Re: [GeneX-dev] Tail (2)

[Harry M. <man...@ho...>]

Nicolas Bertrand wrote:
> 
> Hello
> 
> On Thursday, November 15, 2001, at 09:47 , Harry Mangalam wrote:
> 
> > OK - this is a Mac OSX-specific problem with R and gcc that I can't
> > really help you with except via the grungiest of suggestions.
> >
> > R's SHLIB command calls gcc with the arguments that you see echoed to
> > the screen, so somewhere you cshould be able to set them..
> >
> > AHA! Brian D. Ripley, one of R's authors, indicates:
> >
> > http://www.ens.gu.edu.au/robertk/R/help/01a/0881.html
> >
> > [don't forget that google is your friend..)
> >
> > that you have to enter these flags in R_HOME/etc/Makeconf as part of
> > the CFLAGS string, so you'll probably have to append  '-flat_namespace
> > -undefined suppress' to the CFLAGS string there.  It wasn't
> > cleear to me whether you'll have to recompile R to have this take
> > effect, but I'd try it without the recompile 1st.
> >
> > Helpful...?
> >
> > hjm
> >
> 
> I don't exactly know... I installed R from binaries.

OK - it should still have installed the R_HOME/etc/Makeconf - does it exist?

If so, edit it to add the the options recommended by the guy who gave you the advice previously. ie:

CFLAGS = -g -O2 -flat_namespace -undefined suppress

Taking a longer look at the file, I see that there are a lot of SHLIB-related flags which might benefit from those options as well.  I'm not an R expert, and certainly not on OSX, so your best bet
wold be to query the R user group to see if they have a solution:

r-...@st...

This group is EXCEPTIONALLY good at responding to questions.


> cc -bundle -undefined suppress  -o runa.so runa.o  -L/usr/local/lib
> /usr/bin/ld: -undefined error must be used when -twolevel_namespace is
> in effect
> make: *** [runa.so] Error 1
> 
> Doesn't it mean that runa.so could not be compiled because of a linker
> error? I have been advised by Keisuke Fujii to run cc with the
> -flat_namespace -undefined supress flags.
> That would give the following command to avoid this error:
> cc -bundle -flat_namespace -undefined suppress -o runa.so runa.o
> -L/usr/local/lib

The linker is usually invoked automatically by the compiler if you ask it to produce an object file requiring fn()s from system libs.  I THINK that appro flags are essentially passed thru to the
linker in this case.  Hencve adding these 

> Which Make has to be modified to had this flag?

Seee previous message

> !! System Error: No such file or directory @ line: 2190  (cd
> /Users/Shared/Downloads/GeneX-Server-1.0.4/CyberT-dist; R SHLIB runa.c)
> cp: cannot stat `runa.so': No such file or directory
> 
> !! System Error: No such file or directory @ line: 2195  (cd
> /Users/Shared/Downloads/GeneX-Server-1.0.4/CyberT-dist; cp hdarray
> runa.c runa.so /usr/local/genex/lib/R/library/hdarray/R/)
> 
> I suspect these errors pop up because runa.so failed to compile, right?

Yup.

-- 
Cheers, Harry

Harry J Mangalam -- (949) 856 2847 (v&f) -- man...@ho... 
                    [plain text appreciated]