pymol crashing under Qt on Catalina

[Jack Howarth]

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'


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
>>
>>
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