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

Dirk Eddelbuettel edd at debian.org
Tue Jan 26 02:33:01 CET 2010 

Francois,

Thanks also for your Ubuntu test and confirmation.
On 25 January 2010 at 13:19, François Michonneau wrote:
| 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.

The 'phylobase build-time / install-time' suggestion I made should be
independent of the version of NCL. It simply makes it easier for phylobase to
link to a single static library.

Regards,  Dirk


| 
|   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.
| >>> _______________________________________________
| >>> Phylobase-devl mailing list
| >>> Phylobase-devl at lists.r-forge.r-project.org
| >>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/phylobase-devl
| >>>
| >
| >
| > --
| > 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
| >
| >

-- 
Three out of two people have difficulties with fractions.

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