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

François Michonneau francois.michonneau at gmail.com
Mon Jan 25 19:19:46 CET 2010 

Hi,

  On my system, I was able to update to the most recent version of NCL
within phylobase with almost no problem.

  I can commit the changes, however, I was wondering if maybe we
should first wait to see if it builds currently without problems on
Mac platforms. The rationale being that if I commit the changes now it
might be harder to determine if the problem comes from the changes
that Drik et al implemented or from the newest version of NCL.

  Cheers,
  -- François


On Mon, Jan 25, 2010 at 12:33, Ben Bolker <bolker at ufl.edu> wrote:
>  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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