selfupdate fails with flags supplied by pkg-config installed in /usr/bin

[stejanecek@…]

When running selfupdate today, port tried to update my MacPorts version to 1.9.0:

MacPorts base version 1.8.2 installed,
MacPorts base version 1.9.0 downloaded.

The update failed, I've attached the the full (bzipped) output of "port -d selfupdate". The relevant part seems to be this:

ld: warning: in /Library/Frameworks/Mono.framework/Versions/2.4/lib/libsqlite3.dylib, missing required architecture x86_64 in file
Undefined symbols:
  "_sqlite3_finalize", referenced from:
...

Apparently the configure script found the sqlite3 that comes with the Mono framework (not installed via MacPorts) *before* the one installed in /opt/local, and then fails because the library has the wrong architecture.

I got the upgrade working by temporarily moving away /Library/Frameworks/Mono.framework, but this is not really a permanent fix of the bug...

[stejanecek@…]

Cc Me!

[jmr@…]

Attach config.log please.

[stejanecek@…]

As I moved away Mono.Framwork and successfully ran the upgrade afterwards, the config.log will be from the successful run. Is there something I can do to revert the situation? I can move back the Mono.Framework, but as the upgrade was successful, I guess running "port selfupdate" again time will simply do nothing this time...

[raimue@…]

You can force the rebuild using sudo port -f selfupdate.

[jmr@…]

So it's getting the bad flags from /usr/bin/pkg-config, which doesn't exist in a stock install of OS X. We can't support configurations that modify Apple-owned locations such as /usr/bin.

[stejanecek@…]

Thanks. I did this on my system to see where /usr/bin/pkg-config comes from:

ls -l /usr/bin/pkg-config
lrwxr-xr-x  1 root  wheel  54 21 Apr  2008 /usr/bin/pkg-config -> /Library/Frameworks/Mono.framework/Commands/pkg-config

... So it is the Mono installer that is to blame.

[ryandesign@…]

This issue is now being tracked in #30932.