Macs in Chemistry

Insanely Great Science

XQuartz update

 

XQuartz 2.7.11 is available for download.

Changes in 2.7.11

All changes in 2.7.10 plus:

lib:

  • fontconfig
  • Fix font caching (#97546)

libpng 1.6.26

libX11

  • Plug a memory leak

libXi 1.7.8

  • Plus fixes for a memory leak and improved error handling

mesa 12.0.1


Comments

XQuartz 2.7.10 released

 

XQuartz 2.7.10 has been released. OS X 10.6.3 or later is required to install this package.

I did some very limited (MOE and PYMOL) testing under Mac OSX 10.12 (Sierra) and didn’t find any issues. Changes in 2.7.10 All changes in 2.7.9 plus

app

  • mkfontdir
  • Fix a buffer underrun crash (#96905) quartz-wm
  • Properly handle updates to WM_PROTOCOLS property changes (#92652)
  • xinit
  • Fixed support for enabling TCP server connections (#95379)
  • Added support for enabling IGLX (#96260)
  • defaults write org.macosforge.xquartz.X11 enable_iglx -bool true
  • xterm 326

proto:

  • xcb-proto 1.12
  • xproto 7.0.31

lib:

  • fontconfig 2.12.1
  • CVE-2016-5384
  • freetype 2.7
  • libpng 1.5.27
  • libpng 1.6.25
  • libxcb 1.12
  • libX11 1.6.4
  • libXfixes 5.0.3
  • libXfont 1.5.2
  • Fix a buffer overrun (#83224)
  • libXfont2
  • Fix a buffer overrun (#83224)
  • libXi 1.7.7
  • libXrandr 1.5.1
  • libXrender 0.9.10
  • libXt
  • libXt.6.dylib is now a two-level-namespace dylib
  • libXt.7.dylib is now a stub dylib that re-exports libXt.6.dylib (for binary compatibility with anything built against XQuartz 2.7.9)
  • A flatnamespace version of libXt is available in /opt/X11/lib/flatnamespace to help ease the transition (#96292)
  • Set DYLDLIBRARYPATH=/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.
  • libXtst 1.2.3
  • libXv 1.0.11
  • CVE-2016-5407
  • libXvMC 1.0.10
  • mesa 11.2.2
  • xcb-util-cursor 0.1.3

server:

  • xorg-server 1.18.4 plus other patches
  • Fix the issue where the h key could be come “stuck” after hiding XQuartz with cmd-h (#92648)

Comments

Support of indirect GLX (iGLX) in XQuartz.

 

An update from X11.org

On Thu, 2016-05-26 at 16:34 +0000, Cook, Rich wrote:

Hello, I recently heard on the Apple x11-users mailing list that remote OpenGL rendering (IGLX) is being phased out of XOrg and not being replaced. Is this really the case or am I misunderstanding?

You have heard incorrectly. It is disabled by default for security reasons, as it's been a repeated source of exploitable bugs, but the feature itself isn't going away.

One caveat is there's no easy way to enable it other than the command line, and not all display managers give you a mechanism to pass arbitrary options in (which is reasonable enough). I've added an xorg.conf option to enable IGLX in master, and I'll be backporting that to the various stable branches as well.


Comments

Support of indirect GLX (iGLX) in XQuartz.

 

There is an important discussion taking place on the X11 users list regarding the support of indirect GLX (iGLX) in XQuartz.

Indirect GLX is an extension offered by X11 that enables the transmission of OpenGL commands from an X11 client on a remote machine to an X11 server on your desktop over the network. For example, when your OpenGL science application running on a remote host tries to draw images using OpenGL and display on your local XOrg (XQuartz) desktop, IGLX (red line below) is used to send the commands to your local X server, which then uses OpenGL locally to draw the commands.

siggraph-2012-nvidia-opengl-for-2012-78-728

In seems in the latest version of XQuartz (2.7.9) this is turned off by default and there appears to be a move to deprecate this protocol. This seems to have been prompted by security concerns but I know nothing of the details.

However many scientific applications use this capability and it seems there is no alternative. If this is likely to be an issue for you I suggest you subscribe to the X11 list and make your views known.


