On Thu, May 2, 2013 at 7:37 AM, Dirk Eddelbuettel <e...@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 <sneum...@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 > | > <sneum...@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 > | > | > | > | > | ---------------------------------------------------------------------- > | _______________________________________________ > | Boostheaders-devel mailing list > | boostheaders-de...@lists.r-forge.r-project.org > | > http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/boostheaders-devel > > -- > Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
