[Boostheaders-devel] [Bioc-devel] Boost packaged on rforge
Vincent Carey
stvjc at channing.harvard.edu
Thu May 2 16:01:03 CEST 2013
On Thu, May 2, 2013 at 7:37 AM, Dirk Eddelbuettel <edd at 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 at 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 at 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 at 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 at debian.org | http://dirk.eddelbuettel.com
>
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