Comments

XQuartz update

 

XQuartz 2.7.9_rc1 is available for download. This update contains a workaround for an issue that users have been reporting on El Capitan. If you're on El Capitan and have been seeing OpenGL surfaces remain onscreen after they should have been dismissed, please give this update a try and report back to the developers.

http://www.xquartz.org/releases/XQuartz-2.7.9_rc1.html

Comments

XQuartz updated

 

X11 2.7.7 has been released

The XQuartz project is an open-source effort to develop a version of the ​X.org X Window System that runs on OS X. Together with supporting libraries and applications, it forms the X11.app that Apple has shipped with OS X since version 10.5.

Installation

Download XQuartz-2.7.7_rc1.dmg, and open it with OS X's Installer.

Important Notices

OS X Requirements

OS X 10.6.3 or later is required to install this package.

Default X11 Server

If this is your first time installing XQuartz, you may wish to logout and log back in. This will update your DISPLAY environment variable to point to XQuartz.app rather than X11.app. If you would prefer to keep using X11.app as your default server (you can still launch XQuartz.app manually), you'll want to disable /Library/LaunchAgents/org.macosforge.xquartz.startx.plist using ​launchctl(1).

Changes in 2.7.7

All changes in 2.7.6 plus: app: ​xcursorgen 1.0.6 ​xscope 1.4.1 ​xterm 309 lib: ​libICE 1.0.9 ​libXft 2.3.2 ​libXi 1.7.4 ​pixman 0.32.6 ​xcb-util-renderutil 0.3.9 proto: glproto 1.4.17 ​inputproto 2.3.1 server: ​xorg-server 1.15.2 plus ​other patches Fixes multimonitor support on Mavericks (#832) Fix Xephyr "failed to create root window" bug (#822)

Comments

XQuartz updated

 

Version 2.7.6 of XQuartz has been released. This release requires Mac OSX 10.6.3 or later.

The XQuartz project is an open-source effort to develop a version of the X.Org X Window System that runs on OS X. Together with supporting libraries and applications, it forms the X11.app that Apple has shipped with OS X since version 10.5.

Comments

XQuartz Updated

 

XQuartz has been updated this contains X11 2.7.5 the first release supported on Mavericks. Full details are available here

The XQuartz project is an open-source effort to develop a version of the X.Org X Window System that runs on OS X. Together with supporting libraries and applications, it forms the X11.app that Apple has shipped with OS X since version 10.5.

Comments

XQuartz Updated

A version of the X.Org X Window System that runs on OS X.

The XQuartz project is an open-source effort to develop a version of the X.Org X Window System that runs on OS X. Together with supporting libraries and applications, it forms the X11.app that Apple has shipped with OS X since version 10.5.

For OS X 10.6 or later (including Mountain Lion)

Comments

Mountain Lion and Chemistry

I spent the weekend updating my MacBook Pro to Mountain Lion, this took much longer than I expected due to the fact that apparently my BT business hub is prevented from downloading any files greater than 2 GB. After several discussions with the BT online help they reconfigured things to allow the 4.2GB download. It seems they have had many thousands of complaints so I added my name to the list.

The download and update went very smoothly, I then installed X11. As I mentioned previously, X11 is no longer included as part of the standard distribution of the operating system. In the future this will be downloaded when needed from the XQuartz server. This happens even if you have previously installed XQuartz.

x11

The XQuartz project is an open-source effort to develop a version of the  X.org X Window System that runs on Mac OS X. Together with supporting libraries and applications, it forms the X11.app that Apple has shipped with OS X since version 10.5. It may in fact be better if users download the latest version of XQuartz when needed since they provide regular updates which are unfortunately overwritten when you install a Mac OS update.

I also needed to install the latest version of Java, you will be prompted to install the first time it is required or you can use the command line. First open a Terminal window, then type

java -version

you should get a message stating “No Java runtime present, requesting install” followed by a window prompting you to install Java SE in order to open “java”, click “Install” to get the latest version.

So far I’ve done preliminary tests on the following applications without obvious issues.

