[Bioc-devel] package RBGL requires CRAN dependency on devel branch
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()
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> 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
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
> > >
>
> > >
> > > 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
> > >
> > >
> > >
> > >
> > > This email message may contain legally privileged
and/or
> confidential information. If you are not the intended
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> employee or agent responsible for the delivery of this message
to the
> intended recipient(s), you are hereby notified that any
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> copying, distribution, or use of this email message is
prohibited. If you
> have received this message in error, please notify the sender
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Thank you.
> >
> >
> >
> >
> > This email message may contain legally privileged and/or
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> information. If you are not the intended recipient(s), or the
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