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Date:      Sun, 27 Oct 2019 04:35:15 GMT
From:      pkg-fallout@FreeBSD.org
To:        pkg-fallout@FreeBSD.org
Subject:   [package - head-arm64-default][biology/dsr-pdb] Failed for dsr-pdb-1.0.3_4 in build
Message-ID:  <201910270435.x9R4ZF7c056976@thunderx1.nyi.freebsd.org>

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

Maintainer:     yuri@FreeBSD.org
Last committer: jbeich@FreeBSD.org
Ident:          $FreeBSD: head/biology/dsr-pdb/Makefile 509290 2019-08-19 15:35:27Z jbeich $
Log URL:        http://thunderx1.nyi.freebsd.org/data/head-arm64-default/p514745_s353743/logs/dsr-pdb-1.0.3_4.log
Build URL:      http://thunderx1.nyi.freebsd.org/build.html?mastername=head-arm64-default&build=p514745_s353743
Log:

=>> Building biology/dsr-pdb
build started at Sun Oct 27 04:31:19 UTC 2019
port directory: /usr/ports/biology/dsr-pdb
package name: dsr-pdb-1.0.3_4
building for: FreeBSD head-arm64-default-job-16 13.0-CURRENT FreeBSD 13.0-CURRENT 1300053 arm64
maintained by: yuri@FreeBSD.org
Makefile ident:      $FreeBSD: head/biology/dsr-pdb/Makefile 509290 2019-08-19 15:35:27Z jbeich $
Poudriere version: 3.2.8-5-gc81843e5
Host OSVERSION: 1300002
Jail OSVERSION: 1300053
Job Id: 16




!!! Jail is newer than host. (Jail: 1300053, Host: 1300002) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



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LIBEXECPREFIX=/usr/local/libexec/poudriere
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POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
PWD=/usr/local/poudriere/data/.m/head-arm64-default/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
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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--
--prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/dsr-pdb/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/dsr-pdb/work  HOME=/wrkdirs/usr/ports/biology/dsr-pdb/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/dsr-pdb/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=262144
--End CONFIGURE_ENV--

--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/dsr-pdb/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/dsr-pdb/work  HOME=/wrkdirs/usr/ports/biology/dsr-pdb/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/dsr-pdb/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="cc" CFLAGS="-O2 -pipe  -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing "  CPP="cpp" CPPFLAGS="-isystem /usr/local/include"  LDFLAGS=" -fstack-protector-strong -L/usr/local/lib " LIBS=""  CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -fPIC --std=c++11 -isystem /usr/local/include "  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 0644"  BSD_INSTALL_MAN="install  -m 444"
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--End PLIST_SUB--

--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local  DATADIR=/usr/local/share/dsr-pdb DOCSDIR=/usr/local/share/doc/dsr-pdb EXAMPLESDIR=/usr/local/share/examples/dsr-pdb  WWWDIR=/usr/local/www/dsr-pdb ETCDIR=/usr/local/etc/dsr-pdb
--End SUB_LIST--

