Message-ID: <89d911aa-968e-b822-7e73-de1443f3b172@gmail.com>
Date: 2019-03-27T05:06:31Z
From: Aaron Lun
Subject: [Bioc-devel] package RBGL requires CRAN dependency on devel branch
In-Reply-To: <CAC2h7us5Ks2h=sMbgbs58LT1n6r8PL_AHRS6Xkps_=DC5XJh1w@mail.gmail.com>
> well, we can't fix this in old branches of Bioc.
Sure, but one could say that about breaking changes to any CRAN package.
Nothing particularly special about BH on that point.
> My POV is that we need to consider - in some sense - lock down CRAN with
> a Bioc release.
That's probably worth considering. For example, it would be pretty cool
to just supply a date and BiocManager could figure out the last
successful release versions of all CRAN/BioC packages at that time.
-A
> On Tue, Mar 26, 2019 at 12:45 AM Aaron Lun
> <infinite.monkeys.with.keyboards at gmail.com
> <mailto:infinite.monkeys.with.keyboards at gmail.com>> wrote:
>
> My 2 cents - API-breaking changes to BH are no more of an issue than
> breaking changes to any other CRAN package. We just hope that it
> doesn't
> happen too often and we deal with it when the time comes; that's the
> whole point of getting frequent release builds to check for these cases.
>
> If we were discussing a package that distributed a shared library, then
> greater concern would be warranted if updates to the library
> resulted in
> ABI incompatibilities. This could result in very cryptic errors at link
> time, load time, or possibly segmentation faults, who knows.
>
> But BH is a header-only library, so breaking changes will most likely
> cause compilation errors that are obvious and easy to fix. Well, easy
> enough if you were able to write C++ code in the first place.
>
> -A
>
>
> On 25/03/2019 08:39, Vincent Carey wrote:
> > On Mon, Mar 25, 2019 at 10:57 AM Kasper Daniel Hansen <
> > kasperdanielhansen at gmail.com
> <mailto:kasperdanielhansen at gmail.com>> wrote:
> >
> >> There are no issues with depending on CRAN packages.
> >>
> >> But I would advise caution. On one hand it is great that boost gets
> >> updated regularly. On the other hand, it could lead to
> incompatibilities
> >> with RBGL and then you have to update that package rapidly. Also
> - and this
> >> is something we could consider addressing - the CRAN imports of
> Bioc are
> >> not locked down. By which I mean, you release RBGL in
> Bioconductor X. After
> >> release (or perhaps even after next Bioc release) BH is updated in a
> >> non-backwards compatible way and now the old code is hosed.
> Having said
> >> that, so far we have been ignoring it (I think) and the same
> issue arises
> >> with Rcpp.
> >>
> >> Do you have any idea how often Boost breaks compatibility?? I would
> >> strongly advise to download the last couple of BH releases and
> test with
> >> RBGL. While kind of irrelevant in some sense, it will give you
> an idea of
> >> how fast Boost / BH evolves.
> >>
> >
> > These are good points.? In this particular case I believe that
> Boost Graph
> > Library evolves very slowly and
> > backwards compatibility is not endangered.? It is an early
> component of
> > Boost.? On the other hand, BH has
> > no obligation to provide the graph (BGL) headers, and I believe
> that in
> > early incarnations of BH, some headers
> > needed for RBGL were not there.? So there are maintenance
> vulnerabilities
> > to this approach, but I think it is better
> > if we stick with the maintained BH as long as this works.? Should
> this
> > approach fail (and your scenario of
> > CRAN package changes breaking bioc must be kept in mind) we can
> go back to
> > tarball distribution if necessary.
> >
> >
> >>
> >> On Mon, Mar 25, 2019 at 8:03 AM Martin Morgan
> <mtmorgan.bioc at gmail.com <mailto:mtmorgan.bioc at gmail.com>>
> >> wrote:
> >>
> >>> ...also Bioconductor knows all about CRAN -- see the repositories
> >>> returned by
> >>>
> >>>> BiocManager::repositories()
> >>>? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?BioCsoft
> >>>? ? ? ? ? ? ?"https://bioconductor.org/packages/3.9/bioc"
> >>>? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? BioCann
> >>> "https://bioconductor.org/packages/3.9/data/annotation"
> >>>? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? BioCexp
> >>> "https://bioconductor.org/packages/3.9/data/experiment"
> >>>? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? BioCworkflows
> >>>? ? ? ? "https://bioconductor.org/packages/3.9/workflows"
> >>>? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?CRAN
> >>>? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?"https://cran.rstudio.com"
> >>>>
> >>>
> >>> ?On 3/25/19, 7:42 AM, "Martin Morgan" <mtmorgan.bioc at gmail.com
> <mailto:mtmorgan.bioc at gmail.com>> wrote:
> >>>
> >>>? ? ? 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 at r-project.org
> <mailto:bioc-devel-bounces at r-project.org> on behalf of
> stvjc at channing.harvard.edu <mailto:stvjc at 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 at jimmy.harvard.edu <mailto: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 <mailto: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 <mailto: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 <mailto:ripley at 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}}
> >>>
> >>>? ? ? ? ? _______________________________________________
> >>> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>
> mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>
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