Problems with Gnome 2.8 upgrade after 5.3R & Xorg upgrades

[Scott I. Remick]

Ok, been trying for a couple days now to upgrade to Gnome 2.8 but am having
problems. This is after upgrading to FreeBSD 5.3R and XFree86 -> Xorg.

Hopefully I can demonstrate that I've at least put some effort into
diagnosing this :)

*** UPGRADE FAILED ***

===> /usr/local/sbin/portupgrade failed to run a recursive upgrade on atk
pango.  The output of the failed build is in
/usr/tmp/gnome_upgrade_log.XCzmfM.
If you require additional help in figuring out why the upgrade failed,
please
compress /usr/tmp/gnome_upgrade_log.XCzmfM and send it to
freebsd-gnome at FreeBSD.org.

I tried using gnomeloganalyzer but "The cause of your build failure is not
known to gnomelogalyzer.sh" :(

In studying the log file myself, the first thing that jumps out at me is for
some reason the log is being passed around in the script as if it were a
package to upgrade?

** No such installed package: /usr/tmp/gnome_upgrade_log.XCzmfM

That makes no sense. It appears a couple times. 

mpeg4ip fails due to this:

aclocal.m4:65: error: Autoconf version 2.54 or higher is required
aclocal.m4:65: the top level
autoheader: autom4te failed with exit status: 1
 at /usr/local/bin/autoheader line 163
gmake[3]: *** [config.h.in] Error 1

But I have autoconf 2.59 installed:

bash-2.05b# autoconf -V
autoconf (GNU Autoconf) 2.59
Written by David J. MacKenzie and Akim Demaille.

Copyright (C) 2003 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
bash-2.05b# pkg_info | grep autoconf
autoconf-2.59_2     Automatically configure source code on many Un*x
platforms

Many other ports compile ok but fail due to a "No such file or directory"
error during the install process (after the current version is uninstalled).
Examples:

gok-0.11.16
install: gok-C.omf.out: No such file or directory

yelp-2.6.4
/usr/bin/ld: cannot find -lc_r

file-roller-2.8.3
install: file-roller-C.omf.out: No such file or directory

gnome-terminal-2.8.0
install: gnome-terminal-C.omf.out: No such file or directory

dasher-3.2.11
install: dasher-C.omf.out: No such file or directory

And so on. This is the same error for most the ports that fail. You can read
the whole log yourself in all its glory here:

http://vtbsd.net/gnome_upgrade_log.XCzmfM.bz2

I have a sneaking suspicion this has to do with the transition from libc_r
to libpthread so let me provide this additional info: because of issues I
was having running gnome 2.4 and apps after the upgrade to 5.3, I did the
following:

Modified my /etc/libmap.conf as follows:

# per /usr/src/UPDATING 20040303
libc_r.so.5             libpthread.so.1
libc_r.so               libpthread.so
libkse.so.1             libpthread.so.1
libkse.so               libpthread.so

Removed (well, moved) /usr/lib/libc_r* away.
Added the following line to /etc/make.conf:

NOLIBC_R=true

This allowed apps to run that weren't before but I still had a lot of
instability (for example, Gaim would launch and connect, but crash if I
tried to do most things, or even received an IM) so I decided to proceed
with the Gnome upgrade figuring it'd result in most things being recompiled
and hopefully solve my problems.

Advice appreciated... thanks!