[Bioc-devel] package RBGL requires CRAN dependency on devel branch

Martin Morgan mtmorg@n@b|oc @end|ng |rom gm@||@com
Mon Mar 25 12:42:34 CET 2019


I think the usual incantation in configure files is ${R_HOME}/bin/R ... R_HOME is the path to R set by the command that starts to build or install the package, whereas Rscript is found on the search path.

Martin

On 3/25/19, 7:33 AM, "Bioc-devel on behalf of Vincent Carey" <bioc-devel-bounces using r-project.org on behalf of stvjc using channing.harvard.edu> wrote:

    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 <spollack using 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" <spollack using 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 using 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 using stats.ox.ac.uk
    > >      >      Emeritus Professor of Applied Statistics, University of
    > Oxford
    > >      >
    > >      >
    > >      >
    > >      >
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    > >
    > >
    > > This email message may contain legally privileged and/or confidential
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