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
>> with RBGL and then you have to update that package rapidly. Also
>> is something we could consider addressing - the CRAN imports of
>> not locked down. By which I mean, you release RBGL in
>> release (or perhaps even after next Bioc release) BH is updated in a
>> non-backwards compatible way and now the old code is hosed.
>> that, so far we have been ignoring it (I think) and the same
>> 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
>> RBGL. While kind of irrelevant in some sense, it will give you
>> how fast Boost / BH evolves.
>>
>
> These are good points.? In this particular case I believe that
> Library evolves very slowly and
> backwards compatibility is not endangered.? It is an early
> Boost.? On the other hand, BH has
> no obligation to provide the graph (BGL) headers, and I believe
> early incarnations of BH, some headers
> needed for RBGL were not there.? So there are maintenance
> to this approach, but I think it is better
> if we stick with the maintained BH as long as this works.? Should
> approach fail (and your scenario of
> CRAN package changes breaking bioc must be kept in mind) we can
> 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>>
>>> ...also Bioconductor knows all about CRAN -- see the repositories
>>> returned by
>>>
>>>> BiocManager::repositories()
>>>
>>> ?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 is the path to R set by the command that starts to
>>> 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
>>> 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
##############################################################################
##############################################################################
>>>
>>>
>>>? ? ? ? ? * 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.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
>>> CRAN
>>>? ? ? ? ? > package 'BH' instead of using a local tarball of the
>>> files. We
>>>? ? ? ? ? > consider this an improvement because the 'BH'
>>> update their
>>>? ? ? ? ? > package every time a new version of boost is
>>> 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
>>> we handle
>>>? ? ? ? ? > this?
>>>? ? ? ? ? >
>>>? ? ? ? ? > (Full disclosure: the BH package has all the header
>>> all of
>>>? ? ? ? ? > boost. This is a lot more disk space then we need,
>>> 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
>>> you push
>>>? ? ? ? ? > these changes to the release and devel branches of
>>> 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
>>> the
>>>? ? ? ? ? > difficulty.
>>>? ? ? ? ? > >
>>>? ? ? ? ? > >? ? ? The only routine in RBGL that does not
>>> LLVM-9.0
>>>? ? ? ? ? > system
>>>? ? ? ? ? > >? ? ? is the routine that implements betweenness
>>> clustering.
>>>? ? ? ? ? > This
>>>? ? ? ? ? > >? ? ? seems to be a rarely-used routine, so we have
>>> temporarily removed it
>>>? ? ? ? ? > >? ? ? from RBGL and put in a message explaining how
>>> replace it
>>>? ? ? ? ? > easily.
>>>? ? ? ? ? > >
>>>? ? ? ? ? > >? ? ? I have contacted Professor Jeremy Siek at in
>>> to discuss
>>>? ? ? ? ? > how
>>>? ? ? ? ? > >? ? ? best to proceed. It is possible this will
>>> fixed in BGL,
>>>? ? ? ? ? > >? ? ? probably not in time for boost 1.70.
>>>? ? ? ? ? > >
>>>? ? ? ? ? > >? ? ? For clarity: the incompatibility is not in
>>>? ? ? ? ? > incompatibility is
>>>? ? ? ? ? > >? ? ? in the llvm c++ standard library. Mac users
>>> with clang
>>>? ? ? ? ? > will be
>>>? ? ? ? ? > >? ? ? fine, as long as they don't link in the llvm
>>> which most
>>>? ? ? ? ? > >? ? ? wouldn't think to do and Apple does not
>>>? ? ? ? ? > >
>>>? ? ? ? ? > >? ? ? 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
>>> too (and
>>>? ? ? ? ? > break about
>>>? ? ? ? ? > >? ? ? >? ? ? 50 CRAN packages which depend on them).
>>>? ? ? ? ? > >? ? ? >
>>>? ? ? ? ? > >? ? ? >? ? ? Reminder: this is with clang's native
>>> documented
>>>? ? ? ? ? > at
>>>? ? ? ? ? > >? ? ? >
>>>? ? ? ? ? >
>>>
>>>? ? ? ? ? > >? ? ? >
>>>? ? ? ? ? > >? ? ? >? ? ? We really need fixes in both 3.8 and 3.9.
>>>? ? ? ? ? > >? ? ? >
>>>? ? ? ? ? > >? ? ? >? ? ? BDR
>>>? ? ? ? ? > >? ? ? >
>>>? ? ? ? ? > >? ? ? >? ? ? On 28/02/2019 18:52, Prof Brian Ripley
>>>? ? ? ? ? > >? ? ? >? ? ? > These packages fail to install with
>>> 8.0.0rc3, which
>>>? ? ? ? ? > is supposed to
>>>? ? ? ? ? > >? ? ? >? ? ? > be near-final (it is overdue for
>>> (AFAIR they
>>>? ? ? ? ? > did install with
>>>? ? ? ? ? > >? ? ? >? ? ? > rc1.)? In both cases the problems
>>> 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'
>>> 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
>>> 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
>>> 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,
>>>? ? ? ? ? > 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> >,
>>> 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,
>>>? ? ? ? ? > 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> >'
>>> 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
>>> 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> >'
>>> 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
>>> 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> >'
>>> 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
>>> and/or
>>>? ? ? ? ? > confidential information.? If you are not the intended
>>> recipient(s), or the
>>>? ? ? ? ? > employee or agent responsible for the delivery of
>>> 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
>>> immediately
>>>? ? ? ? ? > by e-mail and delete this email message from your
>>> Thank you.
>>>? ? ? ? ? > >
>>>? ? ? ? ? > >
>>>? ? ? ? ? > >
>>>? ? ? ? ? > >
>>>? ? ? ? ? > > This email message may contain legally privileged
>>> confidential
>>>? ? ? ? ? > information.? If you are not the intended
>>> employee or
>>>? ? ? ? ? > agent responsible for the delivery of this message
>>> intended
>>>? ? ? ? ? > recipient(s), you are hereby notified that any
>>> copying,
>>>? ? ? ? ? > distribution, or use of this email message is
>>> you have
>>>? ? ? ? ? > received this message in error, please notify the sender
>>> immediately by
>>>? ? ? ? ? > e-mail and delete this email message from your
>>> 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>