External Email - Use Caution
Thanks for the explanation and exemplary detective work. Will you push these
changes to the release and devel branches of RBGL? I've given you
permissions... Martin
On 3/22/19, 5:15 AM, "Samuela Pollack" <spoll...@jimmy.harvard.edu> wrote:
We have a temporary fix which we believe will alleviate the difficulty.
The only routine in RBGL that does not compile under the LLVM-9.0 system
is the routine that implements betweenness connectivity clustering. This
seems to be a rarely-used routine, so we have temporarily removed it
from RBGL and put in a message explaining how users may replace it easily.
I have contacted Professor Jeremy Siek at in Bloomington to discuss how
best to proceed. It is possible this will have to be fixed in BGL,
probably not in time for boost 1.70.
For clarity: the incompatibility is not in clang. The incompatibility is
in the llvm c++ standard library. Mac users who build with clang will be
fine, as long as they don't link in the llvm C++ stdlib, which most
wouldn't think to do and Apple does not encourage.
We hope this will be sufficient for now.
- Sam
On 3/22/19 4:18 AM, Morgan, Martin wrote:
> External Email - Use Caution
>
> What's the status for RBGL?
>
> Thanks, Martin
>
> On 3/22/19, 3:57 AM, "Prof Brian Ripley" <rip...@stats.ox.ac.uk> wrote:
>
> clang 8.0.0 is now released, and these fail there too (and break
about
> 50 CRAN packages which depend on them).
>
> Reminder: this is with clang's native libc++, as documented at
>
https://www.stats.ox.ac.uk/pub/bdr/Rconfig/r-devel-linux-x86_64-fedora-clang
>
> We really need fixes in both 3.8 and 3.9.
>
> BDR
>
> On 28/02/2019 18:52, Prof Brian Ripley wrote:
> > These packages fail to install with clang 8.0.0rc3, which is
supposed to
> > be near-final (it is overdue for release). (AFAIR they did
install with
> > rc1.) In both cases the problems are with Boost.
> >
> > RBGL 1.95.1
> >
> > In file included from bbc.cpp:1:
> > In file included from ./RBGL.hpp:7:
> > In file included from
/usr/local/clang8/bin/../include/c++/v1/iostream:38:
> > In file included from
/usr/local/clang8/bin/../include/c++/v1/ios:216:
> > In file included from
/usr/local/clang8/bin/../include/c++/v1/__locale:15:
> > In file included from
/usr/local/clang8/bin/../include/c++/v1/string:505:
> > In file included from
> > /usr/local/clang8/bin/../include/c++/v1/string_view:176:
> > In file included from
/usr/local/clang8/bin/../include/c++/v1/__string:57:
> > /usr/local/clang8/bin/../include/c++/v1/algorithm:2494:5: error:
> > static_assert
> > failed due to requirement
> >
> >
'__is_forward_iterator<boost::detail::undirected_edge_iter<std::__1::__list_iterator<boost::list_edge<unsigned
> >
> > long, boost::property<boost::edge_weight_t, double,
> > boost::property<boost::edge_centrality_t, double,
> > boost::no_property> > >,
> > void *>,
boost::detail::edge_desc_impl<boost::undirected_tag,
> > unsigned
> > long>, long> >::value' "std::max_element requires a
ForwardIterator"
> > static_assert(__is_forward_iterator<_ForwardIterator>::value,
> > ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> > rbgl_trimmed_boost_1_61_0/boost/graph/bc_clustering.hpp:132:26:
note: in
> > instantiation of function template specialization
> >
> >
'std::__1::max_element<boost::detail::undirected_edge_iter<std::__1::__list_iterator<boost::list_edge<unsigned
> >
> > long, boost::property<boost::edge_weight_t, double,
> > boost::property<boost::edge_centrality_t, double,
> > boost::no_property> > >,
> > void *>,
boost::detail::edge_desc_impl<boost::undirected_tag,
> > unsigned
> > long>, long>,
> >
> >
boost::indirect_cmp<boost::adj_list_edge_property_map<boost::undirected_tag,
> >
> > double, double &, unsigned long,
> > boost::property<boost::edge_weight_t,
> > double, boost::property<boost::edge_centrality_t, double,
> > boost::no_property> >, boost::edge_centrality_t>,
> > std::__1::less<double> >
> > >' requested here
> > edge_descriptor e = *max_element(edges_iters.first,
> > edges_iters.seco...
