apbs-3.4.1-0

I am puzzled by the current status of the pull request to update apbs to the current upstream apbs 3.4.1 release so we have arm64 builds of apbs available for the new pymol 3.0.0 packaging to use (which has added the new electrostatics gui interface previously only available in the paid

Sonoma Apple Silicon build machine

What is the situation with MacPorts port builds on the autobuilder for Sonoma? Am I correct to assume that we are waiting for Apple to release Xcode 15.1 to resolve the outstanding linker issues introduced in Xcode 15? I recently switched from a 2017 MacBook Pro i5 to a 20202 MacBook Air M1 and,

Re: Monterey install .pkg and website updates?

Ryan, What is the timeline on getting a package buildbot running for Monterey? Jack ps I've been building through towards my pymol package and so far the biggest blocker is the broken qt5 package on Monterey. It. seems to get confused about finding the SDK (unless those are

port rev-upgrade appearing on gcc9

Despite the fact that the git sources for gcc9 show a revision change to 2 in order to rebuild against the newer isl package, the current package built for darwin18 doesn't seem to be built that way. I get... % sudo port install gcc9 ---> Computing dependencies for gcc9 ---> Fetching

Re: OpenBLAS fixed in Xcode 11.2

und > is automatically dropped when using Xcode 11.3. > > -Marcus > > > On Dec 15, 2019, at 8:49 AM, Jack Howarth > wrote: > > > > FYI, the gmp test suite failure in the t-powm test case when using core2 > optimization with the default stack checking has been

Re: OpenBLAS fixed in Xcode 11.2

was able to pass all of the tests just by setting > CFLAGS (*without* -fcheck-stack). > > -Marcus > > > On Nov 9, 2019, at 8:19 AM, Jack Howarth > wrote: > > > > > > > > On Fri, Nov 8, 2019 at 10:17 PM Ryan Schmidt > wrote: > > On Nov 8, 2019, at 20:03

Re: OpenBLAS fixed in Xcode 11.2

On Fri, Nov 8, 2019 at 10:17 PM Ryan Schmidt wrote: > On Nov 8, 2019, at 20:03, Joshua Root wrote: > > > On 2019-11-9 10:28 , Jack Howarth wrote: > >> I just noticed a really bizarre aspect to this Xcode 11 bug. If you > >> build gmp manually from source with the

Re: OpenBLAS fixed in Xcode 11.2

ens with gcc if that is enabled that > would help... > > Chris > > On 08/11/2019 12:53 pm, Jack Howarth wrote: > > FYI, I got this back on my radar about gmp still being broken in Xcode > > 11.2... > > > > Engineering has provided the following information regard

Re: OpenBLAS fixed in Xcode 11.2

On Fri, Nov 8, 2019 at 7:53 AM Jack Howarth wrote: > FYI, I got this back on my radar about gmp still being broken in Xcode > 11.2... > > Engineering has provided the following information regarding this issue: > It sounds like gmp has a memory corruption issue which -f

Re: OpenBLAS fixed in Xcode 11.2

. For course, the upstream gmp developer constantly rants about how broken clang is so he will probably just blame the llvm developers for the breakage. Jack On Fri, Nov 1, 2019 at 5:09 AM Jack Howarth wrote: > The issues in gmp might not be fixed in Xcode 11.2. The exact issue isn't >

Re: 10.15 builder offline ?

On Sat, Nov 2, 2019 at 11:44 AM Ryan Schmidt wrote: > On Nov 2, 2019, at 07:33, Ryan Schmidt wrote: > > > On Nov 2, 2019, at 07:04, Christopher Jones wrote: > > > >> Looks like the 10.15 builder has gone down ? > >> > >> https://build.macports.org/waterfall > > > > It was requested that I update

Re: OpenBLAS fixed in Xcode 11.2

On Sun, Nov 3, 2019 at 4:55 AM Ryan Schmidt wrote: > > > On Nov 3, 2019, at 03:52, Chris Jones wrote: > > > Hi, > > > > On 2 Nov 2019, at 4:56 pm, Ryan Schmidt wrote: > > > >> Josh told me when Mojave was released that we weren't installing the > CLT anymore on the builders. > >> > >> Then when

