[Boostheaders-devel] iostream in BH package ?

[Dirk Eddelbuettel]

On 1 May 2013 at 23:06, Steffen Neumann wrote:
| Hi Dirk,
| 
| On Wed, 2013-05-01 at 13:46 -0500, Dirk Eddelbuettel wrote:
| [...]
| > Of course, but there are a few notable exceptions. Boost regex is one, and
| > the system / error code library you have here is another.
| 
| And I need both...
| 
| I just created an 
| 	rforge/boostheaders/BoostHeadersROOT/src/Makevars
| 
| with 
| 
| 	OBJECTS=\
| 	../inst/include/libs/system/src/error_code.o \
| 	[...]
| 	../inst/include/libs/regex/src/regex.o \
| 	../inst/include/libs/regex/src/wide_posix_api.o \
| 	[...]
| 
| 	PKG_CPPFLAGS=-I ../inst/include
| 
| and upon R CMD INSTALL BH I got an
| /usr/local/lib/R/site-library/BH/libs/BH.so

Interesting. 

In a way related to how Rcpp also provides its libRcpp.{a,so}.  But recall
that the system linker cannot link against BH.so (you need libBH.so) and that
from having R dynamically load BH we won't yet get the symbols resolved at
package compile/link time.

Also, what I am a little afraid of is ... us dropping the 'configure' step so
that we may silently end up with 32 / 64 bit mixups etc pp (as we're not
using Boost properly installed but just copied).  But we already do that now
so it may not get worse. 
 
| > We can't help with that as this would get us towards the need for linking,
| > configure, ... and all that.
| So far I got away without any need for configure.
| The mzR package then uses PKG_LDFLAGS to link th BH.so into mzR.so

How?  With -LBH.so?

| My main problem at the moment is to get all boost headers
| required for mzR into BH without copying *all* of boost,
| which I do with a very ugly 
| 
| 	system  (paste('find /vol/R/BioC/devel-29/mzR/src/pwiz -type f ',
|             '-exec bcp --scan --boost=', boostroot,
|             ' {}  ', 
|             pkgdir, '/inst/include \\; >> bcp.log ', sep=''))
|
| That'd need a bit of streamlining. My work-in-progress can be found at 
| 
| 	https://github.com/sneumann/mzR/tree/BH
| and	https://github.com/sneumann/boostheaders

I may not have time to play, sadly.

Dirk
 
| Caveat, the boostheaders will create a BH with 1.43.0,
| because the current mzR / pwiz code won't work with 1.51.0 ...
| 
| What do you think ?
| 
| Yours,
| Steffen
| 
| -- 
| 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
| 

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