<br><br><div class="gmail_quote">On Thu, May 2, 2013 at 7:37 AM, Dirk Eddelbuettel <span dir="ltr"><<a href="mailto:edd@debian.org" target="_blank">edd@debian.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im"><br>
On 2 May 2013 at 06:39, Vincent Carey wrote:<br>
| Thanks for inputs from Steffen and Steve. When a considerable block of time<br>
| opens up I will see about the effort required to have RBGL make use of this.<br>
| The compressed size of boost 1.49 is abut 49MB, while the compressed size of<br>
| BH is 1.4 MB, and the subset that I use for RBGL has compressed size 1.9 MB.<br>
| Is there any down side to distributing the entire header set apart from<br>
| expansion to 444 MB on installation? I noticed that bitSeq needed to remove<br>
<br>
</div>Yes, 444mb is considered a downside.<br>
<br>
Our thought process is/was that there are lots of packages that use only a<br>
subset of Boost -- the 80/20 rule clearly applies. I know I have my fingers<br>
in one or two packages that apply, but Jay and Mike drove the concrete first<br>
build of BH by providing what bigmemory needed.<br>
<br>
RBGL may be pushing it, but we would surely try to accomodate it, provided<br>
this would work without linking. We really want to try to limit ourselves to<br>
templates here.<br></blockquote><div><br></div><div>I think this can be done. I'll try and get more precise on the necessary inclusions in the next couple of weeks.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im"><br>
| an inclusion of iostream.h from one of the headers used.... once you need such<br>
| customization the benefits of a centrally managed distribution diminish.<br>
<br>
</div>Are you saying bitSeq only builds when certain Boost headers are removed from<br>
a full Boost installation or copy? That sounds weird.<br>
<br></blockquote><div><br></div><div>Sorry to be unclear. The following is a README from bitSeq src/boost folder. Note the</div><div>"CHANGES" entry.</div><div><br></div><div>Subset of boost libraries, version 1.53.0. (22.3.2013)</div>
<div>------------------------------------------------------</div><div><br></div><div>DEPENDENCY:</div><div>-----------</div><div> boost/random/gamma_distribution.hpp</div><div> boost/random/mersenne_twister.hpp</div><div>
boost/random/normal_distribution.hpp</div><div> boost/random/uniform_01.hpp</div><div><br></div><div>CHANGES:</div><div>--------</div><div>random/uniform_01.hpp</div><div> -> commented out line 19:</div><div> #include<iostream></div>
<div><br></div><div>CREATED VIA:</div><div>------------</div><div>[ no need to build all libraries, just use bcp tool to copy relevant headers ]</div><div>1) download boost sources from (<a href="http://sourceforge.net/projects/boost/">http://sourceforge.net/projects/boost/</a>)</div>
<div>2) unpack</div><div>3) bootstrap and build bcp:</div><div>cd <path_to_boost>/boost_1_53_0</div><div>./bootstrap.sh</div><div>./bjam tools/bcp</div><div>4) run bcp to extract relevant files and save them in directory boost in <destination dir></div>
<div>./dist/bin/bcp \</div><div> boost/random/gamma_distribution.hpp \</div><div> boost/random/mersenne_twister.hpp \</div><div> boost/random/normal_distribution.hpp \</div><div> boost/random/uniform_01.hpp \</div>
<div> <destination dir></div><div>5) copy LICENSE_1_0.txt and create README</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dirk<br>
<div><div class="h5"><br>
| On Thu, May 2, 2013 at 1:50 AM, Steffen Neumann <<a href="mailto:sneumann@ipb-halle.de">sneumann@ipb-halle.de</a>> wrote:<br>
|<br>
| Hi Vincent,<br>
|<br>
| BH currently works the way that the package sources<br>
| (and that includes BH/inst/include/boost/*) are<br>
| automagically created by bcp'ing the dependencies<br>
| of *some* R packages (e.g. bigmemory on rforge).<br>
|<br>
| John and Dirk et al said that people can ask<br>
| for additional dependencies on the tracker [1].<br>
|<br>
| If you want to port your package to BH<br>
| and figure out the required dependencies,<br>
| check out svn://<a href="http://r-forge.r-project.org/svnroot/boostheaders" target="_blank">r-forge.r-project.org/svnroot/boostheaders</a><br>
| and edit boostheaders/CreateBoost.R (see how I munged<br>