Re: OpenBLAS fixed in Xcode 11.2

t; On Oct 31, 2019, at 20:34, Joshua Root wrote: > > > >> On 2019-11-1 11:49 , Jack Howarth wrote: > >>> Although it wasn't fixed in Xcode 11.2 beta 2, the -fcheck-stack > >>> issues with OpenBLAS's test suite are fixed in the final Xcode 11.2 > >>

Re: OpenBLAS fixed in Xcode 11.2

d to hear. However, Xcode 11.2 has not fixed everything, as x265 still > seg. faults when build with clang from Xcode 11.2. > > cheers Chris > > > On 1 Nov 2019, at 12:49 am, Jack Howarth > wrote: > > > > Although it wasn't fixed in Xcode 11.2 beta 2, the -fcheck

Re: OpenBLAS fixed in Xcode 11.2

31, 2019 at 10:51 PM Ryan Schmidt wrote: > > > On Oct 31, 2019, at 20:34, Joshua Root wrote: > > > On 2019-11-1 11:49 , Jack Howarth wrote: > >> Although it wasn't fixed in Xcode 11.2 beta 2, the -fcheck-stack > >> issues with OpenBLAS's test sui

OpenBLAS fixed in Xcode 11.2

Although it wasn't fixed in Xcode 11.2 beta 2, the -fcheck-stack issues with OpenBLAS's test suite are fixed in the final Xcode 11.2 released today. Jack

Re: replacing OpenGL with MoltenVK

On Mon, Oct 21, 2019 at 2:11 PM Christopher Jones wrote: > > > > On 21 Oct 2019, at 6:30 pm, Ryan Schmidt > wrote: > > > > > > > > On Oct 21, 2019, at 12:19, Jack Howarth wrote: > >> > >>Are there any plans for using the MoltenVK pa

replacing OpenGL with MoltenVK

Are there any plans for using the MoltenVK package in MacPorts as a replacement for the macOS OpenGL support that is slated for depreciation? Jack

10.15 builder

I noticed that https://build.macports.org/builders doesn't show a 10.15 builder yet. Is there a schedule for when one will become available? Jack

Re: pymol crashing under Qt on Catalina

Ryan, See https://trac.macports.org/ticket/59358 which has the missing Debian patch for py-pyqt5 that eliminates the crashes. Jack On Wed, Oct 16, 2019 at 7:46 PM Ryan Schmidt wrote: > On Oct 16, 2019, at 17:36, Jack Howarth wrote: > > ps Do the binary servers retain

Re: pymol crashing under Qt on Catalina

under the qt5 interface. https://trac.macports.org/ticket/59358 Jack On Wed, Oct 16, 2019 at 6:36 PM Jack Howarth wrote: > Does the default python27 variant of pymol run without a segfault for > anyone under Mojave? I am finding that a clean installation of MacPorts > agai

Re: pymol crashing under Qt on Catalina

Do the binary servers retain the older versions of the python27 packages? I am tempted to walk back through them and see if I can find a version that still works. On Tue, Oct 15, 2019 at 8:50 PM Jack Howarth wrote: > Another data point. Starting with a clean installation of Mojave 10.1

Re: pymol crashing under Qt on Catalina

? Jack On Mon, Oct 14, 2019 at 5:52 PM Jack Howarth wrote: > I've also been able to test the python27 variant of pymol against both > py27-pyqt5 and python27 packages built with -fno-stack-check passed to > clang and clang++ in Xcode 11.2 beta 2 and the crash in the Qt

Re: legacy-support and Wayland

I asked Jeremy about potential Wayland support for macOS awhile back and his response was that it was pointless duplication as Xquartz already achieved the same goals. Jack On Tue, Oct 15, 2019 at 4:40 AM Chris Jones wrote: > Hi, > > On 15/10/2019 9:20 am, René J. V. Bertin wrote:

Re: pymol crashing under Qt on Catalina

step. Jack On Sun, Oct 13, 2019 at 2:10 PM Jack Howarth wrote: > 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 und

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: pymol crashing under Qt on Catalina

. Jack On Sun, Oct 13, 2019 at 12:07 PM Chris Jones wrote: > > > 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) &a

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. Us

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.

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 in the compiler during the build. > > [Darwin, committed] Pick

Re: pymol crashing under Qt on Catalina

ses -fno-stack-check to the build but the resulting python2.7 doesn't suppress the pymol crashes with the QT interface. Maybe the problem code is in py27-pyqt5? Jack On Sun, Oct 13, 2019 at 11:38 AM Jack Howarth wrote: > It would seem that this failure under Xcode 11.2 beta 2 is due

Re: pymol crashing under Qt on Catalina

t; 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:bu

Re: pymol crashing under Qt on Catalina

enBLAS/work/xianyi-OpenBLAS-5f36f18/test' On Sun, Oct 13, 2019 at 10:49 AM 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 ins

Re: pymol crashing under Qt on Catalina

Jones wrote: > > > > 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 >>> <mailto:jon...@hep.phy.cam.ac.uk>> w

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 > > >

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

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 the stock +python27 variant crashes Qt as foll

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: gcc/g++ failures after xcode11 update

Beyond the /usr/include issue, Xcode 11 should be problematic when its bundled 10.15 SDK is used under either Mojave or Catalina due to the enforced use of the availability attribute in the headers. https://gcc.gnu.org/bugzilla/show_bug.cgi?id=90835 On Wed, Sep 25, 2019 at 5:46 AM Chris Jones

Re: flang port

What I see in https://github.com/iains/darwin-gcc-5/commits/darwin-gcc-5-3r2 is coding for an unavailable attribute which could be the starting point for coding the availability attribute. He would though need to dip into the clang/llvm source code to get the code spec to aim for in handling that

Re: flang port

Even if they cook up a fix includes patch to fix the FSF gcc compiler, they will end up with something that still barfs on the availability attribute when seen by the built compiler. On Wed, Jul 10, 2019 at 12:25 PM Chris Jones wrote: > > > On 10 Jul 2019, at 5:19 pm, Jack Howarth

Re: flang port

gt; On 09/07/2019 11:48 pm, Jack Howarth wrote: > > Just saying that since gcc will be broken on the 10.15 SDK that the path > > of least resistance (and the best long term decision) would be to put > > some effort behind getting flang to build (as older patches exist as a > &

Re: flang port

t; On Jul 8, 2019, at 14:37, Jack Howarth wrote: > > >Since the legacy header support for avoiding the availability > attribute has been dropped from the 10.15 SDK... > > > > https://gcc.gnu.org/bugzilla/show_bug.cgi?id=90835 > > > > and it is unclear w

flang port

Since the legacy header support for avoiding the availability attribute has been dropped from the 10.15 SDK... https://gcc.gnu.org/bugzilla/show_bug.cgi?id=90835 and it is unclear when and if the missing availability attribute support will be added to FSF gcc, the path of least resistance

user "macports" does not exist

Short of fully reinstalling MacPorts is there a way to recreate the "macports" user? It seems that a reinstallation of macOS over macOS purged out that user account and there doesn't seem to be a utility installed by MacPorts to recreate it. Oddly this topic doesn't get any Google

Re: OT: Apple 64-bit changes

Currently in 10.14, the depreciation of the 32-bit support is achieved through restricting the linker behavior when the 10.14 SDK is in use. Using the 10.14 SDK results in the libSystem.tbd being used instead of libSystem.dylib. The libSystem.tbd file masks the i386 symbols contained in

Re: Disabling universal on Mojave

Why aren't we leveraging the -DLIBOMP_OSX_ARCHITECTURES cmake flag to control whether "x86_64;i386" or "x86_64" get built? Jack On Sun, Sep 30, 2018 at 8:03 AM Perry E. Metzger wrote: > On Sun, 30 Sep 2018 00:15:09 -0500 Ryan Schmidt > wrote: > > On Sep 29, 2018, at 08:13, Perry E.

