[package - 120arm64-quarterly][biology/dsr-pdb] Failed for dsr-pdb-1.0.3_1 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Tue May 14 08:21:07 UTC 2019
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
Last committer: yuri at FreeBSD.org
Ident: $FreeBSD: branches/2019Q2/biology/dsr-pdb/Makefile 492270 2019-02-05 19:01:59Z yuri $
Log URL: http://thunderx1.nyi.freebsd.org/data/120arm64-quarterly/501213/logs/dsr-pdb-1.0.3_1.log
Build URL: http://thunderx1.nyi.freebsd.org/build.html?mastername=120arm64-quarterly&build=501213
Log:
=>> Building biology/dsr-pdb
build started at Tue May 14 08:17:52 UTC 2019
port directory: /usr/ports/biology/dsr-pdb
package name: dsr-pdb-1.0.3_1
building for: FreeBSD 120arm64-quarterly-job-09 12.0-RELEASE-p3 FreeBSD 12.0-RELEASE-p3 1200086 arm64
maintained by: yuri at FreeBSD.org
Makefile ident: $FreeBSD: branches/2019Q2/biology/dsr-pdb/Makefile 492270 2019-02-05 19:01:59Z yuri $
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=======================<phase: check-sanity >============================
===> License LGPL21 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> dsr-pdb-1.0.3_1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.10.5_5.txz
[120arm64-quarterly-job-09] Installing pkg-1.10.5_5...
[120arm64-quarterly-job-09] Extracting pkg-1.10.5_5: .......... done
===> dsr-pdb-1.0.3_1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of dsr-pdb-1.0.3_1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License LGPL21 accepted by the user
===> Fetching all distfiles required by dsr-pdb-1.0.3_1 for building
===========================================================================
=======================<phase: checksum >============================
===> License LGPL21 accepted by the user
===> Fetching all distfiles required by dsr-pdb-1.0.3_1 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_1 for building
===> Extracting for dsr-pdb-1.0.3_1
=> SHA256 Checksum OK for dsr-pdb-1.0.3/dsr-pdb.tgz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for dsr-pdb-1.0.3_1
===> Applying FreeBSD patches for dsr-pdb-1.0.3_1
===========================================================================
=======================<phase: build-depends >============================
===> dsr-pdb-1.0.3_1 depends on executable: gmake - not found
===> Installing existing package /packages/All/gmake-4.2.1_3.txz
[120arm64-quarterly-job-09] Installing gmake-4.2.1_3...
[120arm64-quarterly-job-09] `-- Installing gettext-runtime-0.19.8.1_2...
[120arm64-quarterly-job-09] | `-- Installing indexinfo-0.3.1...
[120arm64-quarterly-job-09] | `-- Extracting indexinfo-0.3.1: .... done
[120arm64-quarterly-job-09] `-- Extracting gettext-runtime-0.19.8.1_2: .......... done
[120arm64-quarterly-job-09] Extracting gmake-4.2.1_3: .......... done
===> dsr-pdb-1.0.3_1 depends on executable: gmake - found
===> Returning to build of dsr-pdb-1.0.3_1
===========================================================================
=======================<phase: lib-depends >============================
===> dsr-pdb-1.0.3_1 depends on shared library: libboost_program_options.so - not found
===> Installing existing package /packages/All/boost-libs-1.69.0_2.txz
<snip>
configure: WARNING: ## -------------------------------------------- ##
configure: WARNING: ## Report this to drussel at 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_1
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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if /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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; \
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c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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 -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 -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; \
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c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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 -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 -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 -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 -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 -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 -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 -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 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -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 -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 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -L/usr/local/lib -lboost_program_options -o pdb_stats pdb_stats.o ../lib/libdsrpdb.la
mkdir .libs
c++ -O2 -pipe -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -o pdb_stats pdb_stats.o -L/usr/local/lib ../lib/.libs/libdsrpdb.a -lboost_program_options
/usr/bin/ld: error: undefined symbol: .mcount
>>> referenced by Protein.cc
>>> Protein.o:(dsrpdb::Protein::Protein()) in archive ../lib/.libs/libdsrpdb.a
/usr/bin/ld: error: undefined symbol: .mcount
>>> referenced by Protein.cc
>>> Protein.o:(dsrpdb::Protein::chain() const) in archive ../lib/.libs/libdsrpdb.a
/usr/bin/ld: error: undefined symbol: .mcount
>>> referenced by Protein.cc
>>> Protein.o:(dsrpdb::Protein::set_chain(char)) in archive ../lib/.libs/libdsrpdb.a
/usr/bin/ld: error: undefined symbol: .mcount
>>> referenced by Protein.cc
>>> Protein.o:(dsrpdb::Protein::sequence() const) in archive ../lib/.libs/libdsrpdb.a
/usr/bin/ld: error: undefined symbol: .mcount
>>> referenced by Protein.cc
>>> Protein.o:(dsrpdb::Protein::number_of_atoms() const) in archive ../lib/.libs/libdsrpdb.a
/usr/bin/ld: error: undefined symbol: .mcount
>>> referenced by Protein.cc
>>> Protein.o:(dsrpdb::Protein::number_of_bonds() const) in archive ../lib/.libs/libdsrpdb.a
/usr/bin/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
/usr/bin/ld: error: undefined symbol: .mcount
>>> referenced by Protein.cc
>>> Protein.o:(dsrpdb::Protein::new_residue(dsrpdb::Residue const&)) in archive ../lib/.libs/libdsrpdb.a
/usr/bin/ld: error: undefined symbol: .mcount
>>> referenced by Protein.cc
>>> Protein.o:(dsrpdb::Protein::atoms_begin()) in archive ../lib/.libs/libdsrpdb.a
/usr/bin/ld: error: undefined symbol: .mcount
>>> referenced by Protein.cc
>>> Protein.o:(dsrpdb::Protein::atoms_end()) in archive ../lib/.libs/libdsrpdb.a
/usr/bin/ld: error: undefined symbol: .mcount
>>> referenced by Protein.cc
>>> Protein.o:(dsrpdb::Protein::atoms_begin() const) in archive ../lib/.libs/libdsrpdb.a
/usr/bin/ld: error: undefined symbol: .mcount
>>> referenced by Protein.cc
>>> Protein.o:(dsrpdb::Protein::atoms_end() const) in archive ../lib/.libs/libdsrpdb.a
/usr/bin/ld: error: undefined symbol: .mcount
>>> referenced by Protein.cc
>>> Protein.o:(dsrpdb::Protein::bonds_begin() const) in archive ../lib/.libs/libdsrpdb.a
/usr/bin/ld: error: undefined symbol: .mcount
>>> referenced by Protein.cc
>>> Protein.o:(dsrpdb::Protein::bonds_end() const) in archive ../lib/.libs/libdsrpdb.a
/usr/bin/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
/usr/bin/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
/usr/bin/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
/usr/bin/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
/usr/bin/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
/usr/bin/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
/usr/bin/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
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