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NetPathMiner.install #30

Closed Yikun closed 1 year ago

Yikun commented 1 year ago 
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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL NetPathMiner
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘NetPathMiner’ ...
** using staged installation
'config' variable 'CPP' is defunct
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for xmlParseFile in -lxml2... yes
checking for readSBML in -lsbml... yes
untarring boost include tree...
libSBML found, finding configuration...
pkg-config tool found
libsbml.pc found. Using pkg-config to extract it.
checking for xml2-config... /usr/bin/xml2-config
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/include/libxml2  -I/usr/local/include    -fPIC  -g -O2  -Wall  -c PathRanker.cpp -o PathRanker.o
In file included from ./boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/mpl/arg.hpp:25,
                 from ./boost/mpl/placeholders.hpp:24,
                 from ./boost/iterator/iterator_categories.hpp:17,
                 from ./boost/graph/graph_traits.hpp:25,
                 from ./boost/graph/graph_utility.hpp:29,
                 from PathRanker.cpp:27:
./boost/mpl/assert.hpp:187:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  187 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  188 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  189 |     );
      |     ~                
./boost/mpl/assert.hpp:187:21: note: remove parentheses
  187 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  188 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  189 |     );
      |     ~                
      |     -
./boost/mpl/assert.hpp:192:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  192 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  193 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  194 |     );
      |     ~                
./boost/mpl/assert.hpp:192:21: note: remove parentheses
  192 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  193 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  194 |     );
      |     ~                
      |     -
In file included from ./boost/smart_ptr/detail/shared_count.hpp:30,
                 from ./boost/smart_ptr/shared_ptr.hpp:32,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/property_map/vector_property_map.hpp:14,
                 from ./boost/property_map/property_map.hpp:844,
                 from ./boost/graph/properties.hpp:19,
                 from ./boost/graph/graph_utility.hpp:30,
                 from PathRanker.cpp:27:
./boost/smart_ptr/detail/sp_counted_impl.hpp:81:41: error: ‘boost::detail::sp_typeinfo’ has not been declared
   81 |     virtual void * get_deleter( detail::sp_typeinfo const & )
      |                                         ^~~~~~~~~~~
./boost/smart_ptr/detail/sp_counted_impl.hpp:156:41: error: ‘boost::detail::sp_typeinfo’ has not been declared
  156 |     virtual void * get_deleter( detail::sp_typeinfo const & ti )
      |                                         ^~~~~~~~~~~
./boost/smart_ptr/detail/sp_counted_impl.hpp: In member function ‘virtual void* boost::detail::sp_counted_impl_pd<P, D>::get_deleter(const int&)’:
./boost/smart_ptr/detail/sp_counted_impl.hpp:158:39: error: expected primary-expression before ‘)’ token
  158 |         return ti == BOOST_SP_TYPEID(D)? &reinterpret_cast<char&>( del ): 0;
      |                                       ^
./boost/smart_ptr/detail/sp_counted_impl.hpp:158:22: error: there are no arguments to ‘BOOST_SP_TYPEID’ that depend on a template parameter, so a declaration of ‘BOOST_SP_TYPEID’ must be available [-fpermissive]
  158 |         return ti == BOOST_SP_TYPEID(D)? &reinterpret_cast<char&>( del ): 0;
      |                      ^~~~~~~~~~~~~~~
./boost/smart_ptr/detail/sp_counted_impl.hpp:158:22: note: (if you use ‘-fpermissive’, G++ will accept your code, but allowing the use of an undeclared name is deprecated)
./boost/smart_ptr/detail/sp_counted_impl.hpp: At global scope:
./boost/smart_ptr/detail/sp_counted_impl.hpp:235:41: error: ‘boost::detail::sp_typeinfo’ has not been declared
  235 |     virtual void * get_deleter( detail::sp_typeinfo const & ti )
      |                                         ^~~~~~~~~~~
./boost/smart_ptr/detail/sp_counted_impl.hpp: In member function ‘virtual void* boost::detail::sp_counted_impl_pda<P, D, A>::get_deleter(const int&)’:
./boost/smart_ptr/detail/sp_counted_impl.hpp:237:41: error: expected primary-expression before ‘)’ token
  237 |         return ti == BOOST_SP_TYPEID( D )? &reinterpret_cast<char&>( d_ ): 0;
      |                                         ^
./boost/smart_ptr/detail/sp_counted_impl.hpp:237:22: error: there are no arguments to ‘BOOST_SP_TYPEID’ that depend on a template parameter, so a declaration of ‘BOOST_SP_TYPEID’ must be available [-fpermissive]
  237 |         return ti == BOOST_SP_TYPEID( D )? &reinterpret_cast<char&>( d_ ): 0;
      |                      ^~~~~~~~~~~~~~~
In file included from ./boost/smart_ptr/shared_ptr.hpp:32,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/property_map/vector_property_map.hpp:14,
                 from ./boost/property_map/property_map.hpp:844,
                 from ./boost/graph/properties.hpp:19,
                 from ./boost/graph/graph_utility.hpp:30,
