Skip site navigation (1)Skip section navigation (2)
Date:      Sun, 25 Aug 2019 01:20:47 GMT
From:      pkg-fallout@FreeBSD.org
To:        pkg-fallout@FreeBSD.org
Subject:   [package - 120armv7-quarterly][biology/ncbi-cxx-toolkit] Failed for ncbi-cxx-toolkit-21.0.0_1 in build
Message-ID:  <201908250120.x7P1Kl5J095835@beefy13.nyi.freebsd.org>

next in thread | raw e-mail | index | archive | help

You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.

Maintainer:     yuri@FreeBSD.org
Last committer: gerald@FreeBSD.org
Ident:          $FreeBSD: branches/2019Q3/biology/ncbi-cxx-toolkit/Makefile 487272 2018-12-12 01:35:33Z gerald $
Log URL:        http://beefy13.nyi.freebsd.org/data/120armv7-quarterly/509523/logs/ncbi-cxx-toolkit-21.0.0_1.log
Build URL:      http://beefy13.nyi.freebsd.org/build.html?mastername=120armv7-quarterly&build=509523
Log:

=>> Building biology/ncbi-cxx-toolkit
build started at Sat Aug 24 23:28:42 UTC 2019
port directory: /usr/ports/biology/ncbi-cxx-toolkit
package name: ncbi-cxx-toolkit-21.0.0_1
building for: FreeBSD 120armv7-quarterly-job-11 12.0-RELEASE-p10 FreeBSD 12.0-RELEASE-p10 1200086 arm
maintained by: yuri@FreeBSD.org
Makefile ident:      $FreeBSD: branches/2019Q3/biology/ncbi-cxx-toolkit/Makefile 487272 2018-12-12 01:35:33Z gerald $
Poudriere version: 3.2.8-5-gc81843e5
Host OSVERSION: 1300031
Jail OSVERSION: 1200086
Job Id: 11

---Begin Environment---
SHELL=/bin/csh
UNAME_p=armv7
UNAME_m=arm
ABI_FILE=/usr/lib/crt1.o
OSVERSION=1200086
UNAME_v=FreeBSD 12.0-RELEASE-p10 1200086
UNAME_r=12.0-RELEASE-p10
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
LOCALBASE=/usr/local
QEMU_EMULATING=1
USER=root
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.2.8-5-gc81843e5
MASTERMNT=/usr/local/poudriere/data/.m/120armv7-quarterly/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
PWD=/usr/local/poudriere/data/.m/120armv7-quarterly/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=120armv7-quarterly
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/120armv7-quarterly/ref/.p
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
POUDRIEREPATH=/usr/local/bin/poudriere
---End Environment---

---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=
FLAVOR=
DEPENDS_ARGS=
MAKE_ARGS=
---End Poudriere Port Flags/Env---

---Begin OPTIONS List---
---End OPTIONS List---

--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--

--CONFIGURE_ARGS--
--without-debug --with-dll --without-static --x-libraries=/usr/local/lib --x-includes=/usr/local/include --prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl  PERL_USE_UNSAFE_INC=1 PYTHON="/usr/local/bin/python3.6" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work  HOME=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=262144
--End CONFIGURE_ENV--

--MAKE_ENV--
PERL_USE_UNSAFE_INC=1 OPENSSLBASE=/usr OPENSSLDIR=/etc/ssl OPENSSLINC=/usr/include OPENSSLLIB=/usr/lib XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work  HOME=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local  LOCALBASE=/usr/local  CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe  -fstack-protector-strong -fno-strict-aliasing "  CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS=""  LDFLAGS="  -fstack-protector-strong " LIBS=""  CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing  "  MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install  -s -m 555"  BSD_INSTALL_LIB="install  -s -m 0644"  BSD_INSTALL_SCRIPT="install  -m 555"  BSD_INSTALL_DATA="install  -m 0
 644"  BSD_INSTALL_MAN="install  -m 444"
--End MAKE_ENV--

--PLIST_SUB--
PYTHON_INCLUDEDIR=include/python3.6m  PYTHON_LIBDIR=lib/python3.6  PYTHON_PLATFORM=freebsd12  PYTHON_SITELIBDIR=lib/python3.6/site-packages  PYTHON_SUFFIX=36  PYTHON_VER=3.6  PYTHON_VERSION=python3.6 PYTHON2="@comment " PYTHON3="" OSREL=12.0 PREFIX=%D LOCALBASE=/usr/local  RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.28.2  PERL_VER=5.28  PERL5_MAN1=lib/perl5/site_perl/man/man1  PERL5_MAN3=lib/perl5/site_perl/man/man3  SITE_PERL=lib/perl5/site_perl  SITE_ARCH=lib/perl5/site_perl/mach/5.28 DOCSDIR="share/doc/ncbi-cxx-toolkit"  EXAMPLESDIR="share/examples/ncbi-cxx-toolkit"  DATADIR="share/ncbi-cxx-toolkit"  WWWDIR="www/ncbi-cxx-toolkit"  ETCDIR="etc/ncbi-cxx-toolkit"
--End PLIST_SUB--

