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

Mon Feb 8 20:12:29 CET 2010

On 8 February 2010 at 13:52, François Michonneau wrote:
| Hi Dirk -- That worked. I committed it as well.

Very good catch so thank you!  I had fallen into the trap of this file as I
had a 'svn ignore' on it given that it was a transient file when we still
used configure.

Looks like we're getting there but then I thought that before too :)

Dirk

|   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 I had a 'file out of date' error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!
| >

-- 
  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!