[package - main-arm64-default][biology/dsr-pdb] Failed for dsr-pdb-1.0.3_5 in build

From: <pkg-fallout_at_FreeBSD.org>
Date: Sun, 1 Aug 2021 12:27:48 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://ampere2.nyi.freebsd.org/data/main-arm64-default/pd69639d824b8_s7cbf1de38e/logs/dsr-pdb-1.0.3_5.log
Build URL:      http://ampere2.nyi.freebsd.org/build.html?mastername=main-arm64-default&build=pd69639d824b8_s7cbf1de38e
Log:

=>> Building biology/dsr-pdb
build started at Sun Aug  1 12:26:17 UTC 2021
port directory: /usr/ports/biology/dsr-pdb
package name: dsr-pdb-1.0.3_5
building for: FreeBSD main-arm64-default-job-07 14.0-CURRENT FreeBSD 14.0-CURRENT 1400027 arm64
maintained by: yuri_at_FreeBSD.org
Makefile ident: 
Poudriere version: 3.2.8-20-g137a4a48
Host OSVERSION: 1400008
Jail OSVERSION: 1400027
Job Id: 07




!!! Jail is newer than host. (Jail: 1400027, Host: 1400008) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



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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-1.17.1.pkg
[main-arm64-default-job-07] Installing pkg-1.17.1...
[main-arm64-default-job-07] 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
=> 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.pkg
[main-arm64-default-job-07] Installing gmake-4.3_2...
[main-arm64-default-job-07] `-- Installing gettext-runtime-0.21...
[main-arm64-default-job-07] |   `-- Installing indexinfo-0.3.1...
[main-arm64-default-job-07] |   `-- Extracting indexinfo-0.3.1: .... done
[main-arm64-default-job-07] `-- Extracting gettext-runtime-0.21: .......... done
[main-arm64-default-job-07] Extracting gmake-4.3_2: .......... done
===>   dsr-pdb-1.0.3_5 depends on package: gmake>=4.3 - found
<snip>
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checking how to run the C++ preprocessor... c++ -E
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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 cc object... ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip... strip
checking if cc static flag  works... yes
checking if cc supports -fno-rtti -fno-exceptions... yes
checking for cc option to produce PIC... -fPIC
checking if cc PIC flag -fPIC works... yes
checking if cc supports -c -o file.o... yes
checking whether the cc linker (/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 c++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes
checking for c++ option to produce PIC... -fPIC
checking if c++ PIC flag -fPIC works... yes
checking if c++ supports -c -o file.o... yes
checking whether the c++ linker (/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
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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_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_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 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
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
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 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
 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 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
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 Residue_data.lo -MD -MP -MF .deps/Residue_data.Tpo -c Residue_data.cc -o Residue_data.o >/dev/null 2>&1
 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
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 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 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 Model.lo -MD -MP -MF .deps/Model.Tpo -c Model.cc -o Model.o >/dev/null 2>&1
 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
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
 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
 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
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
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
/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
>>> 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 126 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]: *** Waiting for unfinished jobs....
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
Received on Sun Aug 01 2021 - 12:27:48 UTC

Original text of this message