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

Ben Bolker bolker at ufl.edu
Mon Jan 25 14:00:09 CET 2010


  I got only this far:

  I haven't had a chance to check in to it yet & see what's going on.
(Yes, it implies a permission problem, but I've never had anything like
this ever happen before in building a package, so I wouldn't jump to the
conclusion that my system is mis-configured.)

  Ubuntu Intrepid Ibex: Linux bolker-lap2 2.6.27-16-generic #1 SMP Tue
Dec 1 17:56:54 UTC 2009 i686 GNU/Linux


configure: starting to build libncl.a in ncl
./configure: 465: cannot create configure.lineno: Permission denied
configure: error: cannot create configure.lineno; rerun with a POSIX shell
make  all-recursive
make[1]: Entering directory `/home/ben/lib/R/pkgs/phylobase/pkg/src/ncl'
Making all in ncl
make[2]: Entering directory `/home/ben/lib/R/pkgs/phylobase/pkg/src/ncl/ncl'
/bin/bash ../libtool --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I.
-I..     -O3 -ffast-math  -fPIC -MT nxsassumptionsblock.lo -MD -MP -MF
.deps/nxsassumptionsblock.Tpo -c -o nxsassumptionsblock.lo
nxsassumptionsblock.cpp
 g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT
nxsassumptionsblock.lo -MD -MP -MF .deps/nxsassumptionsblock.Tpo -c
nxsassumptionsblock.cpp  -fPIC -DPIC -o .libs/nxsassumptionsblock.o
nxsassumptionsblock.cpp:481: fatal error: opening dependency file
.deps/nxsassumptionsblock.Tpo: Permission denied
compilation terminated.
make[2]: *** [nxsassumptionsblock.lo] Error 1
make[2]: Leaving directory `/home/ben/lib/R/pkgs/phylobase/pkg/src/ncl/ncl'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/ben/lib/R/pkgs/phylobase/pkg/src/ncl'
make: *** [all] Error 2
Making install in ncl
make[1]: Entering directory `/home/ben/lib/R/pkgs/phylobase/pkg/src/ncl/ncl'
/bin/bash ../libtool --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I.
-I..     -O3 -ffast-math  -fPIC -MT nxsassumptionsblock.lo -MD -MP -MF
.deps/nxsassumptionsblock.Tpo -c -o nxsassumptionsblock.lo
nxsassumptionsblock.cpp
 g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT
nxsassumptionsblock.lo -MD -MP -MF .deps/nxsassumptionsblock.Tpo -c
nxsassumptionsblock.cpp  -fPIC -DPIC -o .libs/nxsassumptionsblock.o
nxsassumptionsblock.cpp:481: fatal error: opening dependency file
.deps/nxsassumptionsblock.Tpo: Permission denied
compilation terminated.
make[1]: *** [nxsassumptionsblock.lo] Error 1
make[1]: Leaving directory `/home/ben/lib/R/pkgs/phylobase/pkg/src/ncl/ncl'
make: *** [install-recursive] Error 1
configure: finished building libncl.a in ncl


Dirk Eddelbuettel wrote:
> 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.
> 


-- 
Ben Bolker
Associate professor, Biology Dep't, Univ. of Florida
bolker at ufl.edu / people.biology.ufl.edu/bolker
GPG key: people.biology.ufl.edu/bolker/benbolker-publickey.asc

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