> > rbgl_trimmed_boost_1_61_0/boost/graph/bc_clustering.hpp:146:3:
note: in
> > instantiation of function template specialization
> >
> >
'boost::betweenness_centrality_clustering<boost::adjacency_list<boost::vecS,
> >
> > boost::vecS, boost::undirectedS,
> > boost::property<boost::vertex_index_t,
> > int, boost::property<boost::vertex_centrality_t, double,
> > boost::no_property> >,
boost::property<boost::edge_weight_t, double,
> > boost::property<boost::edge_centrality_t, double,
> > boost::no_property> >,
> > boost::no_property, boost::listS>, clustering_threshold,
> > boost::adj_list_edge_property_map<boost::undirected_tag,
double,
> > double &,
> > unsigned long, boost::property<boost::edge_weight_t,
double,
> > boost::property<boost::edge_centrality_t, double,
> > boost::no_property> >,
> > boost::edge_centrality_t>,
> >
> >
boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t,
> > int, boost::property<boost::vertex_centrality_t, double,
> > boost::no_property> >, unsigned long> >' requested here
> > betweenness_centrality_clustering(g, done, edge_centrality,
> > ^
> > bbc.cpp:122:3: note: in instantiation of function template
specialization
> >
> >
'boost::betweenness_centrality_clustering<boost::adjacency_list<boost::vecS,
> >
> > boost::vecS, boost::undirectedS,
> > boost::property<boost::vertex_index_t,
> > int, boost::property<boost::vertex_centrality_t, double,
> > boost::no_property> >,
boost::property<boost::edge_weight_t, double,
> > boost::property<boost::edge_centrality_t, double,
> > boost::no_property> >,
> > boost::no_property, boost::listS>, clustering_threshold,
> > boost::adj_list_edge_property_map<boost::undirected_tag,
double,
> > double &,
> > unsigned long, boost::property<boost::edge_weight_t,
double,
> > boost::property<boost::edge_centrality_t, double,
> > boost::no_property> >,
> > boost::edge_centrality_t> >' requested here
> > betweenness_centrality_clustering(g,
> > ^
> >
> > mzR 2.17.1
> >
> > In file included from
pwiz/data/identdata/Serializer_pepXML.cpp:25:
> > In file included from
pwiz/data/identdata/Serializer_pepXML.hpp:27:
> > In file included from pwiz/data/identdata/IdentData.hpp:29:
> > In file included from ./pwiz/utility/misc/Exception.hpp:29:
> > In file included from
/usr/local/clang8/bin/../include/c++/v1/string:505:
> > In file included from
> > /usr/local/clang8/bin/../include/c++/v1/string_view:176:
> > In file included from
/usr/local/clang8/bin/../include/c++/v1/__string:57:
> > /usr/local/clang8/bin/../include/c++/v1/algorithm:2428:5: error:
> > static_assert
> > failed due to requirement
> >
> >
'__is_forward_iterator<boost::iterators::transform_iterator<pwiz::identdata::(anonymous
> >
> > namespace)::EnzymePtr_specificity,
std::__1::__wrap_iter<const
> > boost::shared_ptr<pwiz::identdata::Enzyme> *>,
> > boost::iterators::use_default,
boost::iterators::use_default>
> > >::value'
> > "std::min_element requires a ForwardIterator"
> > static_assert(__is_forward_iterator<_ForwardIterator>::value,
> > ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> > /usr/local/clang8/bin/../include/c++/v1/algorithm:2445:19: note:
in
> > instantiation of function template specialization
> >
> >
'std::__1::min_element<boost::iterators::transform_iterator<pwiz::identdata::(anonymous
> >
> > namespace)::EnzymePtr_specificity,
std::__1::__wrap_iter<const
> > boost::shared_ptr<pwiz::identdata::Enzyme> *>,
> > boost::iterators::use_default,
boost::iterators::use_default>,
> > std::__1::__less<int, int> >' requested here
> > return _VSTD::min_element(__first, __last,
> > ^
> > ./boost/boost/range/algorithm/min_element.hpp:44:17: note: in
> > instantiation of
> > function template specialization
> >
> >
'std::__1::min_element<boost::iterators::transform_iterator<pwiz::identdata::(anonymous
> >
> > namespace)::EnzymePtr_specificity,
std::__1::__wrap_iter<const
> > boost::shared_ptr<pwiz::identdata::Enzyme> *>,
> > boost::iterators::use_default, boost::iterators::use_default>
>'
> > requested
> > here
> > return std::min_element(boost::begin(rng), boost::end(rng));
> >
> >
> >
> > pwiz/data/identdata/Serializer_pepXML.cpp:418:41: note: in
instantiation of
> > function template specialization
> >
> >
'boost::range::min_element<boost::range_detail::transformed_range<pwiz::identdata::(anonymous
> >
> > namespace)::EnzymePtr_specificity, const
> >
std::__1::vector<boost::shared_ptr<pwiz::identdata::Enzyme>,
> >
std::__1::allocator<boost::shared_ptr<pwiz::identdata::Enzyme> >
> > > > >'
> > requested here
> > int minSpecificity =
*boost::range::min_element(sip.enzymes.enzymes
> > ...
