...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.b...@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-boun...@r-project.org on behalf of st...@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 <
spoll...@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" <
spoll...@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" <
rip...@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,
rip...@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}}
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