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

[Dirk Eddelbuettel]

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 I had a 'file out of date' error and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!