---Begin make.conf---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
#### /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
#### /usr/ports/Mk/Scripts/ports_env.sh ####
_CCVERSION_921dbbb2=FreeBSD clang version 9.0.0 (tags/RELEASE_900/final 372316) (based on LLVM 9.0.0) Target: aarch64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin
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CC_OUTPUT_921dbbb2_58173849=yes
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CC_OUTPUT_921dbbb2_67d20829=yes
CC_OUTPUT_921dbbb2_bfa62e83=yes
CC_OUTPUT_921dbbb2_f0b4d593=yes
CC_OUTPUT_921dbbb2_308abb44=yes
CC_OUTPUT_921dbbb2_f00456e5=yes
CC_OUTPUT_921dbbb2_65ad290d=yes
CC_OUTPUT_921dbbb2_f2776b26=yes
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CC_OUTPUT_921dbbb2_380987f7=yes
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HAVE_PORTS_ENV=1
#### Misc Poudriere ####
GID=0
UID=0
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
--Resource limits--
cpu time               (seconds, -t)  unlimited
file size           (512-blocks, -f)  unlimited
data seg size           (kbytes, -d)  1048576
stack size              (kbytes, -s)  1048576
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 LGPL21 accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   dsr-pdb-1.0.3_4 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.12.0.txz
[head-arm64-default-job-16] Installing pkg-1.12.0...
[head-arm64-default-job-16] Extracting pkg-1.12.0: .......... done
===>   dsr-pdb-1.0.3_4 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of dsr-pdb-1.0.3_4
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License LGPL21 accepted by the user
===> Fetching all distfiles required by dsr-pdb-1.0.3_4 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License LGPL21 accepted by the user
===> Fetching all distfiles required by dsr-pdb-1.0.3_4 for building
=> SHA256 Checksum OK for dsr-pdb-1.0.3/dsr-pdb.tgz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>  License LGPL21 accepted by the user
===> Fetching all distfiles required by dsr-pdb-1.0.3_4 for building
===>  Extracting for dsr-pdb-1.0.3_4
=> SHA256 Checksum OK for dsr-pdb-1.0.3/dsr-pdb.tgz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for dsr-pdb-1.0.3_4
===>  Applying FreeBSD patches for dsr-pdb-1.0.3_4
===========================================================================
=======================<phase: build-depends  >============================
===>   dsr-pdb-1.0.3_4 depends on executable: gmake - not found
===>   Installing existing package /packages/All/gmake-4.2.1_3.txz
[head-arm64-default-job-16] Installing gmake-4.2.1_3...
[head-arm64-default-job-16] `-- Installing gettext-runtime-0.20.1...
[head-arm64-default-job-16] |   `-- Installing indexinfo-0.3.1...
[head-arm64-default-job-16] |   `-- Extracting indexinfo-0.3.1: .... done
[head-arm64-default-job-16] `-- Extracting gettext-runtime-0.20.1: .......... done
[head-arm64-default-job-16] Extracting gmake-4.2.1_3: .......... done
===>   dsr-pdb-1.0.3_4 depends on executable: gmake - found
===>   Returning to build of dsr-pdb-1.0.3_4
<snip>
checking for f90... no
checking for xlf90... no
checking for pgf90... no
checking for epcf90... no
checking for f95... no
checking for fort... no
checking for xlf95... no
checking for ifc... no
checking for efc... no
checking for pgf95... no
checking for lf95... no
checking for gfortran... no
checking whether we are using the GNU Fortran 77 compiler... no
checking whether  accepts -g... no
checking the maximum length of command line arguments... (cached) 262144
checking command to parse /usr/bin/nm output from cc object... ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip... strip
checking if cc static flag  works... yes
checking if cc supports -fno-rtti -fno-exceptions... yes
checking for cc option to produce PIC... -fPIC
checking if cc PIC flag -fPIC works... yes
checking if cc supports -c -o file.o... yes
checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... freebsd13.0 ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
configure: creating libtool
appending configuration tag "CXX" to libtool
checking for ld used by c++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes
checking for c++ option to produce PIC... -fPIC
checking if c++ PIC flag -fPIC works... yes
checking if c++ supports -c -o file.o... yes
checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... freebsd13.0 ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
appending configuration tag "F77" to libtool
checking CGAL_MAKEFILE... no
