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

[Dirk Eddelbuettel]

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.

Or, go the other way, and require the user to have a suitable libncl
somewhere.

Dirk

| 
| | (For some reason, the Mac builds aren't updated yet)
| 
| (I see that with my projects too. R-Forge is not so strong on OS X support.)
| 
| Dirk
|  
| |   -- François
| | 
| | On Sun, Jan 31, 2010 at 09:58, Dirk Eddelbuettel <edd at debian.org> wrote:
| | >
| | > All,
| | >
| | > Just as a heads-up, Windows builds were also broken.
| | >
| | > When NCL was updated, a Makefile.win I had added got lost. I restored it,
| | > made the necessary updates. This builds now -- I used the CRAN win-builder to
| | > test it:
| | >
| | >    From: Uwe.Ligges at R-Project.org
| | >    To: edd at debian.org
| | >    Cc: Uwe.Ligges at R-Project.org
| | >    Subject: Package phylobase_0.5.1.tar.gz has been checked and built
| | >
| | >    Dear package maintainer,
| | >
| | >    this notification has been generated automatically.
| | >    Your package phylobase_0.5.1.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/s02150BP6m7i
| | >    The files will be removed after roughly 72 hours.
| | >    Installation time in seconds: 88
| | >    Check time in seconds: 77
| | >    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)
| | >
| | > (where I changed DESCRIPTION locally to have the mail come to me, and
| | > increased the version to 0.5.1).
| | >
| | > I have just committed the Windows fixes as rev 731.
| | >
| | > Regards, Dirk
| | >
| | > --
| | > Three out of two people have difficulties with fractions.
| | >
| 
| -- 
| Three out of two people have difficulties with fractions.

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