Skip site navigation (1)Skip section navigation (2)
Date:      Thu, 17 Oct 2019 04:49:59 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:  <201910170449.x9H4nxbJ035404@thunderx1.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: 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/p513859_s353130/logs/dsr-pdb-1.0.3_4.log
Build URL:      http://thunderx1.nyi.freebsd.org/build.html?mastername=head-arm64-default&build=p513859_s353130
Log:

=>> Building biology/dsr-pdb
build started at Thu Oct 17 04:46:19 UTC 2019
port directory: /usr/ports/biology/dsr-pdb
package name: dsr-pdb-1.0.3_4
building for: FreeBSD head-arm64-default-job-09 13.0-CURRENT FreeBSD 13.0-CURRENT 1300048 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: 1300048
Job Id: 09




!!! Jail is newer than host. (Jail: 1300048, Host: 1300002) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



---Begin Environment---
SHELL=/bin/csh
OSVERSION=1300048
UNAME_v=FreeBSD 13.0-CURRENT 1300048
UNAME_r=13.0-CURRENT
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
USER=root
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.2.8-5-gc81843e5
MASTERMNT=/usr/local/poudriere/data/.m/head-arm64-default/ref
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
MASTERNAME=head-arm64-default
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/head-arm64-default/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--
--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"
--End MAKE_ENV--

--PLIST_SUB--
OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local  RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/dsr-pdb"  EXAMPLESDIR="share/examples/dsr-pdb"  DATADIR="share/dsr-pdb"  WWWDIR="www/dsr-pdb"  ETCDIR="etc/dsr-pdb"
--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 8.0.1 (tags/RELEASE_801/final 366581) (based on LLVM 8.0.1) Target: aarch64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin
_ALTCCVERSION_921dbbb2=none
_CXXINTERNAL_acaad9ca=FreeBSD clang version 8.0.1 (tags/RELEASE_801/final 366581) (based on LLVM 8.0.1) Target: aarch64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--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_921dbbb2_58173849=yes
CC_OUTPUT_921dbbb2_9bdba57c=yes
CC_OUTPUT_921dbbb2_6a4fe7f5=yes
CC_OUTPUT_921dbbb2_6bcac02b=yes
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
CC_OUTPUT_921dbbb2_b2657cc3=yes
CC_OUTPUT_921dbbb2_380987f7=yes
CC_OUTPUT_921dbbb2_160933ec=yes
CC_OUTPUT_921dbbb2_fb62803b=yes
_OBJC_CCVERSION_921dbbb2=FreeBSD clang version 8.0.1 (tags/RELEASE_801/final 366581) (based on LLVM 8.0.1) Target: aarch64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin
_OBJC_ALTCCVERSION_921dbbb2=none
ARCH=aarch64
OPSYS=FreeBSD
_OSRELEASE=13.0-CURRENT
OSREL=13.0
OSVERSION=1300048
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---
--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-09] Installing pkg-1.12.0...
[head-arm64-default-job-09] 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-09] Installing gmake-4.2.1_3...
[head-arm64-default-job-09] `-- Installing gettext-runtime-0.20.1...
[head-arm64-default-job-09] |   `-- Installing indexinfo-0.3.1...
[head-arm64-default-job-09] |   `-- Extracting indexinfo-0.3.1: .... done
[head-arm64-default-job-09] `-- Extracting gettext-runtime-0.20.1: .......... done
[head-arm64-default-job-09] 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>
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

ld: error: undefined symbol: .mcount
>>> referenced by Protein.cc
>>>               Protein.o:(dsrpdb::Protein::chain() const) in archive ../lib/.libs/libdsrpdb.a

ld: error: undefined symbol: .mcount
>>> referenced by Protein.cc
>>>               Protein.o:(dsrpdb::Protein::set_chain(char)) in archive ../lib/.libs/libdsrpdb.a