                 from PathRanker.cpp:27:
./boost/smart_ptr/detail/shared_count.hpp: At global scope:
./boost/smart_ptr/detail/shared_count.hpp:446:25: error: ‘sp_typeinfo’ has not been declared
  446 |     void * get_deleter( sp_typeinfo const & ti ) const
      |                         ^~~~~~~~~~~
./boost/smart_ptr/detail/shared_count.hpp: In member function ‘void* boost::detail::shared_count::get_deleter(const int&) const’:
./boost/smart_ptr/detail/shared_count.hpp:448:39: error: cannot convert ‘const int’ to ‘const sp_typeinfo_&’ {aka ‘const std::type_info&’}
  448 |         return pi_? pi_->get_deleter( ti ): 0;
      |                                       ^~
      |                                       |
      |                                       const int
In file included from ./boost/smart_ptr/detail/sp_counted_base.hpp:60,
                 from ./boost/smart_ptr/detail/shared_count.hpp:29,
                 from ./boost/smart_ptr/shared_ptr.hpp:32,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/property_map/vector_property_map.hpp:14,
                 from ./boost/property_map/property_map.hpp:844,
                 from ./boost/graph/properties.hpp:19,
                 from ./boost/graph/graph_utility.hpp:30,
                 from PathRanker.cpp:27:
/usr/include/boost/smart_ptr/detail/sp_counted_base_sync.hpp:119:54: note:   initializing argument 1 of ‘virtual void* boost::detail::sp_counted_base::get_deleter(const sp_typeinfo_&)’
  119 |     virtual void * get_deleter( sp_typeinfo_ const & ti ) = 0;
      |                                 ~~~~~~~~~~~~~~~~~~~~~^~
In file included from ./boost/shared_ptr.hpp:17,
                 from ./boost/property_map/vector_property_map.hpp:14,
                 from ./boost/property_map/property_map.hpp:844,
                 from ./boost/graph/properties.hpp:19,
                 from ./boost/graph/graph_utility.hpp:30,
                 from PathRanker.cpp:27:
./boost/smart_ptr/shared_ptr.hpp: At global scope:
./boost/smart_ptr/shared_ptr.hpp:700:50: error: ‘boost::detail::sp_typeinfo’ has not been declared
  700 |     void * _internal_get_deleter( boost::detail::sp_typeinfo const & ti ) const BOOST_NOEXCEPT
      |                                                  ^~~~~~~~~~~
In file included from ./boost/shared_ptr.hpp:17,
                 from ./boost/property_map/vector_property_map.hpp:14,
                 from ./boost/property_map/property_map.hpp:844,
                 from ./boost/graph/properties.hpp:19,
                 from ./boost/graph/graph_utility.hpp:30,
                 from PathRanker.cpp:27:
./boost/smart_ptr/shared_ptr.hpp: In function ‘D* boost::detail::basic_get_deleter(const boost::shared_ptr<U>&)’:
./boost/smart_ptr/shared_ptr.hpp:892:71: error: expected primary-expression before ‘)’ token
  892 |     return static_cast<D *>( p._internal_get_deleter(BOOST_SP_TYPEID(D)) );
      |                                                                       ^
./boost/smart_ptr/shared_ptr.hpp:892:54: error: there are no arguments to ‘BOOST_SP_TYPEID’ that depend on a template parameter, so a declaration of ‘BOOST_SP_TYPEID’ must be available [-fpermissive]
  892 |     return static_cast<D *>( p._internal_get_deleter(BOOST_SP_TYPEID(D)) );
      |                                                      ^~~~~~~~~~~~~~~
In file included from ./boost/shared_array.hpp:17,
                 from ./boost/graph/detail/d_ary_heap.hpp:20,
                 from ./boost/graph/named_function_params.hpp:24,
                 from ./boost/graph/depth_first_search.hpp:21,
                 from ./boost/graph/graph_utility.hpp:32,
                 from PathRanker.cpp:27:
./boost/smart_ptr/shared_array.hpp: At global scope:
./boost/smart_ptr/shared_array.hpp:223:50: error: ‘boost::detail::sp_typeinfo’ has not been declared
  223 |     void * _internal_get_deleter( boost::detail::sp_typeinfo const & ti ) const
      |                                                  ^~~~~~~~~~~
./boost/smart_ptr/shared_array.hpp: In function ‘D* boost::get_deleter(const boost::shared_array<T>&)’:
./boost/smart_ptr/shared_array.hpp:283:74: error: expected primary-expression before ‘)’ token
  283 |     return static_cast< D * >( p._internal_get_deleter( BOOST_SP_TYPEID(D) ) );
      |                                                                          ^
./boost/smart_ptr/shared_array.hpp:283:57: error: there are no arguments to ‘BOOST_SP_TYPEID’ that depend on a template parameter, so a declaration of ‘BOOST_SP_TYPEID’ must be available [-fpermissive]
  283 |     return static_cast< D * >( p._internal_get_deleter( BOOST_SP_TYPEID(D) ) );
      |                                                         ^~~~~~~~~~~~~~~
make: *** [/home/biocbuild/bbs-3.17-bioc/R/etc/Makeconf:198: PathRanker.o] Error 1
ERROR: compilation failed for package ‘NetPathMiner’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/NetPathMiner’

https://yikun.github.io/bioconductor-0301/report/NetPathMiner/kunpeng1-install.html

martin-g commented 1 year ago

Reported upstream: https://github.com/ahmohamed/NetPathMiner/issues/14

martin-g commented 1 year ago

PR: https://github.com/ahmohamed/NetPathMiner/pull/15

martin-g commented 1 year ago

New PR: https://github.com/ahmohamed/NetPathMiner/pull/16

martin-g commented 1 year ago

The PR has been merged!

martin-g commented 1 year ago

All is fine in report 23.03.2023