Building from source problems.

On 2/11/2009, at 9:48 AM, Steve Lianoglou wrote:

 Hi,

On Sun, Nov 1, 2009 at 2:46 PM, Rolf Turner <r.turner at auckland.ac.nz>
wrote:

      Checking on what I've got (following your instructions) I
      found that I have version 2.5 of Xcode.

      That appears to be the latest version of Xcode that runs on
      Tiger.  The web page indicates that Xcode 2.5 dates from
      November 2007 which was about when I first installed Xcode.
      So re-installing Xcode 2.5 won't do any good.

It might do some good, because it's possible that something got hosed ...

       The way the Fates treat me, it will do no good with probability =
1!!! :-)

After rereading the thread here (sorry if it feels like your talking
to a wall), I'm guessing it won't, actually ... but it can't hurt.

       I don't ***have*** 4.2 at all, as far as I can tell.  Simon
       Urbanek told me that I ***needed*** to use 4.2 in order to get
       things to build properly from source. He indicated that I should
       make the system ***use*** 4.2 by doing

               sudo gcc_select 4.2

       but as I said, this just tells me that 4.2 ain't there.

OH!

I have a Tiger machine sitting next to me at home, but it has XCode
2.0. I'm d/ling 2.5 to check and see if it comes with gcc-4.2 just in
case ... I'll post back with those results when it's done d/ling and
installing (I guess I should update it anyway ...).

       Thanks.  I look forward to your report with baited breath.
       (Like the cat that ate cheese and then sat by the mousehole ....) :-)

Well, XCode 2.5 is still downloading here ... I pay enough for this
dang cable modem, but it's slower than slow.

In the mean time, do you mind if we take one or two stabs in the dark?

So, if I'm not mistaken, it seems your only problem now is compiling a
package from source, and you're getting some "mtune=core2" problem,
right?

THIS IS PROBABLY A BAD IDEA, BUT ...

If we can't get your compiler to support these optimizations (maybe
because we can't get gcc-4.2 on there), then how about we just don't
use those optimizations when compiling? I'm not sure if that will
cause problems, but perhaps we can try?

Can you find where this is defined in your install? Doing:

$ cd /Library/Frameworks/R.framework/Versions/2.10
$ grep -r mtune=core2 .

for me brings up one file:

./Resources/bin/libtool:LTCFLAGS="-mtune=core2 -g -O2"

Does it for you?

I wonder what happens if you just comment that line out and insert below it:

LTCFLAGS="-g -O2"

Would all of your woes go away?

As I said, it's probably a bad idea, but if you're brave, it might be
worth a try.

(I've been sitting on this email for a while now, because I don't want
to make boneheaded suggestions in public, but my xcode d/l is @ 75%
and I didn't want to leave you hanging for the rest of the day).

-steve

Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact