[package - 130releng-riscv64-quarterly][biology/dsr-pdb] Failed for dsr-pdb-1.0.3_5 in build

From: <pkg-fallout_at_FreeBSD.org>
Date: Thu, 21 Oct 2021 05:18:02 GMT
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.

Maintainer:     yuri_at_FreeBSD.org
Log URL:        http://beefy7.nyi.freebsd.org/data/130releng-riscv64-quarterly/3d9c17481d61/logs/dsr-pdb-1.0.3_5.log
Build URL:      http://beefy7.nyi.freebsd.org/build.html?mastername=130releng-riscv64-quarterly&build=3d9c17481d61
Log:

=>> Building biology/dsr-pdb
build started at Thu Oct 21 05:16:42 UTC 2021
port directory: /usr/ports/biology/dsr-pdb
package name: dsr-pdb-1.0.3_5
building for: FreeBSD 130releng-riscv64-quarterly-job-14 13.0-RELEASE-p4 FreeBSD 13.0-RELEASE-p4 1300139 riscv
maintained by: yuri_at_FreeBSD.org
Makefile ident: 
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=======================<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-1.17.2.pkg
[130releng-riscv64-quarterly-job-14] Installing pkg-1.17.2...
[130releng-riscv64-quarterly-job-14] Extracting pkg-1.17.2: .......... 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
=> 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_5 for building
===>  Extracting for dsr-pdb-1.0.3_5
=> SHA256 Checksum OK for dsr-pdb-1.0.3/dsr-pdb.tgz.
===========================================================================
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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_at_graphics.stanford.edu ##
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configure: creating ./config.status
config.status: creating Makefile
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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
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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'
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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
Received on Thu Oct 21 2021 - 05:18:02 UTC

Original text of this message