_format -lblastxml -lblastxml2 -lxhtml -lxcgi -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 libxblastformat.so /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/lib
/bin/ln -f libxblastformat.so /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/lib/libxblastformat.so
/bin/ln -f .xblastformat.dep /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/status/.xblastformat.dep
gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/blast/format'
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/usr/local/bin/gmake -C blastinput -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/blast/blastinput'
/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/blast/blastinput TMPL=blastinput -w export-headers
gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/blast/blastinput'
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gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/blast/blastinput'
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/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/blast/blastinput TMPL=blastinput -w all
gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/blast/blastinput'
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/blastinput/blast_asn1_input.cpp.
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Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/blastinput/igblastp_args.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/blastinput/igblastn_args.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/blastinput/rpstblastn_args.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/blastinput/rpsblast_args.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/blastinput/psiblast_args.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/blastinput/tblastx_args.cpp.
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Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/blastinput/blastx_args.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/blastinput/rmblastn_args.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/blastinput/blastn_args.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/blastinput/blastp_args.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/blastinput/blast_input_aux.cpp.
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/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 -DNCBI_MODULE=BLAST -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/blast/blastinput/blast_input.cpp -o blast_input.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 -DNCBI_MODULE=BLAST -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/blast/blastinput/blast_fasta_input.cpp -o blast_fasta_input.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 -DNCBI_MODULE=BLAST -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/blast/blastinput/blast_scope_src.cpp -o blast_scope_src.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 -DNCBI_MODULE=BLAST -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/blast/blastinput/blast_args.cpp -o blast_args.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 -DNCBI_MODULE=BLAST -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/blast/blastinput/cmdline_flags.cpp -o cmdline_flags.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 -DNCBI_MODULE=BLAST -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/blast/blastinput/blast_input_aux.cpp -o blast_input_aux.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 -DNCBI_MODULE=BLAST -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/blast/blastinput/blastp_args.cpp -o blastp_args.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 -DNCBI_MODULE=BLAST -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/blast/blastinput/blastn_args.cpp -o blastn_args.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 -DNCBI_MODULE=BLAST -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/blast/blastinput/rmblastn_args.cpp -o rmblastn_args.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 -DNCBI_MODULE=BLAST -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/blast/blastinput/blastx_args.cpp -o blastx_args.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 -DNCBI_MODULE=BLAST -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/blast/blastinput/tblastn_args.cpp -o tblastn_args.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 -DNCBI_MODULE=BLAST -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/blast/blastinput/tblastx_args.cpp -o tblastx_args.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 -DNCBI_MODULE=BLAST -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/blast/blastinput/psiblast_args.cpp -o psiblast_args.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 -DNCBI_MODULE=BLAST -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/blast/blastinput/rpsblast_args.cpp -o rpsblast_args.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 -DNCBI_MODULE=BLAST -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/blast/blastinput/rpstblastn_args.cpp -o rpstblastn_args.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 -DNCBI_MODULE=BLAST -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/blast/blastinput/igblastn_args.cpp -o igblastn_args.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 -DNCBI_MODULE=BLAST -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/blast/blastinput/igblastp_args.cpp -o igblastp_args.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 -DNCBI_MODULE=BLAST -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/blast/blastinput/deltablast_args.cpp -o deltablast_args.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 -DNCBI_MODULE=BLAST -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/blast/blastinput/magicblast_args.cpp -o magicblast_args.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 -DNCBI_MODULE=BLAST -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/blast/blastinput/kblastp_args.cpp -o kblastp_args.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 -DNCBI_MODULE=BLAST -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/blast/blastinput/blast_asn1_input.cpp -o blast_asn1_input.o
/bin/rm -f libblastinput.so .libblastinput.so.stamp
/usr/bin/c++ -stdlib=libc++ -std=gnu++11 -shared -o libblastinput.so -Wl,-rpath,/usr/local/lib -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -fstack-protector-strong -O -fPIC blast_input.o blast_fasta_input.o blast_scope_src.o blast_args.o cmdline_flags.o blast_input_aux.o blastp_args.o blastn_args.o rmblastn_args.o blastx_args.o tblastn_args.o tblastx_args.o psiblast_args.o rpsblast_args.o rpstblastn_args.o igblastn_args.o igblastp_args.o deltablast_args.o magicblast_args.o kblastp_args.o blast_asn1_input.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 -lxblast -lalign_format -lncbi_xloader_blastdb_rmt -lncbi_xloader_blastdb -lseqdb -lxobjread -lvariation -lcreaders -lsubmit -lncbi_xloader_genbank -lncbi_xreader_id1 -lncbi_xreader_id2 -lncbi_xreader_cache -ldbapi_driver -lncbi_xreader -lxconnect -lid1 -lid2 -lxobjmgr -lgeno
me_collection -lseqedit -lseqsplit -lsubmit -lseqset -lseq -lseqcode -lsequtil -lpub -lmedline -lbiblio -lgeneral -lxser -lxutil -lxcompress -lxutil -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 libblastinput.so /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/lib
/bin/ln -f libblastinput.so /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/lib/libblastinput.so
/bin/ln -f .blastinput.dep /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/status/.blastinput.dep
gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/blast/blastinput'
/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/blast/blastinput/unit_test'
NOTE: Skipping project unit_test due to unmet requirements:
Boost.Test.Included
gmake[7]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/blast/blastinput/unit_test'
gmake[7]: Nothing to be done for 'mark-as-disabled_r'.