Re: Xcode 10.0...

On Tue, Sep 18, 2018 at 11:53 AM Ryan Schmidt wrote: > > > On Sep 17, 2018, at 19:39, Perry E. Metzger wrote: > > > Are we currently set up for the new Xcode 10? It was officially > > released today, although Mojave won't show up for another week. > > The minimal changes to have MacPorts

Re: plans to mitigate the OpenGL depreciation?

't expect any change in MacPorts. They're deprecated, not removed. > "Native" ports should transition to Metal, and X11 ports will continue to > use mesa for GLX. > > > On Jun 20, 2018, at 6:26 AM, Jack Howarth > wrote: > > > > Since the 10.14 SDK fu

plans to mitigate the OpenGL depreciation?

Since the 10.14 SDK fully depreciates building against the OpenGL API, what are the plans going forward for OpenGL support in MacPorts? More importantly, what will be the performance impacts on 10.14? I have the impression that the video card drivers have to provide hardware level OpenGL

build failures and lack of logs

Can someone explain to me how to parse the output from the build failure reports of the build machines? I found a number of them from the pymol package update yesterday across all the build machines however a local build using rsync of the same packaging files produces no build issues. As far as I

pymol update to restore compiler optimization flags

Can someone commit the proposed changes on https://trac.macports.org/ticket/56373 which restores the use of compiler optimization flags to the pymol build. The upstream pymol developers have been not passing optimization flags on Darwin for a couple years now due to a clang compiler ICE which

Re: updating pymol to 2.1.0 and PyQt interface

Okay. I believe I have addressed all the concerns cited on https://trac.macports.org/ticket/56139 Can someone commit the latest files for me? Jack On Mon, Apr 16, 2018 at 11:51 AM, Jack Howarth < howarth.at.macpo...@gmail.com> wrote: > Could someone please commit the

updating pymol to 2.1.0 and PyQt interface

Could someone please commit the proposed Portfile.diff and patches on the ticket... https://trac.macports.org/ticket/56139 which updates pymol to the current 2.1.0 release and adds the additional dependencies required for the new PyQt based GUI? The packages notes on installation that the legacy

let's actually fix the ccpnmr build

Can someone please commit the changes that I posted in the ticket... https://trac.macports.org/ticket/56292 so that ccpnmr actually builds again? People keep committing changes to this package without actually checking that they work. We need to resort to a compiler.blacklist to avoid all

Ticket #56139 update to pymol 2.1.0 with PyQt interface support

Can someone commit my final update to pymol 2.1.0 with PyQt interface support? The packaging switches pymol to use the new PyQt based interface while retaining the tcl/k/pmw dependencies for the legacy plugins. Regarding the legacy plugins, the apbstools one only properly functions on the default

Re: polari broken?

Never-mind. The issue was solved by executing... launchctl load -w /opt/local/Library/LaunchDaemons/org.freedesktop.dbus-system.plist launchctl load -w /opt/local/Library/LaunchAgents/org.freedesktop.dbus-session.plist and logging out. On Thu, Apr 12, 2018 at 8:08 PM, Jack Howarth

polari broken?

Is anyone on 10.13 able to start polari such that a window appears? It seems to cause the xors-server app to launch but only produces the following output in the terminal without opening the Polari window... $ polari (.:18119): Gjs-*WARNING* **: 20:07:49.426: Some code accessed the property

Re: port version reports 2.4.2 when built from tag v2.4.3

On Thu, Apr 12, 2018 at 6:47 PM, Rainer Müller <rai...@macports.org> wrote: > On 2018-04-13 00:42, Jack Howarth wrote: > > This issue might also be impacting the High Sierra macports 2.4.3 > > installer image as well. After installing it on a machine with no > > /opt