On Thu, May 2, 2013 at 7:37 AM, Dirk Eddelbuettel <edd@debian.org> wrote:

>
> On 2 May 2013 at 06:39, Vincent Carey wrote:
> | Thanks for inputs from Steffen and Steve.  When a considerable block of
> time
> | opens up I will see about the effort required to have RBGL make use of
> this.
> |  The compressed size of boost 1.49 is abut 49MB, while the compressed
> size of
> | BH is 1.4 MB, and the subset that I use for RBGL has compressed size 1.9
> MB.
> |  Is there any down side to distributing the entire header set apart from
> | expansion to 444 MB on installation?  I noticed that bitSeq needed to
> remove
>
> Yes, 444mb is considered a downside.
>
> Our thought process is/was that there are lots of packages that use only a
> subset of Boost -- the 80/20 rule clearly applies.  I know I have my
> fingers
> in one or two packages that apply, but Jay and Mike drove the concrete
> first
> build of BH by providing what bigmemory needed.
>
> RBGL may be pushing it, but we would surely try to accomodate it, provided
> this would work without linking.  We really want to try to limit ourselves
> to
> templates here.
>

I think this can be done.  I'll try and get more precise on the necessary
inclusions in the next couple of weeks.


>
> | an inclusion of iostream.h from one of the headers used.... once you
> need such
> | customization the benefits of a centrally managed distribution diminish.
>
> Are you saying bitSeq only builds when certain Boost headers are removed
> from
> a full Boost installation or copy?  That sounds weird.
>
>
Sorry to be unclear.  The following is a README from bitSeq src/boost
folder.  Note the
"CHANGES" entry.

Subset of boost libraries, version 1.53.0. (22.3.2013)
------------------------------------------------------

DEPENDENCY:
-----------
 boost/random/gamma_distribution.hpp
 boost/random/mersenne_twister.hpp
 boost/random/normal_distribution.hpp
 boost/random/uniform_01.hpp

CHANGES:
--------
random/uniform_01.hpp
 -> commented out line 19:
   #include<iostream>

CREATED VIA:
------------
[ no need to build all libraries, just use bcp tool to copy relevant
headers ]
1) download boost sources from (http://sourceforge.net/projects/boost/)
2) unpack
3) bootstrap and build bcp:
cd <path_to_boost>/boost_1_53_0
./bootstrap.sh
./bjam tools/bcp
4) run bcp to extract relevant files and save them in directory boost in
<destination dir>
./dist/bin/bcp \
   boost/random/gamma_distribution.hpp \
   boost/random/mersenne_twister.hpp \
   boost/random/normal_distribution.hpp \
   boost/random/uniform_01.hpp \
   <destination dir>
5) copy LICENSE_1_0.txt and create README


> Dirk
>
> | On Thu, May 2, 2013 at 1:50 AM, Steffen Neumann <sneumann@ipb-halle.de>
> wrote:
> |
> |     Hi Vincent,
> |
> |     BH currently works the way that the package sources
> |     (and that includes BH/inst/include/boost/*) are
> |     automagically created by bcp'ing the dependencies
> |     of *some* R packages (e.g. bigmemory on rforge).
> |
> |     John and Dirk et al said that people can ask
> |     for additional dependencies on the tracker [1].
> |
> |     If you want to port your package to BH
> |     and figure out the required dependencies,
> |     check out svn://r-forge.r-project.org/svnroot/boostheaders
> |     and edit boostheaders/CreateBoost.R (see how I munged
> |     that file on [2] ...)
> |
> |     Then iterate over
> |
> |             cd boostheaders
> |             rm -rf pkg/BH
> |             R --vanilla <CreateBoost.R
> |             R CMD INSTALL pkg/BH
> |             R CMD INSTALL /your/package/
> |
> |     until success. Unfortunately with boost, it might not
> |     be as straightforward as adding " graph ",
> |     that's why I have that insane "find /my/package -exec bcp -scan"
> |     in my hacked [2]. Also note that in a hacked version of
> |     CreateBoost.R it is possible to switch between boost versions.
> |
> |     Yours,
> |     Steffen
> |
> |
> |     [1]
> https://r-forge.r-project.org/tracker/?atid=5310&group_id=1469&func=
> |     browse
> |     [2]
> https://github.com/sneumann/boostheaders/blob/master/CreateBoost.R
> |
> |
> |
> |
> |
> |
> |
> |
> |     On Wed, 2013-05-01 at 22:47 -0400, Vincent Carey wrote:
> |     > are the headers for the "boost graph library" purposely excluded?
>  i
> |     > do not see them in BH/include
> |     >
> |     > On Wed, May 1, 2013 at 6:19 PM, Steffen Neumann
> |     > <sneumann@ipb-halle.de> wrote:
> |     >         Hi BioC world,
> |     >
> |     >         I'd like to draw the attention to the boostheaders (or BH)
> |     >         package on rforge.org [1], which packages the boost
> headers
> |     >         so that other packages can link/include them.
> |     >
> |     >         I know a few packages on BioC are using -- and embedding --
> |     >         boost.
> |     >         There have also been some discussion a long time ago [2]
> |     >
> |     >         This might be a chance to get a single package that
> contains
> |     >         boost ?
> |     >
> |     >         Yours,
> |     >         Steffen
> |     >
> |     >         [1] http://r-forge.r-project.org/projects/boostheaders/
> |     >         [2]
> |     >         https://stat.ethz.ch/pipermail/bioc-devel/2009-February/
> |     001808.html
> |     >
> |     >
> |     >
> |     >         --
> |     >         IPB Halle                    AG Massenspektrometrie
> |     &
> |     >         Bioinformatik
> |     >         Dr. Steffen Neumann          http://www.IPB-Halle.DE
> |     >         Weinberg 3                   http://msbi.bic-gh.de
> |     >         06120 Halle                  Tel. +49 (0) 345 5582 -
> |     1470
> |     >                                           +49 (0)
> |     345 5582 - 0
> |     >         sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409
> |     >
> |     >         _______________________________________________
> |     >         Bioc-devel@r-project.org mailing list
> |     >         https://stat.ethz.ch/mailman/listinfo/bioc-devel
> |     >
> |
> |
> |     --
> |     IPB Halle                    AG Massenspektrometrie &
> |     Bioinformatik
> |     Dr. Steffen Neumann          http://www.IPB-Halle.DE
> |     Weinberg 3                   http://msbi.bic-gh.de
> |     06120 Halle                  Tel. +49 (0) 345 5582 - 1470
> |                                       +49 (0) 345 5582 - 0
> |     sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409
> |
> |
> |
> |
> | ----------------------------------------------------------------------
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> |
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>
> --
> Dirk Eddelbuettel | edd@debian.org | http://dirk.eddelbuettel.com
>

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