checking CGAL/Exact_predicates_inexact_constructions_kernel.h usability... no
checking CGAL/Exact_predicates_inexact_constructions_kernel.h presence... no
checking for CGAL/Exact_predicates_inexact_constructions_kernel.h... no
checking CGAL... no
checking boost/program_options.hpp usability... no
checking boost/program_options.hpp presence... yes
configure: WARNING: boost/program_options.hpp: present but cannot be compiled
configure: WARNING: boost/program_options.hpp:     check for missing prerequisite headers?
configure: WARNING: boost/program_options.hpp: see the Autoconf documentation
configure: WARNING: boost/program_options.hpp:     section "Present But Cannot Be Compiled"
configure: WARNING: boost/program_options.hpp: proceeding with the preprocessor's result
configure: WARNING: boost/program_options.hpp: in the future, the compiler will take precedence
configure: WARNING:     ## -------------------------------------------- ##
configure: WARNING:     ## Report this to drussel@graphics.stanford.edu ##
configure: WARNING:     ## -------------------------------------------- ##
checking for boost/program_options.hpp... yes
checking for main in -lboost_program_options... yes
checking for main in -lMagick++... no
checking Magick++.h usability... no
checking Magick++.h presence... no
checking for Magick++.h... no
configure: creating ./config.status
config.status: creating Makefile
config.status: creating doc/Makefile
config.status: creating doc/html/Makefile
config.status: creating include/Makefile
config.status: creating include/dsrpdb/Makefile
config.status: creating include/dsrpdb_internal/Makefile
config.status: creating include/tnt/Makefile
config.status: creating lib/Makefile
config.status: creating test/Makefile
config.status: creating tools/Makefile
config.status: creating config.h
config.status: executing depfiles commands
ImageMagick++ not found, writing of images will be disabled.
===========================================================================
=======================<phase: build          >============================
===>  Building for dsr-pdb-1.0.3_4
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3'
gmake  all-recursive
gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3'
Making all in lib
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/lib'
if /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I. -I..  -I../include -pg -isystem /usr/local/include  -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -fPIC --std=c++11 -isystem /usr/local/include  -MT Residue.lo -MD -MP -MF ".deps/Residue.Tpo" -c -o Residue.lo Residue.cc; \
then mv -f ".deps/Residue.Tpo" ".deps/Residue.Plo"; else rm -f ".deps/Residue.Tpo"; exit 1; fi
mkdir .libs
 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Residue.lo -MD -MP -MF .deps/Residue.Tpo -c Residue.cc  -fPIC -DPIC -o .libs/Residue.o
 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Residue.lo -MD -MP -MF .deps/Residue.Tpo -c Residue.cc -o Residue.o >/dev/null 2>&1
if /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I. -I..  -I../include -pg -isystem /usr/local/include  -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -fPIC --std=c++11 -isystem /usr/local/include  -MT Protein.lo -MD -MP -MF ".deps/Protein.Tpo" -c -o Protein.lo Protein.cc; \
then mv -f ".deps/Protein.Tpo" ".deps/Protein.Plo"; else rm -f ".deps/Protein.Tpo"; exit 1; fi
 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Protein.lo -MD -MP -MF .deps/Protein.Tpo -c Protein.cc  -fPIC -DPIC -o .libs/Protein.o
 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Protein.lo -MD -MP -MF .deps/Protein.Tpo -c Protein.cc -o Protein.o >/dev/null 2>&1
if /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I. -I..  -I../include -pg -isystem /usr/local/include  -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -fPIC --std=c++11 -isystem /usr/local/include  -MT Residue_data.lo -MD -MP -MF ".deps/Residue_data.Tpo" -c -o Residue_data.lo Residue_data.cc; \
then mv -f ".deps/Residue_data.Tpo" ".deps/Residue_data.Plo"; else rm -f ".deps/Residue_data.Tpo"; exit 1; fi
 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Residue_data.lo -MD -MP -MF .deps/Residue_data.Tpo -c Residue_data.cc  -fPIC -DPIC -o .libs/Residue_data.o
 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Residue_data.lo -MD -MP -MF .deps/Residue_data.Tpo -c Residue_data.cc -o Residue_data.o >/dev/null 2>&1
if /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I. -I..  -I../include -pg -isystem /usr/local/include  -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -fPIC --std=c++11 -isystem /usr/local/include  -MT Protein_pdb.lo -MD -MP -MF ".deps/Protein_pdb.Tpo" -c -o Protein_pdb.lo Protein_pdb.cc; \
