[Bioc-devel] [Boostheaders-devel] Boost packaged on rforge

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
|
|
|
|
| ----------------------------------------------------------------------
| _______________________________________________
| Boostheaders-devel mailing list
| Boostheaders-devel at lists.r-forge.r-project.org
|
http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/boostheaders-devel

--
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com

	[[alternative HTML version deleted]]