On Mon, Mar 25, 2019 at 10:57 AM Kasper Daniel Hansen <
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>
wrote:
...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> 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 on behalf of 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>
wrote:
> Dear Bioconductor,
>
> The devel version of package RBGL is flunking build.
>
> This package has been modified to include header files in the
> package 'BH' instead of using a local tarball of the header
> consider this an improvement because the 'BH' maintainers
> package every time a new version of boost is released, but
> the included tarball is unreliable.
>
> Is it possible to request inclusion of a CRAN package
> Bioconductor package? If not, how would Bioconductor recommend
> this?
>
> (Full disclosure: the BH package has all the header files for
> boost. This is a lot more disk space then we need, because we
> 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.
> these changes to the release and devel branches of RBGL? I've
> >
> > ?On 3/22/19, 5:15 AM, "Samuela Pollack" <
spollack at jimmy.harvard.edu>
> >
> > We have a temporary fix which we believe will alleviate
> >
> > The only routine in RBGL that does not compile under
> > is the routine that implements betweenness connectivity
> > seems to be a rarely-used routine, so we have
> > from RBGL and put in a message explaining how users may
> >
> > I have contacted Professor Jeremy Siek at in
> > best to proceed. It is possible this will have to be
> > probably not in time for boost 1.70.
> >
> > For clarity: the incompatibility is not in clang. The
> > in the llvm c++ standard library. Mac users who build
> > fine, as long as they don't link in the llvm C++
> > 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>
> > >
> > > clang 8.0.0 is now released, and these fail
> > > 50 CRAN packages which depend on them).
> > >
> > > Reminder: this is with clang's native libc++, as
> > >
> > > 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
> > > > be near-final (it is overdue for release).
> > > > rc1.) In both cases the problems are with
> > > >
> > > > 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:
> > > > static_assert
> > > > failed due to requirement
> > > >
> > > >
'__is_forward_iterator<boost::detail::undirected_edge_iter<std::__1::__list_iterator<boost::list_edge<unsigned
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
> 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
'std::__1::max_element<boost::detail::undirected_edge_iter<std::__1::__list_iterator<boost::list_edge<unsigned
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,
> > > > 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:
> > > > instantiation of function template
'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,
> > > > 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>,
> boost::adj_list_edge_property_map<boost::undirected_tag,
> > > > 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,
boost::property<boost::vertex_centrality_t,
> > > > boost::no_property> >, unsigned long>
> > > > betweenness_centrality_clustering(g, done,
> > > > ^
> > > > bbc.cpp:122:3: note: in instantiation of
'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,
> > > > 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>,
> boost::adj_list_edge_property_map<boost::undirected_tag,
> > > > 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
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:
> > > > 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>
> > > > "std::min_element requires a
> static_assert(__is_forward_iterator<_ForwardIterator>::value,
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/clang8/bin/../include/c++/v1/algorithm:2445:19:
> > > > instantiation of function template
'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
> > > > return _VSTD::min_element(__first, __last,
> > > > ^
> > > >
./boost/boost/range/algorithm/min_element.hpp:44:17: note:
> > > > 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),
> > > >
> > > >
> > > >
> > > >
pwiz/data/identdata/Serializer_pepXML.cpp:418:41: note: in
> > > > 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:
> > > > 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>
> > > > "std::max_element requires a
> static_assert(__is_forward_iterator<_ForwardIterator>::value,
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/clang8/bin/../include/c++/v1/algorithm:2512:19:
> > > > instantiation of function template
'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
> > > > return _VSTD::max_element(__first, __last,
> > > > ^
> > > >
./boost/boost/range/algorithm/max_element.hpp:44:17: note:
> > > > 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),
> > >
> > >
> > > --
> > > Brian D. Ripley,
> > > Emeritus Professor of Applied Statistics,
> > >
> > >
> > >
> > >
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> >
> >
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