Re: Pick up SDKROOT as the sysroot fallback.

> > Also, note that if you execute the buried clang compilers in > /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin > or /Library/Developer/CommandLineTools/usr/bin that they can't find the SDK. > Jack > The logic to add SDKROOT to the

Re: Pick up SDKROOT as the sysroot fallback.

On Sun, Oct 13, 2019 at 4:22 PM Ken Cunningham < ken.cunningham.web...@gmail.com> wrote: > >* I did not want to touch that at this point. The gcc bug report is still > *>* open, as far as I can see. > *>>* If someone wants try a build using —with-build-sysroot instead, they are > *>* very welcome

Re: Pick up SDKROOT as the sysroot fallback.

> > I did not want to touch that at this point. The gcc bug report is still > > open, as far as I can see. > > > > If someone wants try a build using —with-build-sysroot instead, they are > > very welcome to try... > > > > Cheers chris > > > > Chris, > I'll try your changes with that hunk

Re: pymol crashing under Qt on Catalina

A few more data points. Testing builds of the pymol with the +python34, +python35, +python36 and +python37 on Catalina built with Xcode 11.2 beta 2 shows that none of them have issues running under the Qt interface. So this crash seems entirely specific to the +python27 variant of pymol.

Re: Pick up SDKROOT as the sysroot fallback.

On Sun, Oct 13, 2019 at 1:30 PM Chris Jones wrote: > > > On 13 Oct 2019, at 6:20 pm, Jack Howarth > wrote: > >  > Shouldn't that also strip out... > > if {${configure.sdkroot} ne ""} { > # We should be using --with-build-sysroot here. Using > --with-sysroot > # changes the

Re: Pick up SDKROOT as the sysroot fallback.

> On 13 Oct 2019, at 6:20 pm, Jack Howarth > wrote: > >  > Shouldn't that also strip out... > > if {${configure.sdkroot} ne ""} { > # We should be using --with-build-sysroot here. Using --with-sysroot > # changes the behavior of the installed gcc to look in that sysroot

Re: Pick up SDKROOT as the sysroot fallback.

Shouldn't that also strip out... if {${configure.sdkroot} ne ""} { # We should be using --with-build-sysroot here. Using --with-sysroot # changes the behavior of the installed gcc to look in that sysroot # by default instead of /. Using --with-build-sysroot is

Re: Pick up SDKROOT as the sysroot fallback.

https://github.com/macports/macports-ports/commit/1850136d289019f3b29a5b24d3ec8ef9b23913ee Chris > On 13 Oct 2019, at 5:49 pm, Kenneth F. Cunningham > wrote: > >> Chris, >> FYI, this has

Re: Pick up SDKROOT as the sysroot fallback.

> Chris, > FYI, this has already been committed upstream. > > https://gcc.gnu.org/ml/gcc-cvs/2019-10/msg00148.html > > Jack Yes, this plan is coming along nicely -- some of us know how this came to pass :> I sent that link to Josh a while back when it came out, as support for

Re: Pick up SDKROOT as the sysroot fallback.

Yes, I know. We need a version for the gcc 9.2.0 version/branch, and the master one does not apply directly. cheers Chris > On 13 Oct 2019, at 5:30 pm, Jack Howarth > wrote: > > Chris, > FYI, this has already been committed upstream. > >

Re: Pick up SDKROOT as the sysroot fallback.

Chris, FYI, this has already been committed upstream. https://gcc.gnu.org/ml/gcc-cvs/2019-10/msg00148.html Jack On Sun, Oct 13, 2019 at 12:02 PM Chris Jones wrote: > Hi, > > Interesting thanks . Was wondering about something like this. Let me see > about porting it to the gcc9

Re: pymol crashing under Qt on Catalina

> On 13 Oct 2019, at 4:57 pm, Jack Howarth > wrote: > >  > Another data point. Rebuilding python27 with this addition to the Portfile... > > if { ([vercmp ${os.major} 19] >= 0) && ([vercmp $xcodeversion 11.3] < 0) } { > if {[string match clang ${configure.compiler}]} { >

Re: pymol crashing under Qt on Catalina

> On 13 Oct 2019, at 4:38 pm, Jack Howarth > wrote: > >  > It would seem that this failure under Xcode 11.2 beta 2 is due to the current > patch dropping -fno-stack-check for Xcode 11.2 in anticipation of a fix. > > # Workaround for test failure :- > # > ./sblat2 < ./sblat2.dat > # Program

Re: Xcode bug (was: pymol crashing under Qt on Catalina)

>> >> >> Thanks, >> Jeremy > > Hope that doesn’t mean 12 Apple lawyers will be calling me Tuesday. Happy (Canadian) Thanksgiving! (It’s cold up here, harvest comes a month earlier than down in the USA). Ken

Re: Pick up SDKROOT as the sysroot fallback.