--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local  DATADIR=/usr/local/share/ncbi-cxx-toolkit DOCSDIR=/usr/local/share/doc/ncbi-cxx-toolkit EXAMPLESDIR=/usr/local/share/examples/ncbi-cxx-toolkit  WWWDIR=/usr/local/www/ncbi-cxx-toolkit ETCDIR=/usr/local/etc/ncbi-cxx-toolkit
--End SUB_LIST--

---Begin make.conf---
.sinclude "/etc/make.nxb.conf"
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
MACHINE=arm
MACHINE_ARCH=armv7
ARCH=${MACHINE_ARCH}
#### /usr/local/etc/poudriere.d/make.conf ####
# XXX: We really need this but cannot use it while 'make checksum' does not
# try the next mirror on checksum failure.  It currently retries the same
# failed mirror and then fails rather then trying another.  It *does*
# try the next if the size is mismatched though.
#MASTER_SITE_FREEBSD=yes
# Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs
MAKE_JOBS_NUMBER=2

# stable/10 includes src.conf too late but make.conf is in sys.mk
.if ${.CURDIR:M/poudriere/jails/10*/usr/src/usr.bin/xlint*}
# Disable build of llib now that head no longer has lint(1)
LINT=	true
.endif
#### /usr/ports/Mk/Scripts/ports_env.sh ####
_CCVERSION_9d218390=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: armv7-unknown-freebsd12.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin
_ALTCCVERSION_9d218390=none
_CXXINTERNAL_9c45a5b1=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: armv7-unknown-freebsd12.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin "/nxb-bin/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o"
CC_OUTPUT_9d218390_58173849=yes
CC_OUTPUT_9d218390_9bdba57c=yes
CC_OUTPUT_9d218390_6a4fe7f5=yes
CC_OUTPUT_9d218390_6bcac02b=yes
CC_OUTPUT_9d218390_67d20829=yes
CC_OUTPUT_9d218390_bfa62e83=yes
CC_OUTPUT_9d218390_f0b4d593=yes
CC_OUTPUT_9d218390_308abb44=yes
CC_OUTPUT_9d218390_f00456e5=yes
CC_OUTPUT_9d218390_65ad290d=yes
CC_OUTPUT_9d218390_f2776b26=yes
CC_OUTPUT_9d218390_b2657cc3=yes
CC_OUTPUT_9d218390_380987f7=yes
CC_OUTPUT_9d218390_160933ec=yes
CC_OUTPUT_9d218390_fb62803b=yes
_OBJC_CCVERSION_9d218390=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: armv7-unknown-freebsd12.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin
_OBJC_ALTCCVERSION_9d218390=none
ARCH=armv7
OPSYS=FreeBSD
_OSRELEASE=12.0-RELEASE-p10
OSREL=12.0
OSVERSION=1200086
PYTHONBASE=/usr/local
CONFIGURE_MAX_CMD_LEN=262144
HAVE_PORTS_ENV=1
#### Misc Poudriere ####
GID=0
UID=0
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
---Begin make.nxb.conf---
CC=/nxb-bin/usr/bin/cc
CPP=/nxb-bin/usr/bin/cpp
CXX=/nxb-bin/usr/bin/c++
AS=/nxb-bin/usr/bin/as
NM=/nxb-bin/usr/bin/nm
LD=/nxb-bin/usr/bin/ld
OBJCOPY=/nxb-bin/usr/bin/objcopy
SIZE=/nxb-bin/usr/bin/size
STRIPBIN=/nxb-bin/usr/bin/strip
SED=/nxb-bin/usr/bin/sed
RANLIB=/nxb-bin/usr/bin/ranlib
YACC=/nxb-bin/usr/bin/yacc
MAKE=/nxb-bin/usr/bin/make
STRINGS=/nxb-bin/usr/bin/strings
AWK=/nxb-bin/usr/bin/awk
FLEX=/nxb-bin/usr/bin/flex
---End make.nxb.conf---
--Resource limits--
cpu time               (seconds, -t)  unlimited
file size           (512-blocks, -f)  unlimited
data seg size           (kbytes, -d)  33554432
stack size              (kbytes, -s)  524288
core file size      (512-blocks, -c)  unlimited
max memory size         (kbytes, -m)  unlimited
locked memory           (kbytes, -l)  unlimited
max user processes              (-u)  89999
open files                      (-n)  1024
virtual mem size        (kbytes, -v)  unlimited
swap limit              (kbytes, -w)  unlimited
socket buffer size       (bytes, -b)  unlimited
pseudo-terminals                (-p)  unlimited
kqueues                         (-k)  unlimited
umtx shared locks               (-o)  unlimited
--End resource limits--
=======================<phase: check-sanity   >============================
===>  License PD accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   ncbi-cxx-toolkit-21.0.0_1 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.11.1.txz
[120armv7-quarterly-job-11] Installing pkg-1.11.1...
[120armv7-quarterly-job-11] Extracting pkg-1.11.1: .......... done
===>   ncbi-cxx-toolkit-21.0.0_1 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of ncbi-cxx-toolkit-21.0.0_1
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License PD accepted by the user
===> Fetching all distfiles required by ncbi-cxx-toolkit-21.0.0_1 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License PD accepted by the user
===> Fetching all distfiles required by ncbi-cxx-toolkit-21.0.0_1 for building
=> SHA256 Checksum OK for ncbi_cxx--21_0_0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
<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
/bin/ln -f .xalgoalignsplign.dep /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



Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?201908250120.x7P1Kl5J095835>