Build failure on Linux ARM64
martin-g opened this issue · comments
Hello,
We are working on adding support for R/Bioconductor packages for Linux ARM64 and we face an issue with the build of the NetPathMiner package:
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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’
The build is OK on Linux x86_64: https://bioconductor.org/checkResults/3.17/bioc-LATEST/NetPathMiner/
And it has a different but probably related problem on Mac ARM64: https://bioconductor.org/checkResults/3.17/bioc-mac-arm64-LATEST/NetPathMiner/kjohnson2-install.html :
...
In file included from ./boost/smart_ptr/detail/shared_count.hpp:29:
./boost/smart_ptr/detail/sp_counted_base.hpp:60:11: fatal error: 'boost/smart_ptr/detail/sp_counted_base_sync.hpp' file not found
# include <boost/smart_ptr/detail/sp_counted_base_sync.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1 error generated.
make: *** [PathRanker.o] Error 1
ERROR: compilation failed for package ‘NetPathMiner’
It looks like the issue is an old version of the Boost library
Closed via #16