Hi, Interesting thanks . Was wondering about something like this. Let me see about porting it to the gcc9 build. Chris > On 13 Oct 2019, at 3:24 pm, Jack Howarth > wrote: > >  >We might want to back port this patch into out gcc9 package in order to > avoid hard coding the SDKROOT path

Re: Xcode bug (was: pymol crashing under Qt on Catalina)

> On Oct 13, 2019, at 7:26 AM, Joshua Root wrote: >>> >>> 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... > > Ken? > Hey Ken, > > There's a bug in Xcode 11's llvm that is biting

Re: pymol crashing under Qt on Catalina

Another data point. Rebuilding python27 with this addition to the Portfile... if { ([vercmp ${os.major} 19] >= 0) && ([vercmp $xcodeversion 11.3] < 0) } { if {[string match clang ${configure.compiler}]} { configure.cc-append -fno-stack-check } } successfully passes

Re: pymol crashing under Qt on Catalina

It would seem that this failure under Xcode 11.2 beta 2 is due to the current patch dropping -fno-stack-check for Xcode 11.2 in anticipation of a fix. # Workaround for test failure :- # > ./sblat2 < ./sblat2.dat # Program received signal SIGSEGV: Segmentation fault - invalid memory reference. #

Re: pymol crashing under Qt on Catalina

> On 13 Oct 2019, at 4:02 pm, Jack Howarth > 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

Re: pymol crashing under Qt on Catalina

On 2019-10-14 01:49 , Jack Howarth 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? >          

Re: pymol crashing under Qt on Catalina

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

Re: pymol crashing under Qt on Catalina

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

Xcode bug (was: pymol crashing under Qt on Catalina)

On 2019-10-14 01:13 , Chris Jones wrote: > > >> On 13 Oct 2019, at 3:11 pm, Joshua Root wrote: >> On Sun, Oct 13, 2019 at 9:49 AM Chris Jones >>> > wrote: >>>Agreed. Accordingly to Jeremy though its a Xcode bug expected to be >>>fixed in 11.2.

Pick up SDKROOT as the sysroot fallback.

We might want to back port this patch into out gcc9 package in order to avoid hard coding the SDKROOT path in the compiler during the build. [Darwin, committed] Pick up SDKROOT as the sysroot fallback. Jack

Re: pymol crashing under Qt on Catalina

On Sun, Oct 13, 2019 at 10:04 AM Chris Jones wrote: > > > On 13 Oct 2019, at 2:56 pm, Jack Howarth > wrote: > >  > Chris, > This is a fresh build of all the MacPorts packages from last night's > port files using Xcode 11.1. > Jack > > > Ok, then next I would try either using

Re: pymol crashing under Qt on Catalina

> On 13 Oct 2019, at 3:11 pm, Joshua Root wrote: > > On 2019-10-14 00:59 , Jack Howarth wrote: >> >> >>> On Sun, Oct 13, 2019 at 9:49 AM Chris Jones >> > wrote: >>> >>> >>> >>>On 13 Oct 2019, at 2:46 pm, Joshua Root >>>

Re: pymol crashing under Qt on Catalina

On 2019-10-14 00:59 , Jack Howarth wrote: > > > On Sun, Oct 13, 2019 at 9:49 AM Chris Jones > wrote: > > > >> On 13 Oct 2019, at 2:46 pm, Joshua Root > > wrote: >> >> On 2019-10-14 00:35 , Chris Jones wrote: >>> >>>

Re: pymol crashing under Qt on Catalina

> On 13 Oct 2019, at 2:56 pm, Jack Howarth > wrote: > >  > Chris, > This is a fresh build of all the MacPorts packages from last night's > port files using Xcode 11.1. > Jack Ok, then next I would try either using the Xcode 11.2 beta, or patch python with the

Re: pymol crashing under Qt on Catalina

On Sun, Oct 13, 2019 at 9:49 AM Chris Jones wrote: > > > On 13 Oct 2019, at 2:46 pm, Joshua Root 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

Re: pymol crashing under Qt on Catalina

Chris, This is a fresh build of all the MacPorts packages from last night's port files using Xcode 11.1. Jack On Sun, Oct 13, 2019 at 9:31 AM Chris Jones wrote: > Hi, > > What Xcode version are you using ? If 11.0, first try updating to 11.1 and > then rebuild the various

Re: pymol crashing under Qt on Catalina

> On 13 Oct 2019, at 2:46 pm, Joshua Root 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 >> >>

Re: pymol crashing under Qt on Catalina

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 > >

Re: pymol crashing under Qt on Catalina

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 > On 13 Oct 2019, at 2:31

Re: pymol crashing under Qt on Catalina

Hi, What Xcode version are you using ? If 11.0, first try updating to 11.1 and then rebuild the various ports (including python). Chris > On 13 Oct 2019, at 1:52 pm, Jack Howarth > wrote: > >  > The +python37 variant of pymol runs fine under its Qt interface on > Catalina, however

pymol crashing under Qt on Catalina

The +python37 variant of pymol runs fine under its Qt interface on Catalina, however the stock +python27 variant crashes Qt as follows... Process: Python [46230] Path: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python

Re: Perl module Privileges::Drop Portfile Fails to Build on Azure

On 2019-10-13 21:29 , Steven Smith wrote: >> Add the needed dependencies so that that does not happen. > > Everything in PR https://github.com/macports/macports-ports/pull/5482 is > working now except for the remaining issue that one azure build fails > because of some issue with perl building

Re: Perl module Privileges::Drop Portfile Fails to Build on Azure

> Add the needed dependencies so that that does not happen. Everything in PR https://github.com/macports/macports-ports/pull/5482 is working now except for the remaining issue that one azure build fails because of some issue with perl