[package - head-armv7-default][biology/libsbml] Failed for libsbml-5.17.0 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Thu Aug 16 00:46:32 UTC 2018
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: ports at FreeBSD.org
Last committer: wen at FreeBSD.org
Ident: $FreeBSD: head/biology/libsbml/Makefile 473289 2018-06-25 01:37:52Z wen $
Log URL: http://beefy16.nyi.freebsd.org/data/head-armv7-default/p477123_s337732/logs/libsbml-5.17.0.log
Build URL: http://beefy16.nyi.freebsd.org/build.html?mastername=head-armv7-default&build=p477123_s337732
Log:
=>> Building biology/libsbml
build started at Thu Aug 16 00:44:32 UTC 2018
port directory: /usr/ports/biology/libsbml
package name: libsbml-5.17.0
building for: FreeBSD head-armv7-default-job-04 12.0-ALPHA1 FreeBSD 12.0-ALPHA1 1200077 arm
maintained by: ports at FreeBSD.org
Makefile ident: $FreeBSD: head/biology/libsbml/Makefile 473289 2018-06-25 01:37:52Z wen $
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=======================<phase: check-sanity >============================
===> NOTICE:
The libsbml port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:
https://bugs.freebsd.org/bugzilla
More information about port maintainership is available at:
<snip>
-- Check for working C compiler: /nxb-bin/usr/bin/cc
-- Check for working C compiler: /nxb-bin/usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /nxb-bin/usr/bin/c++
-- Check for working CXX compiler: /nxb-bin/usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for working C compiler: /nxb-bin/usr/bin/cc -- works
-- Detecting C compile features
-- Detecting C compile features - done
-- Could NOT find SWIG (missing: SWIG_EXECUTABLE SWIG_DIR)
-- Looking for BZ2_bzCompressInit in /usr/lib/libbz2.so
-- Looking for BZ2_bzCompressInit in /usr/lib/libbz2.so - found
-- Looking for gzopen in /usr/lib/libz.so
-- Looking for gzopen in /usr/lib/libz.so - found
-- Looking for include file check.h
-- Looking for include file check.h - not found
-- Looking for include file expat.h
-- Looking for include file expat.h - not found
-- Looking for include file errno.h
-- Looking for include file errno.h - found
-- Looking for include file ieeefp.h
-- Looking for include file ieeefp.h - found
-- Looking for include file math.h
-- Looking for include file math.h - found
-- Looking for include file sys/types.h
-- Looking for include file sys/types.h - found
-- Looking for include file float.h
-- Looking for include file float.h - found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for sqrt in m
-- Looking for sqrt in m - found
--
----------------------------------------------------------------------
libSBML version 5.17.0
----------------------------------------------------------------------
More information and the latest version are available online at
http://sbml.org/Software/libSBML
Please report problems using the issue tracker at
http://sbml.org/Software/libsbml/issue-tracker
To contact the developers directly, email libsbml-team at googlegroups.com
Configured on host 'head-armv7-default-job-04'
host type = FreeBSD
host operating system = FreeBSD 12.0-ALPHA1
host CPU architecture = armv7
General build flags:
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CXX = /nxb-bin/usr/bin/c++
CPPFLAGS = -DLINUX
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LDFLAGS = -L/usr/lib
XML parser library configuration:
XML library = libxml2
CPPFLAGS for XML = -I/usr/local/include/libxml2
LIBS for XML = /usr/local/lib/libxml2.so
Other libSBML configuration settings:
Installation $prefix = /usr/local
-- Value of $LD_LIBRARY_PATH =
-- Using SWIG = SWIG_EXECUTABLE-NOTFOUND (Version )
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-- Build examples = no
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--
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-- Compression support is enabled for .bz2 files
--
----------------------------------------------------------------------
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
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CMAKE_CXX_FLAGS_DEBUG
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CMAKE_MODULE_LINKER_FLAGS
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ICONV_LIBRARIES
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LIBICONV_INCLUDE_DIR
LIBICONV_LIBRARIES
LIBICONV_LIBRARY
THREADS_HAVE_PTHREAD_ARG
-- Build files have been written to: /wrkdirs/usr/ports/biology/libsbml/work/.build
===========================================================================
=======================<phase: build >============================
===> Building for libsbml-5.17.0
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[49/465] /nxb-bin/usr/bin/c++ -DLIBSBML_COMPILED_IN_SRC -DLINUX -DUSE_BZ2 -DUSE_LIBXML -DUSE_ZLIB -Isrc/src/sbml -Isrc/src -Isrc -I/wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src -I/wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml -I/usr/local/include/libxml2 -O2 -pipe -I/usr/include -DLIBICONV_PLUG -fno-strict-aliasing -DLIBICONV_PLUG -fno-strict-aliasing -fPIC -O2 -pipe -I/usr/include -DLIBICONV_PLUG -fno-strict-aliasing -DLIBICONV_PLUG -MD -MT src/CMakeFiles/sbml-static.dir/sbml/LocalParameter.cpp.o -MF src/CMakeFiles/sbml-static.dir/sbml/LocalParameter.cpp.o.d -o src/CMakeFiles/sbml-static.dir/sbml/LocalParameter.cpp.o -c /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/LocalParameter.cpp