then mv -f ".deps/Protein_pdb.Tpo" ".deps/Protein_pdb.Plo"; else rm -f ".deps/Protein_pdb.Tpo"; exit 1; fi
 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Protein_pdb.lo -MD -MP -MF .deps/Protein_pdb.Tpo -c Protein_pdb.cc  -fPIC -DPIC -o .libs/Protein_pdb.o
 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Protein_pdb.lo -MD -MP -MF .deps/Protein_pdb.Tpo -c Protein_pdb.cc -o Protein_pdb.o >/dev/null 2>&1
if /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I. -I..  -I../include -pg -isystem /usr/local/include  -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -fPIC --std=c++11 -isystem /usr/local/include  -MT pdb_utils.lo -MD -MP -MF ".deps/pdb_utils.Tpo" -c -o pdb_utils.lo pdb_utils.cc; \
then mv -f ".deps/pdb_utils.Tpo" ".deps/pdb_utils.Plo"; else rm -f ".deps/pdb_utils.Tpo"; exit 1; fi
 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT pdb_utils.lo -MD -MP -MF .deps/pdb_utils.Tpo -c pdb_utils.cc  -fPIC -DPIC -o .libs/pdb_utils.o
 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT pdb_utils.lo -MD -MP -MF .deps/pdb_utils.Tpo -c pdb_utils.cc -o pdb_utils.o >/dev/null 2>&1
if /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I. -I..  -I../include -pg -isystem /usr/local/include  -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -fPIC --std=c++11 -isystem /usr/local/include  -MT Model.lo -MD -MP -MF ".deps/Model.Tpo" -c -o Model.lo Model.cc; \
then mv -f ".deps/Model.Tpo" ".deps/Model.Plo"; else rm -f ".deps/Model.Tpo"; exit 1; fi
 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Model.lo -MD -MP -MF .deps/Model.Tpo -c Model.cc  -fPIC -DPIC -o .libs/Model.o
 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Model.lo -MD -MP -MF .deps/Model.Tpo -c Model.cc -o Model.o >/dev/null 2>&1
if /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I. -I..  -I../include -pg -isystem /usr/local/include  -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -fPIC --std=c++11 -isystem /usr/local/include  -MT PDB.lo -MD -MP -MF ".deps/PDB.Tpo" -c -o PDB.lo PDB.cc; \
then mv -f ".deps/PDB.Tpo" ".deps/PDB.Plo"; else rm -f ".deps/PDB.Tpo"; exit 1; fi
 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT PDB.lo -MD -MP -MF .deps/PDB.Tpo -c PDB.cc  -fPIC -DPIC -o .libs/PDB.o
 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT PDB.lo -MD -MP -MF .deps/PDB.Tpo -c PDB.cc -o PDB.o >/dev/null 2>&1
if /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I. -I..  -I../include -pg -isystem /usr/local/include  -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -fPIC --std=c++11 -isystem /usr/local/include  -MT align.lo -MD -MP -MF ".deps/align.Tpo" -c -o align.lo align.cc; \
then mv -f ".deps/align.Tpo" ".deps/align.Plo"; else rm -f ".deps/align.Tpo"; exit 1; fi
 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT align.lo -MD -MP -MF .deps/align.Tpo -c align.cc  -fPIC -DPIC -o .libs/align.o
In file included from align.cc:5:
In file included from ../include/dsrpdb_internal/align_points.h:6:
In file included from ../include/tnt/tnt_array2d.h:31:
./include/tnt/tnt_array1d.h:238:15: warning: '&&' within '||' [-Wlogical-op-parentheses]
        if ((i0 > 0) && (i1 < n_) || (i0 <= i1))
            ~~~~~~~~~^~~~~~~~~~~~ ~~
./include/tnt/tnt_array1d.h:238:15: note: place parentheses around the '&&' expression to silence this warning
        if ((i0 > 0) && (i1 < n_) || (i0 <= i1))
                     ^
            (                    )
1 warning generated.
 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT align.lo -MD -MP -MF .deps/align.Tpo -c align.cc -o align.o >/dev/null 2>&1
if /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I. -I..  -I../include -pg -isystem /usr/local/include  -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -fPIC --std=c++11 -isystem /usr/local/include  -MT distance.lo -MD -MP -MF ".deps/distance.Tpo" -c -o distance.lo distance.cc; \
then mv -f ".deps/distance.Tpo" ".deps/distance.Plo"; else rm -f ".deps/distance.Tpo"; exit 1; fi
 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT distance.lo -MD -MP -MF .deps/distance.Tpo -c distance.cc  -fPIC -DPIC -o .libs/distance.o
In file included from distance.cc:1:
In file included from ../include/dsrpdb/distance.h:28:
In file included from ../include/dsrpdb/Matrix.h:4:
In file included from ../include/tnt/tnt_array2d.h:31:
./include/tnt/tnt_array1d.h:238:15: warning: '&&' within '||' [-Wlogical-op-parentheses]
        if ((i0 > 0) && (i1 < n_) || (i0 <= i1))
            ~~~~~~~~~^~~~~~~~~~~~ ~~
