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

[François Michonneau]

Hi Dirk -- That worked. I committed it as well.
  Thanks!
  -- François

On Mon, Feb 8, 2010 at 13:38, Dirk Eddelbuettel <edd at debian.org> wrote:

>
> On 8 February 2010 at 13:24, François Michonneau wrote:
> | Hi Dirk,
> |
> |   With a fresh svn checkout, I can't build the package on my machine.
> | I get the following error message.
> |
> |   Cheers,
> |   -- François
> |
> | francois at francois-laptop:~/Desktop/phylobase$ R CMD build pkg/
> | * checking for file 'pkg/DESCRIPTION' ... OK
> | * preparing 'pkg':
> | * checking DESCRIPTION meta-information ... OK
> | * cleaning src
> | * running cleanup
> | * installing the package to re-build vignettes
> | * installing *source* package ‘phylobase’ ...
> | ** libs
> | g++ -I/usr/share/R/include      -fpic  -g -O2 -c NCLInterface.cpp -o
> | NCLInterface.o
> | g++ -I/usr/share/R/include      -fpic  -g -O2 -c ReadWithNCL.cpp -o
> | ReadWithNCL.o
> | ReadWithNCL.cpp:27:18: error: Rcpp.h: No such file or directory
> | ReadWithNCL.cpp:44: error: ‘RcppExport’ does not name a type
> | ReadWithNCL.cpp:121: error: ‘RcppExport’ does not name a type
> | ReadWithNCL.cpp:169: error: ‘RcppExport’ does not name a type
> | make: *** [ReadWithNCL.o] Error 1
> | ERROR: compilation failed for package ‘phylobase’
> | * removing ‘/tmp/Rinst2338445123/phylobase’
> |  ERROR
> | Installation failed.
> | Removing '/tmp/Rinst2338445123'
>
> src/Makevars got hosed. Do you have one?  Try dropping this one in:
>
> --- cut
> -----------------------------------------------------------------------
> RCPP_FLAGS=`${R_HOME}/bin/Rscript -e "Rcpp:::CxxFlags()"`
> RCPP_LIBS=`${R_HOME}/bin/Rscript -e "Rcpp:::LdFlags()"`
> #
> PKG_CPPFLAGS=-I. ${RCPP_FLAGS} -DHAVE_INTTYPES_H
> PKG_LIBS=${RCPP_LIBS}
> --- cut
> -----------------------------------------------------------------------
>
> That file was accidentally deleted in cleanup, (on line three or so); check
> if that is fixed in the script cleanup. I had a 'file out of date' error
> and
> commit and may not have checked a clean version.
>
> I'll try a fresh svn checkout myself later.
>
> Dirk
>
>
> |
> |
> | On Mon, Feb 8, 2010 at 12:40, Dirk Eddelbuettel <edd at debian.org> wrote:
> | >
> | > On 2 February 2010 at 10:44, Dirk Eddelbuettel wrote:
> | > | [ Resending with 7-bit clean headers without Francois's cedille ]
> | > |
> | > | On 1 February 2010 at 12:41, Dirk Eddelbuettel wrote:
> | > | | On 1 February 2010 at 13:22, François Michonneau wrote:
> | > | | | Hi all,
> | > | | |
> | > | | | It looks that we're still having some troubles building the
> package on R-forge.
> | > | | |
> | > | | | Now, we get the following error message for the linux builds:
> | > | | | g++ -shared -L/usr/local/lib64 -o phylobase.so NCLInterface.o
> | > | | | ReadWithNCL.o ancestors.o descendants.o phyloXX.o reorderBinary.o
> | > | | | reorderRobust.o -L/home/rforge/lib/R/2.10/Rcpp/lib -lRcpp
> | > | | | -Wl,-rpath,/home/rforge/lib/R/2.10/Rcpp/lib -Llib/ncl -lncl
> | > | | | -L/srv/R/R-patched/build.10-01-29/lib -lR
> | > | | | /usr/bin/ld: lib/ncl/libncl.a(nxsassumptionsblock.o): relocation
> | > | | | R_X86_64_32 against `.rodata.str1.1' can not be used when making
> a
> | > | | | shared object; recompile with -fPIC
> | > | | | lib/ncl/libncl.a: could not read symbols: Bad value
> | > | | | collect2: ld returned 1 exit status
> | > | |
> | > | | Good catch. I never need that on 32bit where it works automatically
> so I
> | > | | forgot. This basically means that out plan of using
> | > | |
> | > | |     configure --enable-static --disable-shared
> | > | |
> | > | | doesn't work as configure no longer seems to add -fPIC. That
> stinks.
> | > | |
> | > | | I think the simplest solution is to tell configure to stuff itself,
> and to
> | > | | use the same Makefile we already use for Windows, maybe with an
> explicit
> | > | | -fPIC thrown in for good measure.
> | > |
> | > | Didn't work. I wasn't thinking hard enough.
> | > |
> | > | For OS X, three builds are attempted for three architectures.  That
> cannot
> | > | work with a single configure.
> | > |
> | > | Maybe we need to throw our arms up in the air and just import the
> sources
> | > | files from pkg/src/ncl/ncl into pkg/src/ and treat them as part of
> the
> | > | package.
> | >
> | > After discussing this some more with Francois, I have now made this
> change
> | > and committed it as a 'request for comment' type commit. So now we no
> longer
> | > have a seperate source directory for ncl but simply comingle the ncl
> sources
> | > with the phylobase sources.
> | >
> | > Advantage:  R knows how to build
> | >
> | > Disadvantage: comingled :-/
> | >
> | > It works for me on Linux, and I submitted it to the automated
> win-builder (by
> | > locally altering DESCRIPTION to make me Maintainer:, and I also like to
> | > change the version). The result is in:
> | >
> | >   From: Uwe.Ligges at R-Project.org
> | >   To: edd at debian.org
> | >   Cc: Uwe.Ligges at R-Project.org
> | >   Subject: Package phylobase_0.5.2.tar.gz has been checked and built
> | >   Date: Mon, 08 Feb 2010 18:20:59 +0100
> | >
> | >   Dear package maintainer,
> | >
> | >   this notification has been generated automatically.
> | >   Your package phylobase_0.5.2.tar.gz has been built (if working) and
> checked for Windows.
> | >   Please check the log files and (if working) the binary package at:
> | >   http://win-builder.r-project.org/oIyt0KC6A03C
> | >   The files will be removed after roughly 72 hours.
> | >   Installation time in seconds: 124
> | >   Check time in seconds: 113
> | >   Check result: WARNING
> | >   R version 2.10.1 (2009-12-14) (32-bit)
> | >
> | >   All the best,
> | >   Uwe Ligges
> | >   (CRAN maintainer of binary packages for Windows)
> | >
> | > So if anyone with OS X could try this, preferably over multiarch etc,
> it
> | > would be great. Maybe we can _finally_ put this to bed in a few days.
> | >
> | > Dirk
> | >
> | >
> | > --
> | >  Registration is open for the 2nd International conference R / Finance
> 2010
> | >  See http://www.RinFinance.com for details, and see you in Chicago in
> April!
> | >
>
> --
>   Registration is open for the 2nd International conference R / Finance
> 2010
>  See http://www.RinFinance.com for details, and see you in Chicago in
> April!
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.r-forge.r-project.org/pipermail/phylobase-devl/attachments/20100208/1b0db2be/attachment-0001.htm