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

Mon Jan 25 18:33:53 CET 2010

  mea culpa.
  I took out some old leftover junk that was root-owned and it R CMD
checks OK.

   is the next step to try replacing NCL with a newer version ... ?

  cheers
   Ben

François Michonneau wrote:
> I can build, install and start with no problem with Ubuntu 9.10 (Jaunty).
>   -- François
> 
> 
> On Mon, Jan 25, 2010 at 08:14, Dirk Eddelbuettel <edd at debian.org> wrote:
>> On 25 January 2010 at 08:00, Ben Bolker wrote:
>> |   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
>>
>> I think that is a hint. On Ubuntu /bin/sh is not bash, and we get bitten.
>> Why, I do not know. Something is still odd.  You did that in your home
>> directory and the files from the tarball look good otherwise?
>>
>> What I had done way back for cran2deb was similar in spirit --- a patch that
>> provides a Makefile that creates libncl.a.  It's more brute force. But if we
>> cannot run configure for ncl let's make an endrun around configure for ncl.
>>
>> Dirk
>>
>> | 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
>> |
>> |
>> | [GNUPG:] ERRSIG 7395291A3C337A73 17 2 01 1264424409 9
>> | [GNUPG:] NO_PUBKEY 7395291A3C337A73
>>
>> --
>> Three out of two people have difficulties with fractions.
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>>

-- 
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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