[Bioc-devel] [Boostheaders-devel] Boost packaged on rforge
Peter Glaus
glaus at cs.man.ac.uk
Fri May 3 11:42:22 CEST 2013
Hi Vincent,
regarding BitSeq:
As far as I can remember we only removed the #include<iostream> as
earlier versions of R CMD check used to complain about using iostream in
the source code. I can't fully verify it as current version of R builds
and checks without warning even without that change. (The other option
is that I wanted to make sure that iostream won't be used as it can
cause problems with R.).
Other than that, I don't recall any problems with Boost and iostream.
However, BitSeq uses just a very small subset of Boost headers (3.8M
unpacked).
Peter.
On 02/05/13 15:01, Vincent Carey wrote:
> 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
>>
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