[package - 121arm64-quarterly][biology/dsr-pdb] Failed for dsr-pdb-1.0.3_5 in build

pkg-fallout at FreeBSD.org pkg-fallout at FreeBSD.org
Sun Jan 24 05:52:51 UTC 2021


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: jbeich at FreeBSD.org
Ident:          $FreeBSD: branches/2021Q1/biology/dsr-pdb/Makefile 519824 2019-12-11 17:53:48Z jbeich $
Log URL:        http://ampere1.nyi.freebsd.org/data/121arm64-quarterly/562432/logs/dsr-pdb-1.0.3_5.log
Build URL:      http://ampere1.nyi.freebsd.org/build.html?mastername=121arm64-quarterly&build=562432
Log:

=>> Building biology/dsr-pdb
build started at Sun Jan 24 05:51:50 UTC 2021
port directory: /usr/ports/biology/dsr-pdb
package name: dsr-pdb-1.0.3_5
building for: FreeBSD 121arm64-quarterly-job-01 12.1-RELEASE FreeBSD 12.1-RELEASE arm64
maintained by: yuri at FreeBSD.org
Makefile ident:      $FreeBSD: branches/2021Q1/biology/dsr-pdb/Makefile 519824 2019-12-11 17:53:48Z jbeich $
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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-1.16.1.txz
[121arm64-quarterly-job-01] Installing pkg-1.16.1...
[121arm64-quarterly-job-01] Extracting pkg-1.16.1: .......... 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
=> 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.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for dsr-pdb-1.0.3_5
===>  Applying FreeBSD patches for dsr-pdb-1.0.3_5 from /usr/ports/biology/dsr-pdb/files
===========================================================================
=======================<phase: build-depends  >============================
===>   dsr-pdb-1.0.3_5 depends on package: gmake>=4.3 - not found
===>   Installing existing package /packages/All/gmake-4.3_2.txz
[121arm64-quarterly-job-01] Installing gmake-4.3_2...
[121arm64-quarterly-job-01] `-- Installing gettext-runtime-0.21...
[121arm64-quarterly-job-01] |   `-- Installing indexinfo-0.3.1...
[121arm64-quarterly-job-01] |   `-- Extracting indexinfo-0.3.1: .... done
[121arm64-quarterly-job-01] `-- Extracting gettext-runtime-0.21: .......... done
[121arm64-quarterly-job-01] Extracting gmake-4.3_2: .......... done
===>   dsr-pdb-1.0.3_5 depends on package: gmake>=4.3 - found
===>   Returning to build of dsr-pdb-1.0.3_5
===========================================================================
=======================<phase: lib-depends    >============================
===>   dsr-pdb-1.0.3_5 depends on shared library: libboost_program_options.so - not found
===>   Installing existing package /packages/All/boost-libs-1.72.0_3.txz
[121arm64-quarterly-job-01] Installing boost-libs-1.72.0_3...
[121arm64-quarterly-job-01] `-- Installing icu-68.2,1...
[121arm64-quarterly-job-01] `-- Extracting icu-68.2,1: .......... done
[121arm64-quarterly-job-01] Extracting boost-libs-1.72.0_3: .......... done
=====
Message from boost-libs-1.72.0_3:

<snip>
./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))
                     ^
            (                    )
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
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
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
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_split.o -MD -MP -MF ".deps/pdb_split.Tpo" -c -o pdb_split.o pdb_split.cc; \
then mv -f ".deps/pdb_split.Tpo" ".deps/pdb_split.Po"; else rm -f ".deps/pdb_split.Tpo"; exit 1; fi
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_transform.o -MD -MP -MF ".deps/pdb_transform.Tpo" -c -o pdb_transform.o pdb_transform.cc; \
then mv -f ".deps/pdb_transform.Tpo" ".deps/pdb_transform.Po"; else rm -f ".deps/pdb_transform.Tpo"; exit 1; fi
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_cat.o -MD -MP -MF ".deps/pdb_cat.Tpo" -c -o pdb_cat.o pdb_cat.cc; \
then mv -f ".deps/pdb_cat.Tpo" ".deps/pdb_cat.Po"; else rm -f ".deps/pdb_cat.Tpo"; exit 1; fi
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_align.o -MD -MP -MF ".deps/pdb_align.Tpo" -c -o pdb_align.o pdb_align.cc; \
then mv -f ".deps/pdb_align.Tpo" ".deps/pdb_align.Po"; else rm -f ".deps/pdb_align.Tpo"; exit 1; fi
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_align_points.o -MD -MP -MF ".deps/pdb_align_points.Tpo" -c -o pdb_align_points.o pdb_align_points.cc; \
then mv -f ".deps/pdb_align_points.Tpo" ".deps/pdb_align_points.Po"; else rm -f ".deps/pdb_align_points.Tpo"; exit 1; fi
In file included from pdb_align.cc:27:
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))
                     ^
            (                    )
In file included from pdb_align_points.cc:28:
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.
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_distance_matrix.o -MD -MP -MF ".deps/pdb_distance_matrix.Tpo" -c -o pdb_distance_matrix.o pdb_distance_matrix.cc; \
then mv -f ".deps/pdb_distance_matrix.Tpo" ".deps/pdb_distance_matrix.Po"; else rm -f ".deps/pdb_distance_matrix.Tpo"; exit 1; fi
1 warning generated.
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_distance.o -MD -MP -MF ".deps/pdb_distance.Tpo" -c -o pdb_distance.o pdb_distance.cc; \
then mv -f ".deps/pdb_distance.Tpo" ".deps/pdb_distance.Po"; else rm -f ".deps/pdb_distance.Tpo"; exit 1; fi
In file included from pdb_distance_matrix.cc:25:
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.
/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]: *** Waiting for unfinished jobs....
In file included from pdb_distance.cc:27:
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.
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'
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1

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


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