./include/tnt/tnt_array1d.h:238:15: note: place parentheses around the '&&' expression to silence this warning
        if ((i0 > 0) && (i1 < n_) || (i0 <= i1))
                     ^
            (                    )
1 warning generated.
 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT distance.lo -MD -MP -MF .deps/distance.Tpo -c distance.cc -o distance.o >/dev/null 2>&1
if /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I. -I..  -I../include -pg -isystem /usr/local/include  -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -fPIC --std=c++11 -isystem /usr/local/include  -MT Error_logger.lo -MD -MP -MF ".deps/Error_logger.Tpo" -c -o Error_logger.lo Error_logger.cc; \
then mv -f ".deps/Error_logger.Tpo" ".deps/Error_logger.Plo"; else rm -f ".deps/Error_logger.Tpo"; exit 1; fi
 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Error_logger.lo -MD -MP -MF .deps/Error_logger.Tpo -c Error_logger.cc  -fPIC -DPIC -o .libs/Error_logger.o
 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Error_logger.lo -MD -MP -MF .deps/Error_logger.Tpo -c Error_logger.cc -o Error_logger.o >/dev/null 2>&1
/bin/sh ../libtool --tag=CXX --mode=link c++  -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -fPIC --std=c++11 -isystem /usr/local/include   -fstack-protector-strong -L/usr/local/lib  -lboost_program_options -o libdsrpdb.la -rpath /usr/local/lib -static Residue.lo Protein.lo Residue_data.lo Protein_pdb.lo pdb_utils.lo Model.lo PDB.lo align.lo distance.lo Error_logger.lo  
ar cru .libs/libdsrpdb.a  Residue.o Protein.o Residue_data.o Protein_pdb.o pdb_utils.o Model.o PDB.o align.o distance.o Error_logger.o
ranlib .libs/libdsrpdb.a
creating libdsrpdb.la
(cd .libs && rm -f libdsrpdb.la && ln -s ../libdsrpdb.la libdsrpdb.la)
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/lib'
Making all in tools
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/tools'
if c++ -DHAVE_CONFIG_H -I. -I. -I..  -I../include -isystem /usr/local/include  -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -fPIC --std=c++11 -isystem /usr/local/include  -MT pdb_stats.o -MD -MP -MF ".deps/pdb_stats.Tpo" -c -o pdb_stats.o pdb_stats.cc; \
then mv -f ".deps/pdb_stats.Tpo" ".deps/pdb_stats.Po"; else rm -f ".deps/pdb_stats.Tpo"; exit 1; fi
/bin/sh ../libtool --tag=CXX --mode=link c++  -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -fPIC --std=c++11 -isystem /usr/local/include   -fstack-protector-strong -L/usr/local/lib  -lboost_program_options -o pdb_stats  pdb_stats.o ../lib/libdsrpdb.la 
mkdir .libs
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -fstack-protector-strong -o pdb_stats pdb_stats.o  -L/usr/local/lib ../lib/.libs/libdsrpdb.a -lboost_program_options
ld: error: undefined symbol: .mcount
>>> referenced by Protein.cc
>>>               Protein.o:(dsrpdb::Protein::Protein()) in archive ../lib/.libs/libdsrpdb.a
>>> referenced by Protein.cc
>>>               Protein.o:(dsrpdb::Protein::chain() const) in archive ../lib/.libs/libdsrpdb.a
>>> referenced by Protein.cc
>>>               Protein.o:(dsrpdb::Protein::set_chain(char)) in archive ../lib/.libs/libdsrpdb.a
>>> referenced by Protein.cc
>>>               Protein.o:(dsrpdb::Protein::sequence() const) in archive ../lib/.libs/libdsrpdb.a
>>> referenced by Protein.cc
>>>               Protein.o:(dsrpdb::Protein::number_of_atoms() const) in archive ../lib/.libs/libdsrpdb.a
>>> referenced by Protein.cc
>>>               Protein.o:(dsrpdb::Protein::number_of_bonds() const) in archive ../lib/.libs/libdsrpdb.a
>>> referenced by Protein.cc
>>>               Protein.o:(dsrpdb::Protein::dump(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) const) in archive ../lib/.libs/libdsrpdb.a
>>> referenced by Protein.cc
>>>               Protein.o:(dsrpdb::Protein::new_residue(dsrpdb::Residue const&)) in archive ../lib/.libs/libdsrpdb.a
>>> referenced by Protein.cc
>>>               Protein.o:(dsrpdb::Protein::atoms_begin()) in archive ../lib/.libs/libdsrpdb.a
>>> referenced by Protein.cc
>>>               Protein.o:(dsrpdb::Protein::atoms_end()) in archive ../lib/.libs/libdsrpdb.a
>>> referenced 121 more times
clang-cpp: error: linker command failed with exit code 1 (use -v to see invocation)
gmake[3]: *** [Makefile:317: pdb_stats] Error 1
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/tools'
gmake[2]: *** [Makefile:250: all-recursive] Error 1
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3'
gmake[1]: *** [Makefile:179: all] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3'
*** Error code 1

Stop.
make: stopped in /usr/ports/biology/dsr-pdb



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