[50/465] /nxb-bin/usr/bin/c++ -DLIBSBML_COMPILED_IN_SRC -DLINUX -DUSE_BZ2 -DUSE_LIBXML -DUSE_ZLIB -Isrc/src/sbml -Isrc/src -Isrc -I/wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src -I/wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml -I/usr/local/include/libxml2 -O2 -pipe -I/usr/include -DLIBICONV_PLUG -fno-strict-aliasing -DLIBICONV_PLUG -fno-strict-aliasing -fPIC -O2 -pipe -I/usr/include -DLIBICONV_PLUG -fno-strict-aliasing -DLIBICONV_PLUG -MD -MT src/CMakeFiles/sbml-static.dir/sbml/Model.cpp.o -MF src/CMakeFiles/sbml-static.dir/sbml/Model.cpp.o.d -o src/CMakeFiles/sbml-static.dir/sbml/Model.cpp.o -c /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/Model.cpp
FAILED: src/CMakeFiles/sbml-static.dir/sbml/Model.cpp.o
/nxb-bin/usr/bin/c++ -DLIBSBML_COMPILED_IN_SRC -DLINUX -DUSE_BZ2 -DUSE_LIBXML -DUSE_ZLIB -Isrc/src/sbml -Isrc/src -Isrc -I/wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src -I/wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml -I/usr/local/include/libxml2 -O2 -pipe -I/usr/include -DLIBICONV_PLUG -fno-strict-aliasing -DLIBICONV_PLUG -fno-strict-aliasing -fPIC -O2 -pipe -I/usr/include -DLIBICONV_PLUG -fno-strict-aliasing -DLIBICONV_PLUG -MD -MT src/CMakeFiles/sbml-static.dir/sbml/Model.cpp.o -MF src/CMakeFiles/sbml-static.dir/sbml/Model.cpp.o.d -o src/CMakeFiles/sbml-static.dir/sbml/Model.cpp.o -c /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/Model.cpp
In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/Model.cpp:41:
In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/SBMLDocument.h:298:
In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/SBMLTransforms.h:48:
In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/FunctionDefinition.h:129:
In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/SBO.h:207:
/usr/include/c++/v1/map:629:15: error: object of type 'std::__1::pair<std::__1::pair<const std::__1::basic_string<char>, int>, FormulaUnitsData *>' cannot be assigned because its copy assignment operator is implicitly deleted
{__nc = __v.__cc; return *this;}
^
/usr/include/c++/v1/__tree:1645:35: note: in instantiation of member function 'std::__1::__value_type<std::__1::pair<const std::__1::basic_string<char>, int>, FormulaUnitsData *>::operator=' requested here
__cache->__value_ = *__first;
^
/usr/include/c++/v1/__tree:1575:9: note: in instantiation of function template specialization 'std::__1::__tree<std::__1::__value_type<std::__1::pair<const std::__1::basic_string<char>, int>, FormulaUnitsData *>, std::__1::__map_value_compare<std::__1::pair<const std::__1::basic_string<char>, int>, std::__1::__value_type<std::__1::pair<const std::__1::basic_string<char>, int>, FormulaUnitsData *>, std::__1::less<std::__1::pair<const std::__1::basic_string<char>, int> >, true>, std::__1::allocator<std::__1::__value_type<std::__1::pair<const std::__1::basic_string<char>, int>, FormulaUnitsData *> > >::__assign_multi<std::__1::__tree_const_iterator<std::__1::__value_type<std::__1::pair<const std::__1::basic_string<char>, int>, FormulaUnitsData *>, std::__1::__tree_node<std::__1::__value_type<std::__1::pair<const std::__1::basic_string<char>, int>, FormulaUnitsData *>, void *> *, int> >' requested here
__assign_multi(__t.begin(), __t.end());
^
/usr/include/c++/v1/map:912:21: note: in instantiation of member function 'std::__1::__tree<std::__1::__value_type<std::__1::pair<const std::__1::basic_string<char>, int>, FormulaUnitsData *>, std::__1::__map_value_compare<std::__1::pair<const std::__1::basic_string<char>, int>, std::__1::__value_type<std::__1::pair<const std::__1::basic_string<char>, int>, FormulaUnitsData *>, std::__1::less<std::__1::pair<const std::__1::basic_string<char>, int> >, true>, std::__1::allocator<std::__1::__value_type<std::__1::pair<const std::__1::basic_string<char>, int>, FormulaUnitsData *> > >::operator=' requested here
__tree_ = __m.__tree_;
^
/wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/Model.cpp:243:19: note: in instantiation of member function 'std::__1::map<std::__1::pair<const std::__1::basic_string<char>, int>, FormulaUnitsData *, std::__1::less<std::__1::pair<const std::__1::basic_string<char>, int> >, std::__1::allocator<std::__1::pair<const std::__1::pair<const std::__1::basic_string<char>, int>, FormulaUnitsData *> > >::operator=' requested here
mUnitsDataMap = rhs.mUnitsDataMap;
^
/usr/include/c++/v1/utility:325:5: note: copy assignment operator is implicitly deleted because 'pair<std::__1::pair<const std::__1::basic_string<char>, int>, FormulaUnitsData *>' has a user-declared move constructor
pair(pair&&) = default;
^
1 error generated.
ninja: build stopped: subcommand failed.
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/libsbml
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