| that file on [2] ...)<br>
|<br>
| Then iterate over<br>
|<br>
| cd boostheaders<br>
| rm -rf pkg/BH<br>
| R --vanilla <CreateBoost.R<br>
| R CMD INSTALL pkg/BH<br>
| R CMD INSTALL /your/package/<br>
|<br>
| until success. Unfortunately with boost, it might not<br>
| be as straightforward as adding " graph ",<br>
| that's why I have that insane "find /my/package -exec bcp -scan"<br>
| in my hacked [2]. Also note that in a hacked version of<br>
| CreateBoost.R it is possible to switch between boost versions.<br>
|<br>
| Yours,<br>
| Steffen<br>
|<br>
|<br>
| [1] <a href="https://r-forge.r-project.org/tracker/?atid=5310&group_id=1469&func=" target="_blank">https://r-forge.r-project.org/tracker/?atid=5310&group_id=1469&func=</a><br>
| browse<br>
| [2] <a href="https://github.com/sneumann/boostheaders/blob/master/CreateBoost.R" target="_blank">https://github.com/sneumann/boostheaders/blob/master/CreateBoost.R</a><br>
|<br>
|<br>
|<br>
|<br>
|<br>
|<br>
|<br>
|<br>
| On Wed, 2013-05-01 at 22:47 -0400, Vincent Carey wrote:<br>
| > are the headers for the "boost graph library" purposely excluded? i<br>
| > do not see them in BH/include<br>
| ><br>
| > On Wed, May 1, 2013 at 6:19 PM, Steffen Neumann<br>
| > <<a href="mailto:sneumann@ipb-halle.de">sneumann@ipb-halle.de</a>> wrote:<br>
| > Hi BioC world,<br>
| ><br>
| > I'd like to draw the attention to the boostheaders (or BH)<br>
| > package on <a href="http://rforge.org" target="_blank">rforge.org</a> [1], which packages the boost headers<br>
| > so that other packages can link/include them.<br>
| ><br>
| > I know a few packages on BioC are using -- and embedding --<br>
| > boost.<br>
| > There have also been some discussion a long time ago [2]<br>
| ><br>
| > This might be a chance to get a single package that contains<br>
| > boost ?<br>
| ><br>
| > Yours,<br>
| > Steffen<br>
| ><br>
| > [1] <a href="http://r-forge.r-project.org/projects/boostheaders/" target="_blank">http://r-forge.r-project.org/projects/boostheaders/</a><br>
| > [2]<br>
| > <a href="https://stat.ethz.ch/pipermail/bioc-devel/2009-February/" target="_blank">https://stat.ethz.ch/pipermail/bioc-devel/2009-February/</a><br>
| 001808.html<br>
| ><br>
| ><br>
| ><br>
| > --<br>
| > IPB Halle AG Massenspektrometrie<br>
| &<br>
| > Bioinformatik<br>
| > Dr. Steffen Neumann <a href="http://www.IPB-Halle.DE" target="_blank">http://www.IPB-Halle.DE</a><br>
| > Weinberg 3 <a href="http://msbi.bic-gh.de" target="_blank">http://msbi.bic-gh.de</a><br>
| > 06120 Halle Tel. <a href="tel:%2B49%20%280%29%20345%205582" value="+493455582">+49 (0) 345 5582</a> -<br>
| 1470<br>
| > +49 (0)<br>
| 345 5582 - 0<br>
| > sneumann(at)IPB-Halle.DE Fax. <a href="tel:%2B49%20%280%29%20345%205582%20-%201409" value="+4934555821409">+49 (0) 345 5582 - 1409</a><br>
| ><br>
| > _______________________________________________<br>
| > <a href="mailto:Bioc-devel@r-project.org">Bioc-devel@r-project.org</a> mailing list<br>
| > <a href="https://stat.ethz.ch/mailman/listinfo/bioc-devel" target="_blank">https://stat.ethz.ch/mailman/listinfo/bioc-devel</a><br>
| ><br>
|<br>
|<br>
| --<br>
| IPB Halle AG Massenspektrometrie &<br>
| Bioinformatik<br>
| Dr. Steffen Neumann <a href="http://www.IPB-Halle.DE" target="_blank">http://www.IPB-Halle.DE</a><br>
| Weinberg 3 <a href="http://msbi.bic-gh.de" target="_blank">http://msbi.bic-gh.de</a><br>
| 06120 Halle Tel. <a href="tel:%2B49%20%280%29%20345%205582%20-%201470" value="+4934555821470">+49 (0) 345 5582 - 1470</a><br>
| <a href="tel:%2B49%20%280%29%20345%205582%20-%200" value="+4934555820">+49 (0) 345 5582 - 0</a><br>
| sneumann(at)IPB-Halle.DE Fax. <a href="tel:%2B49%20%280%29%20345%205582%20-%201409" value="+4934555821409">+49 (0) 345 5582 - 1409</a><br>
|<br>
|<br>
|<br>
|<br>
</div></div>| ----------------------------------------------------------------------<br>
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<span class="HOEnZb"><font color="#888888"><br>
--<br>
Dirk Eddelbuettel | <a href="mailto:edd@debian.org">edd@debian.org</a> | <a href="http://dirk.eddelbuettel.com" target="_blank">http://dirk.eddelbuettel.com</a><br>
</font></span></blockquote></div><br>