R devel - Oct 2009 - compiling packages without Framework and CoreFoundation options on OSX

I've been trying to get R+PostgreSQL+PL/R to work together on a OSX  
machine without the Framework and CoreFoundation options and have  
noticed some suspicious switches when compiling packages.

I've installed R (on OSX) with the following ./configure:

./configure \
  CC="gcc -arch i386" \
  CXX="g++ -arch i386" \
  OBJC="gcc -arch i386" \
  F77="gfortran -arch i386" \
  FC="gfortran -arch i386" \
  --enable-R-framework=no \
  --enable-R-shlib \
  --without-blas \
  --x-includes=/usr/X11/include \
  --x-libraries=/usr/X11/lib

Notice the

  --enable-R-framework=no \
  --enable-R-shlib \

No flames please.I'm sure I'm breaking lot's of R purist-isms.
There's
a bigger picture here than trying to get R and packages to build by  
themselves.

When I build packages, using sudo R, for example:

 > install.packages(c("rconifers"),
+  lib="/usr/local/lib/R/library",
+  repos="http://cran.r-project.org",
+  dependencies=TRUE )

the package seems to get built with the "-Wl,-framework - 
Wl,CoreFoundation" switches, even when R isn't built with the  
framework (and CoreFoundation) options. For example:

gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names  
-undefined dynamic_lookup -single_module -multiply_defined suppress -L/ 
usr/local/lib -o rconifers.so coeffs.o file_io.o grow.o mortality.o  
plot.o rconifers.o sample.o smc_coeffs.o smc_model.o stats.o  
swo_coeffs.o swo_model.o thin.o -L/usr/local/lib/R/lib -lR -Wl,- 
framework -Wl,CoreFoundation

I would like to build packages without the "-Wl,-framework - 
Wl,CoreFoundation" options because I'm going to install it on other OS
(FreeBSD, Linux, whatever)

Does this cause a problem? Will this cause a problem? I'm guessing the  
CoreFoundations are an artifact of the XCode compiler. What's with the  
-Wl,-framework stuff? Can I make it stop? Will I be okay?

Thanks,
Jeff.




Jeff Hamann, PhD
PO Box 1421
Corvallis, Oregon 97339-1421
541-754-2457
jeff.hamann[at]forestinformatics[dot]com
http://www.forestinformatics.com


	[[alternative HTML version deleted]]

Jeff,

On Oct 7, 2009, at 18:48 , Jeff Hamann wrote:
> I've been trying to get R+PostgreSQL+PL/R to work together on a OSX
> machine without the Framework and CoreFoundation options and have
> noticed some suspicious switches when compiling packages.
>
> I've installed R (on OSX) with the following ./configure:
>
> ./configure \
>  CC="gcc -arch i386" \
>  CXX="g++ -arch i386" \
>  OBJC="gcc -arch i386" \
>  F77="gfortran -arch i386" \
>  FC="gfortran -arch i386" \
>  --enable-R-framework=no \
>  --enable-R-shlib \
>  --without-blas \
>  --x-includes=/usr/X11/include \
>  --x-libraries=/usr/X11/lib
>
> Notice the
>
>  --enable-R-framework=no \
>  --enable-R-shlib \
>
> No flames please.I'm sure I'm breaking lot's of R purist-isms.
> There's a bigger picture here than trying to get R and packages to  
> build by themselves.
>
> When I build packages, using sudo R, for example:
>
>> install.packages(c("rconifers"),
> +  lib="/usr/local/lib/R/library",
> +  repos="http://cran.r-project.org",
> +  dependencies=TRUE )
>
> the package seems to get built with the "-Wl,-framework - 
> Wl,CoreFoundation" switches, even when R isn't built with the  
> framework (and CoreFoundation) options.
You're confusing entirely different things here - "-Wl,-framework - 
Wl,CoreFoundation" is simply a safe form of "-framework  
CoreFoundation" which means that R uses the CoreFoundation framework  
which is part of OS X. It has nothing to do with the --enable-R- 
framework option which is about creating *R* as a framework.

> For example:
>
> gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names
> -undefined dynamic_lookup -single_module -multiply_defined suppress - 
> L/
> usr/local/lib -o rconifers.so coeffs.o file_io.o grow.o mortality.o
> plot.o rconifers.o sample.o smc_coeffs.o smc_model.o stats.o
> swo_coeffs.o swo_model.o thin.o -L/usr/local/lib/R/lib -lR -Wl,-
> framework -Wl,CoreFoundation
>
Note the "-lR" which is caused by --enable-R-framework=no, in the  
normal R on OS X you'd have seen "-framework R" instead.

> I would like to build packages without the "-Wl,-framework -
> Wl,CoreFoundation" options because I'm going to install it on
other OS
> (FreeBSD, Linux, whatever)
>
If you install it on other OS, you'll get entirely different switches,  
of course. CF is needed on OS X for certain OS-specific functionality  
such as locales support, Quartz graphics etc.

Clearly, a binary is specific for given OS, so you have to build a  
binary of your package for each single OS you want to support in  
binary form (with different switches each time).

> Does this cause a problem? Will this cause a problem? I'm guessing  
> the CoreFoundations are an artifact of the XCode compiler.
"XCode compiler" is gcc, so, no.

> What's with the   -Wl,-framework stuff?
It's roughly the same as -l but it's more powerful as it covers  
umbrellas, resources etc. You may want to read more about frameworks:
http://developer.apple.com/mac/library/documentation/MacOSX/Conceptual/BPFrameworks/Frameworks.html

> Can I make it stop?
Not really without hacking R.

> Will I be okay?
>
I have the suspicion that you're heading in a very wrong direction  
(but you didn't tell us what you're really up to so that's just a  
speculation). It should be entirely irrelevant for you what switches  
are used, because packages get all necessary switches from R, so they  
never need to worry about them. If you do, then it's highly likely  
that you're doing something wrong.

Cheers,
Simon