Aabel Avogadro BBEdit ChemBioDraw 13 ChemDoodle DevonThink Pro Elemental MarvinSketch MarvinView MarvinSpace MOE (X11 enviroment) PYMOL Swiss-PdbViewer Vortex

Comments

X11 in Mountain Lion

As I mentioned previously, X11 is no longer included as part of the standard distribution of the operating system. In the future this will be downloaded when needed from the XQuartz server. This happens even if you have previously installed XQuartz.

x11

The XQuartz project is an open-source effort to develop a version of the  X.org X Window System that runs on Mac OS X. Together with supporting libraries and applications, it forms the X11.app that Apple has shipped with OS X since version 10.5. It may in fact be better if users download the latest version of XQuartz when needed since they provide regular updates which are unfortunately overwritten when you install a Mac OS update.

Comments

XQuartz 2.7.2 released

The XQuartz project is an open-source effort to develop a version of the X.Org X Window System that runs on OS X. Together with supporting libraries and applications, it forms the X11.app that Apple has shipped with OS X since version 10.5.

The latest version is available from here together with a list of the changes.

Comments

XQuartz release candidate 3

The XQuartz project is an open-source effort to develop a version of the  X.org X Window System that runs on OS X. Together with supporting libraries and applications, it forms the X11.app that Apple has shipped with OS X since version 10.5.

This development release are now signed with an Apple DeveloperID for increased security.

Download XQuartz-2.7.2_rc3.dmg, and open it with OS X's Installer.

Full details of the changes are here.

Comments

XQuartz release candiate 2

The XQuartz project is an open-source effort to develop a version of the  X.org X Window System that runs on OS X. Together with supporting libraries and applications, it forms the X11.app that Apple has shipped with OS X since version 10.5.

This development release are now signed with an Apple DeveloperID for increased security.

Download XQuartz-2.7.2_rc2.dmg, and open it with OS X's Installer.

Full details of the changes are here.

Comments

XQuartz 2.7.2 beta 5 released

The latest beta test version of XQuartz has been released. Mac OS X 10.6.3 or later is required to install this package.

The XQuartz project is an open-source effort to develop a version of the  X.org X Window System that runs on OS X. Together with supporting libraries and applications, it forms the X11.app that Apple has shipped with OS X since version 10.5.

Comments

X11 in Mountain Lion

A couple of people have contacted me about the news that X11will not part of the standard distribution of the next version of the Mac operating system. X11 is a key UNIX windowing system for a number scientific applications and I can understand the concern. However whilst X11 has been included in the past it should be noted that the distributed version is simply a snapshot of XQuartz, in the future this will be automatically downloaded.

x11

The XQuartz project is an open-source effort to develop a version of the  X.org X Window System that runs on Mac OS X. Together with supporting libraries and applications, it forms the X11.app that Apple has shipped with OS X since version 10.5. It may in fact be better if users download the latest version of XQuartz when needed since they provide regular updates which are unfortunately overwritten when you install a Mac OS update.

Indeed the team have already provided a latest development version that is compatible with Mountain Lion (XQuartz  2.7.1 rc4 - 2012.02.11), if you find any bugs or issues I urge you to report them to the XQuartz team !

Comments

XQuartz 2.7.0 released

The XQuartz project is an open-source effort to develop a version of the  X.org X Window System that runs on Mac OS X. Together with supporting libraries and applications, it forms the X11.app that Apple has shipped with OS X since version 10.5.

X11 2.7.0
Released: 2011.11.04
This release contains xorg-server 1.11.2
Installation
Download XQuartz-2.7.0.dmg (Snow Leopard and Lion), and open it with Mac OSX's Installer.
Important Notices
OS-X Requirements
OS-X 10.6.3 or later is required to install this package.

Comments

XQuartz updated

XQuartz has been updated to version 2.6.3 Read More...
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XQuartz 2.6.2 released

XQuartz 2.6.2 released Read More...
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XQuartz update

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Knime and XQuartz updated

Knime and XQuartz updated

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XQuartz Updated

XQuartz was updated recently to version 2.5.3

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XQuartz Updated

XQuartz has been updated to version 2.5.2 Read More...
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XQuartz update

Important X11 update Read More...
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X11 for Mac OS X updated

X11 2.4.0 Released: 2009.08.14 Read More...
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X11

Update to X11 app. Read More...
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X11

New X11 update. Read More...
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X11 in Leopard problems

In Leopard, Apple switched from XFree86 to X.org for its X11 implementation. This seems to have caused a number of issues.
Read More...
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