pymol crashing under Qt on Catalina

[Chris Jones]

> On 13 Oct 2019, at 4:02 pm, Jack Howarth <howarth.at.macports at gmail.com> wrote:
> 
> 
> Well this is interesting. After installing Xcode 11 Beta 2, Command Line tools and setting the Xcode-select path to the Xcode-beta.app, I find that 'sudo port build OpenBLAS' now fails with...
> 
> :info:build OPENBLAS_NUM_THREADS=1 OMP_NUM_THREADS=1 ./sblat2 < ./sblat2.dat
> :info:build Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
> :info:build Backtrace for this error:
> :info:build #0  0x1029863e4
> :info:build #1  0x102985b06
> :info:build #2  0x7fff688fab1c
> :info:build /bin/sh: line 1: 22671 Segmentation fault: 11  OPENBLAS_NUM_THREADS=1 OMP_NUM_THREADS=1 ./sblat2 < ./sblat2.dat
> :info:build make[1]: *** [level2] Error 139
> :info:build make[1]: *** Waiting for unfinished jobs....
> :info:build make[1]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_OpenBLAS/OpenBLAS/work/xianyi-OpenBLAS-5f36f18/test'

That just means the stack check issue is in fact not addressed in 11.2, or there is in fact a real issue with the openblas source.

> 
> 
>> On Sun, Oct 13, 2019 at 10:49 AM Jack Howarth <howarth.at.macports at gmail.com> wrote:
>> Okay, I have Xcode 11.2 beta 2 and the associated Command Line Tools installed. Is there some permutation of options to pass to 'port' that will rebuild and reinstall a currently installed MacPorts package without uninstalling it first?
>>             Jack
>> 
>>> On Sun, Oct 13, 2019 at 10:13 AM Chris Jones <jonesc at hep.phy.cam.ac.uk> wrote:
>>> 
>>> 
>>> > On 13 Oct 2019, at 3:11 pm, Joshua Root <jmr at macports.org> wrote:
>>> > 
>>> > On 2019-10-14 00:59 , Jack Howarth wrote:
>>> >> 
>>> >> 
>>> >>> On Sun, Oct 13, 2019 at 9:49 AM Chris Jones <jonesc at hep.phy.cam.ac.uk
>>> >>> <mailto:jonesc at hep.phy.cam.ac.uk>> wrote:
>>> >>> 
>>> >>> 
>>> >>> 
>>> >>>    On 13 Oct 2019, at 2:46 pm, Joshua Root <jmr at macports.org
>>> >>>    <mailto:jmr at macports.org>> wrote:
>>> >>> 
>>> >>>    On 2019-10-14 00:35 , Chris Jones wrote:
>>> >>>> 
>>> >>>>    After that, my next guess would perhaps another issue related to the
>>> >>>>    stack-check issue with Xcode 11. See e.g. the fix I added for
>>> >>>>    OpenBLAS
>>> >>>> 
>>> >>>>    https://github.com/macports/macports-ports/commit/6e78e5c9495b4dc4e7e050fae2b41dd5b9accfdd#diff-a755de84ca7f97ab071328807d829e0b
>>> >>> 
>>> >>>    I'd be wary of removing a hardening measure and leaving it at that. It
>>> >>>    could be revealing a genuine stack-smashing bug.
>>> >> 
>>> >>    Agreed. Accordingly to Jeremy though its a Xcode bug expected to be
>>> >>    fixed in 11.2. Thats why I subsequently added a version check, see e.g.
>>> > 
>>> > Ah, good to know. Do you have a link to Jeremy's statement out of curiosity?
>>> 
>>> No I don’t, I only know this second hand from a comment by Ken...
>>> 
>>> > 
>>> >>    https://github.com/macports/macports-ports/blob/master/math/OpenBLAS/Portfile
>>> >> 
>>> >>    Line 109.
>>> >> 
>>> >>> 
>>> >>>    - Josh
>>> >> 
>>> >> 
>>> >> Josh,
>>> >>      Does anyone know if this is already fixed in the posted Xcode 11.2
>>> >> beta 2? If so, would rebuilding the OpenBLAS package with it be
>>> >> sufficient or aren't we sure where the offending code lies?
>>> >>             Jack
>>> > 
>>> > I don't know sorry.
>>> > 
>>> > - Josh
>>> 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.macports.org/pipermail/macports-dev/attachments/20191013/3e661540/attachment.html>