gmake[7]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/blast/blastinput/unit_test'
gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/blast/blastinput/unit_test'
/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/blast/blastinput/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/blast/blastinput/demo TMPL=blastinput_demo -w all
ld: error: /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/lib/libvalid.so: undefined reference to ncbi::CRegexp::CRegexp(ncbi::CTempStringEx, unsigned int)
ld: error: /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/lib/libvalid.so: undefined reference to ncbi::CRegexp::~CRegexp()
c++: error: linker command failed with exit code 1 (use -v to see invocation)
gmake[7]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/Makefile.app:156: blastinput_demo] Error 1
gmake[7]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/blast/blastinput/demo'
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/blastinput/demo/blastinput_demo.cpp.
/usr/bin/c++ -stdlib=libc++ -std=gnu++11 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/util/lmdb -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/util/lmdb /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/blast/blastinput/demo/blastinput_demo.cpp -o blastinput_demo.o
/usr/bin/c++ -stdlib=libc++ -std=gnu++11 -Wl,-rpath,/usr/local/lib -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -fstack-protector-strong -O blastinput_demo.o -Wl,-rpath-link,/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/lib -L/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/lib -lblastinput -lncbi_xloader_blastdb_rmt -lncbi_xloader_blastdb -lxblastformat -lalign_format -ltaxon1 -lblastdb_format -lgene_info -lxformat -lxcleanup -lgbseq -lmlacli -lmla -lmedlars -lpubmed -lvalid -ltaxon3 -lxalnmgr -lblastxml -lblastxml2 -lxcgi -lxhtml -lentrez2cli -lentrez2 -lproteinkmer -lxblast -lxalgoblastdbindex -lcomposition_adjustment -lxalgodustmask -lxalgowinmask -lseqmasks_io -lseqdb -lblast_services -lxalnmgr -lxobjutil -lxobjread -lvariation -lcreaders -lsubmit -lxnetblastcli -lxnetblast -lblastdb -lscoremat -ltables -llmdb -lncbi_xloader_genbank -lncbi_xreader_id1 -lncbi_xreader_id2 -lncbi_xreader_cache -ld
bapi_driver -lncbi_xreader -lxconnect -lid1 -lid2 -lxobjmgr -lgenome_collection -lseqedit -lseqsplit -lsubmit -lseqset -lseq -lseqcode -lsequtil -lpub -lmedline -lbiblio -lgeneral -lxser -lxutil -lxncbi -lxcompress -pthread -lz -lz -lbz2 -lm -pthread -o blastinput_demo
gmake[7]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/blast/blastinput/demo'
FAILED: src/algo/blast/blastinput/demo/Makefile.blastinput_demo.app
gmake[7]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/blast/blastinput/demo'
/bin/rm -f blastinput_demo .blastinput_demo.stamp
gmake[7]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/blast/blastinput/demo'
gmake[6]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/build-system/Makefile.meta_l:304: all.nonusr] Error 2
gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/blast/blastinput/demo'
gmake[5]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/build-system/Makefile.meta_r:41: all_r.real] Error 5
gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/blast/blastinput'
gmake[4]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/build-system/Makefile.meta_r:41: all_r.real] Error 5
gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo/blast'
gmake[3]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/build-system/Makefile.meta_r:41: all_r.real] Error 5
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build/algo'
gmake[2]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/build-system/Makefile.meta_r:41: all_r.real] Error 5
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL64/build'
gmake[1]: *** [Makefile:24: all] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0'
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/ncbi-cxx-toolkit
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