> > ^
> > In file included from
pwiz/data/identdata/Serializer_pepXML.cpp:25:
> > In file included from
pwiz/data/identdata/Serializer_pepXML.hpp:27:
> > In file included from pwiz/data/identdata/IdentData.hpp:29:
> > In file included from ./pwiz/utility/misc/Exception.hpp:29:
> > In file included from
/usr/local/clang8/bin/../include/c++/v1/string:505:
> > In file included from
> > /usr/local/clang8/bin/../include/c++/v1/string_view:176:
> > In file included from
/usr/local/clang8/bin/../include/c++/v1/__string:57:
> > /usr/local/clang8/bin/../include/c++/v1/algorithm:2494:5: error:
> > static_assert
> > failed due to requirement
> >
> >
'__is_forward_iterator<boost::iterators::transform_iterator<pwiz::identdata::(anonymous
> >
> > namespace)::EnzymePtr_missedCleavages,
std::__1::__wrap_iter<const
> > boost::shared_ptr<pwiz::identdata::Enzyme> *>,
> > boost::iterators::use_default,
boost::iterators::use_default>
> > >::value'
> > "std::max_element requires a ForwardIterator"
> > static_assert(__is_forward_iterator<_ForwardIterator>::value,
> > ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> > /usr/local/clang8/bin/../include/c++/v1/algorithm:2512:19: note:
in
> > instantiation of function template specialization
> >
> >
'std::__1::max_element<boost::iterators::transform_iterator<pwiz::identdata::(anonymous
> >
> > namespace)::EnzymePtr_missedCleavages,
std::__1::__wrap_iter<const
> > boost::shared_ptr<pwiz::identdata::Enzyme> *>,
> > boost::iterators::use_default,
boost::iterators::use_default>,
> > std::__1::__less<int, int> >' requested here
> > return _VSTD::max_element(__first, __last,
> > ^
> > ./boost/boost/range/algorithm/max_element.hpp:44:17: note: in
> > instantiation of
> > function template specialization
> >
> >
'std::__1::max_element<boost::iterators::transform_iterator<pwiz::identdata::(anonymous
> >
> > namespace)::EnzymePtr_missedCleavages,
std::__1::__wrap_iter<const
> > boost::shared_ptr<pwiz::identdata::Enzyme> *>,
> > boost::iterators::use_default, boost::iterators::use_default>
>'
> > requested
> > here
> > return std::max_element(boost::begin(rng), boost::end(rng));
> > ...
> >
>
>
> --
> Brian D. Ripley, rip...@stats.ox.ac.uk
> Emeritus Professor of Applied Statistics, University of Oxford
>
>
>
>
> This email message may contain legally privileged and/or confidential
information. If you are not the intended recipient(s), or the employee or agent
responsible for the delivery of this message to the intended recipient(s), you are
hereby notified that any disclosure, copying, distribution, or use of this email
message is prohibited. If you have received this message in error, please notify
the sender immediately by e-mail and delete this email message from your computer.
Thank you.
This email message may contain legally privileged and/or confidential
information. If you are not the intended recipient(s), or the employee or
agent responsible for the delivery of this message to the intended
recipient(s), you are hereby notified that any disclosure, copying,
distribution, or use of this email message is prohibited. If you have received
this message in error, please notify the sender immediately by e-mail and
delete this email message from your computer. Thank you.