ld: error: undefined symbol: .mcount
>>> referenced by Protein.cc
>>>               Protein.o:(dsrpdb::Protein::sequence() const) in archive ../lib/.libs/libdsrpdb.a

ld: error: undefined symbol: .mcount
>>> referenced by Protein.cc
>>>               Protein.o:(dsrpdb::Protein::number_of_atoms() const) in archive ../lib/.libs/libdsrpdb.a

ld: error: undefined symbol: .mcount
>>> referenced by Protein.cc
>>>               Protein.o:(dsrpdb::Protein::number_of_bonds() const) in archive ../lib/.libs/libdsrpdb.a

ld: error: undefined symbol: .mcount
>>> 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

ld: error: undefined symbol: .mcount
>>> referenced by Protein.cc
>>>               Protein.o:(dsrpdb::Protein::new_residue(dsrpdb::Residue const&)) in archive ../lib/.libs/libdsrpdb.a

ld: error: undefined symbol: .mcount
>>> referenced by Protein.cc
>>>               Protein.o:(dsrpdb::Protein::atoms_begin()) in archive ../lib/.libs/libdsrpdb.a

ld: error: undefined symbol: .mcount
>>> referenced by Protein.cc
>>>               Protein.o:(dsrpdb::Protein::atoms_end()) in archive ../lib/.libs/libdsrpdb.a

ld: error: undefined symbol: .mcount
>>> referenced by Protein.cc
>>>               Protein.o:(dsrpdb::Protein::atoms_begin() const) in archive ../lib/.libs/libdsrpdb.a

ld: error: undefined symbol: .mcount
>>> referenced by Protein.cc
>>>               Protein.o:(dsrpdb::Protein::atoms_end() const) in archive ../lib/.libs/libdsrpdb.a

ld: error: undefined symbol: .mcount
>>> referenced by Protein.cc
>>>               Protein.o:(dsrpdb::Protein::bonds_begin() const) in archive ../lib/.libs/libdsrpdb.a

ld: error: undefined symbol: .mcount
>>> referenced by Protein.cc
>>>               Protein.o:(dsrpdb::Protein::bonds_end() const) in archive ../lib/.libs/libdsrpdb.a

ld: error: undefined symbol: .mcount
>>> referenced by Protein.cc
>>>               Protein.o:(dsrpdb::Protein::residue(dsrpdb::PDB_index<dsrpdb::Residue>) const) in archive ../lib/.libs/libdsrpdb.a

ld: error: undefined symbol: .mcount
>>> referenced by Protein.cc
>>>               Protein.o:(dsrpdb::Protein::residue_offset(dsrpdb::PDB_index<dsrpdb::Residue>) const) in archive ../lib/.libs/libdsrpdb.a

ld: error: undefined symbol: .mcount
>>> referenced by Protein.cc
>>>               Protein.o:(dsrpdb::Protein::has_residue(dsrpdb::PDB_index<dsrpdb::Residue>) const) in archive ../lib/.libs/libdsrpdb.a

ld: error: undefined symbol: .mcount
>>> referenced by Protein.cc
>>>               Protein.o:(dsrpdb::Protein::residue_offset_of_atom_index(dsrpdb::PDB_index<dsrpdb::Atom>) const) in archive ../lib/.libs/libdsrpdb.a

ld: error: undefined symbol: .mcount
>>> referenced by Protein.cc
>>>               Protein.o:(dsrpdb::Protein::set_atom(dsrpdb::PDB_index<dsrpdb::Atom>, dsrpdb::Atom const&)) in archive ../lib/.libs/libdsrpdb.a

ld: error: undefined symbol: .mcount
>>> referenced by Protein.cc
>>>               Protein.o:(dsrpdb::Protein::atom(dsrpdb::PDB_index<dsrpdb::Atom>) const) in archive ../lib/.libs/libdsrpdb.a

ld: error: too many errors emitted, stopping now (use -error-limit=0 to see all errors)
c++: 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



Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?201910170449.x9H4nxbJ035404>