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

[François Michonneau]

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'


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
>
>
> --
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