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

Mon, Mar 25, 2019 4:32 AM

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

Thread (13 messages)