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>
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>
> 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.
>

-- 
The information in this e-mail is intended only for the ...{{dropped:18}}

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