[package - main-riscv64-default][biology/dsr-pdb] Failed for dsr-pdb-1.0.3_5 in build
- Go to: [ bottom of page ] [ top of archives ] [ this month ]
Date: Thu, 02 Sep 2021 10:21:53 UTC
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
Log URL: http://beefy7.nyi.freebsd.org/data/main-riscv64-default/pfda1da2d7917_s9939af1a16/logs/dsr-pdb-1.0.3_5.log
Build URL: http://beefy7.nyi.freebsd.org/build.html?mastername=main-riscv64-default&build=pfda1da2d7917_s9939af1a16
Log:
=>> Building biology/dsr-pdb
build started at Thu Sep 2 10:20:05 UTC 2021
port directory: /usr/ports/biology/dsr-pdb
package name: dsr-pdb-1.0.3_5
building for: FreeBSD main-riscv64-default-job-04 14.0-CURRENT FreeBSD 14.0-CURRENT 1400032 riscv
maintained by: yuri@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-21-g883afb07
Host OSVERSION: 1400008
Jail OSVERSION: 1400032
Job Id: 04
!!! Jail is newer than host. (Jail: 1400032, Host: 1400008) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
---Begin Environment---
SHELL=/bin/csh
UNAME_p=riscv64
UNAME_m=riscv
ABI_FILE=/usr/lib/crt1.o
OSVERSION=1400032
UNAME_v=FreeBSD 14.0-CURRENT 1400032
UNAME_r=14.0-CURRENT
BLOCKSIZE=K
MAIL=/var/mail/root
MM_CHARSET=UTF-8
LANG=C.UTF-8
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=3.2.8-21-g883afb07
MASTERMNT=/usr/local/poudriere/data/.m/main-riscv64-default/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
PWD=/usr/local/poudriere/data/.m/main-riscv64-default/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=main-riscv64-default
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/main-riscv64-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=524288
--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="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -march=rv64imafdc -mabi=lp64d -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=14.0 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---
.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=riscv
MACHINE_ARCH=riscv64
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
#### /usr/ports/Mk/Scripts/ports_env.sh ####
_CCVERSION_9d218390=FreeBSD clang version 12.0.1 (git@github.com:llvm/llvm-project.git llvmorg-12.0.1-0-gfed41342a82f) Target: riscv64-unknown-freebsd14.0 Thread model: posix InstalledDir: /nxb-bin/usr/bin
_ALTCCVERSION_9d218390=none
_CXXINTERNAL_9c45a5b1=FreeBSD clang version 12.0.1 (git@github.com:llvm/llvm-project.git llvmorg-12.0.1-0-gfed41342a82f) Target: riscv64-unknown-freebsd14.0 Thread model: posix InstalledDir: /nxb-bin/usr/bin "/nxb-bin/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--enable-new-dtags" "-m" "elf64lriscv" "-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 12.0.1 (git@github.com:llvm/llvm-project.git llvmorg-12.0.1-0-gfed41342a82f) Target: riscv64-unknown-freebsd14.0 Thread model: posix InstalledDir: /nxb-bin/usr/bin
_OBJC_ALTCCVERSION_9d218390=none
ARCH=riscv64
OPSYS=FreeBSD
_OSRELEASE=14.0-CURRENT
OSREL=14.0
OSVERSION=1400032
PYTHONBASE=/usr/local
CONFIGURE_MAX_CMD_LEN=524288
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++
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 LGPL21 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> dsr-pdb-1.0.3_5 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.17.1.pkg
[main-riscv64-default-job-04] Installing pkg-1.17.1...
[main-riscv64-default-job-04] Extracting pkg-1.17.1: .......... done
===> dsr-pdb-1.0.3_5 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of dsr-pdb-1.0.3_5
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License LGPL21 accepted by the user
===> Fetching all distfiles required by dsr-pdb-1.0.3_5 for building
===========================================================================
=======================<phase: checksum >============================
===> License LGPL21 accepted by the user
===> Fetching all distfiles required by dsr-pdb-1.0.3_5 for building
<snip>
checking whether we are using the GNU C compiler... yes
checking whether /nxb-bin/usr/bin/cc accepts -g... yes
checking for /nxb-bin/usr/bin/cc option to accept ANSI C... none needed
checking dependency style of /nxb-bin/usr/bin/cc... gcc3
checking how to run the C preprocessor... /nxb-bin/usr/bin/cpp
checking for a BSD-compatible install... /usr/bin/install -c
checking whether ln -s works... yes
checking whether gmake sets $(MAKE)... (cached) yes
checking build system type... riscv64-portbld-freebsd14.0
checking host system type... riscv64-portbld-freebsd14.0
checking for a sed that does not truncate output... /usr/bin/sed
checking for egrep... grep -E
checking for ld used by /nxb-bin/usr/bin/cc... /nxb-bin/usr/bin/ld
checking if the linker (/nxb-bin/usr/bin/ld) is GNU ld... yes
checking for /nxb-bin/usr/bin/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm
checking how to recognise dependent libraries... pass_all
checking for ANSI C header files... (cached) yes
checking for sys/types.h... (cached) yes
checking for sys/stat.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for memory.h... (cached) yes
checking for strings.h... (cached) yes
checking for inttypes.h... (cached) yes
checking for stdint.h... (cached) yes
checking for unistd.h... (cached) yes
checking for dlfcn.h... (cached) yes
checking how to run the C++ preprocessor... /nxb-bin/usr/bin/c++ -E
checking for g77... no
checking for f77... no
checking for xlf... no
checking for frt... no
checking for pgf77... no
checking for fort77... no
checking for fl32... no
checking for af77... no
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) 524288
checking command to parse /usr/bin/nm output from /nxb-bin/usr/bin/cc object... ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip... strip
checking if /nxb-bin/usr/bin/cc static flag works... yes
checking if /nxb-bin/usr/bin/cc supports -fno-rtti -fno-exceptions... yes
checking for /nxb-bin/usr/bin/cc option to produce PIC... -fPIC
checking if /nxb-bin/usr/bin/cc PIC flag -fPIC works... yes
checking if /nxb-bin/usr/bin/cc supports -c -o file.o... yes
checking whether the /nxb-bin/usr/bin/cc linker (/nxb-bin/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... freebsd14.0 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 /nxb-bin/usr/bin/c++... /nxb-bin/usr/bin/ld
checking if the linker (/nxb-bin/usr/bin/ld) is GNU ld... yes
checking whether the /nxb-bin/usr/bin/c++ linker (/nxb-bin/usr/bin/ld) supports shared libraries... yes
checking for /nxb-bin/usr/bin/c++ option to produce PIC... -fPIC
checking if /nxb-bin/usr/bin/c++ PIC flag -fPIC works... yes
checking if /nxb-bin/usr/bin/c++ supports -c -o file.o... yes
checking whether the /nxb-bin/usr/bin/c++ linker (/nxb-bin/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... freebsd14.0 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_5
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 /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -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
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -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
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -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 /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -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
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -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
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -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 /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -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
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -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
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -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 /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -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
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -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
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -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 /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -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
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -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
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -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 /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -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
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -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
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -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 /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -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
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -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
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -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 /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -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
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -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
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -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 /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -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
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -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
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -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 /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -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
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -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
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -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 /nxb-bin/usr/bin/c++ -O2 -pipe -march=rv64imafdc -mabi=lp64d -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 /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -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 /nxb-bin/usr/bin/c++ -O2 -pipe -march=rv64imafdc -mabi=lp64d -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
/nxb-bin/usr/bin/c++ -O2 -pipe -march=rv64imafdc -mabi=lp64d -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 127 more times
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