[Phylobase-devl] New phylobase build approach using static libncl (Was: Rcpp and OS X compiliation)

Dirk Eddelbuettel edd at debian.org
Mon Jan 25 13:39:23 CET 2010

On 23 January 2010 at 21:04, Dirk Eddelbuettel wrote:
| Thanks to the excellent debugging work by Mark Holder, as well as some help
| from Simon Urbanek, we finally got OS X and Rcpp to be nice to each other:
| static linking lets everybody be friends.

Rcpp 0.7.3 will not do. Yesterday I learned from Simon U that I 'broke' Rcpp
by including a configure file which means no universal OS X binary with x86,
ppc, x86_64 content get created. We will reverse this ASAP for 0.7.4 but it
may take a day.

Hopefully with 0.7.4 all will be good.  The rest of the mail is still valid I
would appreciate tests of the new libncl builds though.

Sorry, Dirk

| This was encoded in Rcpp 0.7.3 which was released earlier this week. So I
| figured it was time to get back to the rest of the phylobase build.  And a
| few days earlier I had suggested:
| On 11 January 2010 at 08:55, Dirk Eddelbuettel wrote:
| | I am still game. I see a three-pronged approach:
| | 
| |   i)    Suggestion Let's fix NCL and have a locally built version outside 
| |         of phylobase on all test platforms
| | 
| |   ii)   With that, fix/simplify Rcpp usage. Should be easy
| | 
| |   iii)  With that, get back to i) and clean up NCL's configure.
| | 
| | I think it would be easier to disentangle Rcpp and NCL inside phylobase while
| | we make this more.
| And I just committed a simple and easy fix to phylobase's SVN on R-Forge.  In
| a nutshell, we were just descending down to ncl's source directory and saying
| 'configure; make' which leaves the ncl library unfinished. The mighty libtool
| would normally run over it once more during 'make install'.
| So I changed it to this (and recall that this is relative to top-level
| directory for phylobase):
|    cd src/ncl
|    ./configure --quiet --enable-static --disable-shared --prefix=`pwd`/..
|    make
|    make install
|    cd ../..
| So we ask for a static library (and no dynamic library), and we tell
| configure to put it simply one directory up. That works well enough!  I also
| changed the CPPFLAGS and LDFLAGS accordingly: include/ncl and lib/ncl are now
| created during that new 'make install' step:
|    ## configure include/load flags and copy sample source to inst/doc
|    AC_SUBST([CPPFLAGS],["${CPPFLAGS} ${rcpp_cxxflags} -Iinclude/ncl"])
|    AC_SUBST([LDFLAGS],["${LDFLAGS} ${rcpp_ldflags} -Llib/ncl -lncl"])
| With that phylobase builds and installs fine on my Linux machine and
| (finger's crossed!!) should do the same on other people's Linux and OS X
| boxen.  So if over the next few days you have a moment, could you update from
| SVN and give it a whirl?
| Cheers, Dirk
| -- 
| Three out of two people have difficulties with fractions.

Three out of two people have difficulties with fractions.

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