Could be an issue with the configure script. Will check. - Sam
On 3/25/19 7:32 AM, Vincent Carey wrote: > > External Email - Use Caution > > The error on linux for 3.9: > > ############################################################################## > ############################################################################## > ### > ### Running command: > ### > ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL RBGL > ### > ############################################################################## > ############################################################################## > > > * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ > * installing *source* package ‘RBGL’ ... > ** using staged installation > checking R package BH ... no > configure: error: R package BH not found. > ERROR: configuration failed for package ‘RBGL’ > * removing ‘/home/biocbuild/bbs-3.9-bioc/R/library/RBGL’ > * restoring previous ‘/home/biocbuild/bbs-3.9-bioc/R/library/RBGL’ > Note that BiocParallel also uses BH and succeeds > configure: creating ./config.status > config.status: creating src/Makevars > ** libs > g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG > -I"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I/usr/local/include > -fpic -g -O2 -Wall -c ipcmutex.cpp -o ipcmutex.o > In file included from > /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0, > from > /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19, > from > /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23, > from > /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/seed_impl.hpp:26, > from > /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/mersenne_twister.hpp:30, > from > /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:17, > So could it be an issue with the configure script? > > On Mon, Mar 25, 2019 at 7:22 AM Samuela Pollack > <spoll...@jimmy.harvard.edu <mailto:spoll...@jimmy.harvard.edu>> wrote: > > 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: > > 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 <mailto: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 <mailto: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 > <mailto: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. > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel