[ccp4bb] Latest XQuartz upgrade breaks Coot

[William G. Scott]

More regarding" XQuartz upgrade breaks Coot”  from people who know more than I 
do (which admittedly is most everyone, but I digress …):


> 
> Today's Topics:
> 
>   1. Xquartz 2.7.10-rc2 breakage (Jack Howarth)
>   2. fink-0.41.0-101 du_sk.t build failure (Patrick Carmack)
> 
> 
> --
> 
>  
>Xquartz is currently testing the upcoming 2.7.10 release which has the
> following significant change
> 
> libXt
> 
> Both libXt.6.dylib and libXt.7.dylib are two-level-namespaced now
> A flat_namespace version of libXt is available in
> /opt/X11/lib/flat_namespace to help ease the transition (#96292)
> 
> Set DYLD_LIBRARY_PATH=/opt/X11/lib/flat_namespace when executing older
> non-compliant software (eg: Motif-based applications)
> Motif users are encouraged to file bugs against Motif to encourage them to
> fix that library
> 
> Upstream is attempting to deprecate out the libXt.7.dylib with a
> symlink to libXt.6.dylib (as both are now linked as two-level namespace).
> Unfortunately, they didn't think this one through as it breaks all binaries
> linked against libXt under Xquartz 2.7.9 (as those expect the library to
> have the 8.0.0 soversion from libXt.7.dylib instead of the 7.0.0 one from
> libXt.6.dylib). Currently you have to rebuild any packages built under
> Xquartz 2.7.9 which linked libXt after upgrading to Xquartz 2.7.10-rc2.
> 
> I've alerted upstream of this issue
> 
> https://lists.macosforge.org/pipermail/xquartz-dev/2016-September/004008.html
> 
> and expect they will solve this by releasing an -rc3 with the symlink for
> libXt.7.dylib replaced by the actual shared library as in 2.7.9. Note that
> in 2.7.10, libXt.dyib points at libXt.6.dylib since its flat-namespace
> linkage has been replaced with two-level namespace linkage for both.
>Jack
> ps Note that the flat-namespace libXt.6.dylib provided by Xquartz in 2.7.10
> in /opt/X11/lib/flat_namespace can't be used for builds as the path in its
> install name is intentionally set to /opt/X11/lib.
> 
> I've placed proposed libxt-flat-namespace-shlibs packaging on fink tracker
> to provide the missing flat-namespace libXt.6.dylib for use in builds of
> and against openmotif4. I've also placed updated packaging for those
> packages that use openmotif4 on fink tracking which uses this new
> libxt-flat-namespace-shlibs package.

Re: [ccp4bb] Latest XQuartz upgrade breaks Coot

[Derek Logan]

Hi Logan,

Thanks for this useful information. Didn't know it was possible to rejig 
binaries in that way! I'm taking the liberty of cc:ing your answer to the list. 
I forgot to say that this problem affected both the CCP4-distributed Coot and 
an old stand-alone from Bill Scott that I had in /Library/Coot/bin. It seems 
from your experience that it doesn't affect the latest compiled versions from 
Bill. Regarding the contents of /opt/X11/lib, I have:

lrwxr-xr-x  1 root  wheel  26 Sep 27 17:19 /opt/X11/lib/libXt.6.dylib -> 
/opt/X11/lib/libXt.7.dylib
-rwxr-xr-x  1 root  wheel  698896 Sep 27 07:45 /opt/X11/lib/libXt.7.dylib
lrwxr-xr-x  1 501   wheel  13 Sep 27 10:43 /opt/X11/lib/libXt.dylib -> 
libXt.7.dylib
-rwxr-xr-x  1 root  wheel   71104 Sep 27 07:45 /opt/X11/lib/libXtst.6.dylib
lrwxr-xr-x  1 501   wheel  15 Sep 27 10:43 /opt/X11/lib/libXtst.dylib -> 
libXtst.6.dylib

where the first line is the link I made myself. So libXt.6.dylib seems to have 
been removed in the latest release.

/Derek

On 28 Sep 2016, at 13:16, Logan Donaldson 
> wrote:

I’m running 10.12.1b2 but not the newest X11 yet.

The quick and dirty permanent way would be to use

install_name_tool -change /opt/X11/lib/libXt.6.dylib /opt/X11/lib/libXt.7.dylib 
coot-bin

I just installed coot-0.8.6.pkg from the Scott lab (for 10.11) and when I 
checked the binary, it already knew to look for libXt.7

LDMBP2015 [7:12am] /Library/Coot/bin
16 % otool -L 
coot-bin | grep libXt
/opt/X11/lib/libXt.7.dylib (compatibility version 8.0.0, current version 8.0.0)

19 % ls -l /opt/X11/lib/libXt*
-rwxr-xr-x  1 root   wheel  725856 May  5 04:33 /opt/X11/lib/libXt.6.dylib
-rwxr-xr-x  1 root   wheel  694640 May  5 04:33 /opt/X11/lib/libXt.7.dylib
lrwxr-xr-x  1 logan  wheel  13 May  5 13:56 /opt/X11/lib/libXt.dylib -> 
libXt.7.dylib
-rwxr-xr-x  1 root   wheel   71088 May  5 04:33 /opt/X11/lib/libXtst.6.dylib
lrwxr-xr-x  1 logan  wheel  15 May  5 13:56 /opt/X11/lib/libXtst.dylib -> 
libXtst.6.dylib

-logan donaldson

[ccp4bb] Latest XQuartz upgrade breaks Coot

[Derek Logan]

Hi,

I recently upgraded my Mac to Sierra (I know, early adopter...) and thereafter 
the latest XQuartz (2.7.10_rc3). The latter step seemed to break Coot, 
apparently because Coot requires the run-time library 
/opt/X11/lib/libXt.6.dylib and this has been replaced by 
/opt/X11/lib/libXt.7.dylib. I solved this temporarily by soft-linking 
libXt.6.dylib to libXt.7.dylib. Has anyone else run into this and are there 
alternative solutions?

/Derek