[Bioc-devel] package RBGL requires CRAN dependency on devel branch
Dear Bioconductor, The devel version of package RBGL is flunking build. This package has been modified to include header files in the CRAN package 'BH' instead of using a local tarball of the header files. We consider this an improvement because the 'BH' maintainers update their package every time a new version of boost is released, but rebuilding the included tarball is unreliable. Is it possible to request inclusion of a CRAN package dependency in a Bioconductor package? If not, how would Bioconductor recommend we handle this? (Full disclosure: the BH package has all the header files for all of boost. This is a lot more disk space then we need, because we only need the BGL.) thanks, - Sam
On 3/22/19 7:28 AM, Morgan, Martin wrote:
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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" <spollack at 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" <ripley at 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, ripley at stats.ox.ac.uk
> Emeritus Professor of Applied Statistics, University of Oxford
>
>
>
>
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