Subject: Re: [nmr_sparky] (unknown)
From: kk sinha
Date: Jan 23, 2014

Previous: 908

Hi,
Just wanted to let you all know that Sparky is working now with Mavericks. All I had to do was to uninstall it (I had the version 3.113) and reinstall the version 3.115. Now it works even when I double click the sparky icon.
Thanks


On Wednesday, 22 January 2014 2:05 PM, kk sinha kkalyansinha@... wrote:
Hi,
Thanks for the replies. I tried changing the sparky script as Andy suggested. After doing that I tried to launch Sparky by typing sparky when in the MacOS directory. I get the following message in the terminal: bad CPU type in executable. Following that a pop-up window appeared with following message:
Could not connect to the X server.
You must start the X window system before starting sparky. The Apple X server is found in the Applications/Utilities folder, called x11. It is available from http://www.apple.com/macosx/x11.


On Wednesday, 22 January 2014 11:48 AM, Hinck, Andrew Peterson hinck@... wrote:
I am running Sparky successfully under 10.9.1 mavericks.

However, I must start the program by invoking the startup script called sparky on the XQuartz command line (I was not successful getting it to launch from the icon in my toolbar, as I had under 10.7 where I was running X11).

On my system, the sparky startup script is found in/Applications/Sparky.app/Contents/MacOS.

One further note ... I found that I had to slightly modify the sparky startup script (relative to that supplied by the download) ... specifically mine now looks like this:

[Andrew-Hincks-MacBook-Pro-2:Sparky.app/Contents/MacOS] ahinck% more sparky
#!/bin/sh

SPARKY_APP=/Applications/Sparky.app/
SPARKY=$SPARKY_APP/Contents/Resources

if [ ! $DISPLAY ]
then
DISPLAY=:0
export DISPLAY
fi

#
# Try connecting to X server. Show a warning dialog on failure.
#
XTEST=$SPARKY_APP/Contents/MacOS/xtest
if test -x $XTEST ! $XTEST
then
exec osascript -e display dialog Could not connect to the X server.r rYou must start the X windowing system before starting Sparky. The Apple X server is found in the /Applications/Utilities folder, called X11. It is available fromrrhttp://www.apple.com/macosx/x11 buttons {Ok} with icon 2
fi

# Increase stack limit. Default is 512Kb
ulimit -s 4096

#
# Mac OS makes the first command-line argument -psn_xxx where xxx is the
# process serial number when Sparky is started by clicking an icon.
# Dont pass this argument to Sparky.
#
if test ${1:0:4} == -psn
then
exec $SPARKY/bin/sparky ${@:2}
else
exec $SPARKY/bin/sparky ${@:1}
fi

===========

A diff commands the following differences relative to the sparky startup script that was supplied with the download:

[andrewhncksmbp2:Sparky.app/Contents/MacOS] ahinck% diff sparky /Applications/Sparky.app/Contents/MacOS/sparky
3c3
SPARKY_APP=`dirname $0`/../..
---
SPARKY_APP=/Applications/Sparky.app/
15c15
XTEST=$SPARKY_APP/Contents/MacOS/xtest
---
XTEST=$SPARKY_APP/Contents/MacOS/xtest

So, in other words, I had to adjust the definition of SPARKY_APP and add double quotes to the XTEST definition .. that was it.

One last thing ... once you get the sparky startup script working, you can make this easier to use by adding a symbolic link that points to the sparky script from a directory thats already on your PATH. On my MAC, I setup things up so that I am running C-shell by default and in my .cshrc file in my homedir I added /usr/local/bin to my PATH ... so in this case, I just cdd to /usr/local/bin and then ran the following:

sudo ln -s /Applications/Sparky.app/Contents/MacOS/sparky ./sparky

command to create the symbolic link.

This makes things easy now ... all you have to do is open an XQuartz shell and without changing from your homedir you can start sparky by just typing sparky.

I hope that helps.

Andy

On Jan 22, 2014, at 2:42 AM, Martin Ballaschk ballaschk@... wrote:

Hi,

Sparky starts without issues here (OS 10.9.1) ... but I remember that it didnt come up the first time I tried to start it, second time no problems.

Does it give you any error messages? Does yor X11 work with other applications?

Cheers,
Martin

On 21.01.2014, at 23:02, kk sinha kkalyansinha@... wrote:

Im having issues with sparky since I upgraded my mac to the new OS Mavericks. Basically, I cant open it anymore. Apparently, the new OS doesnt include x11. It however gave me a link to the site where x11 can be obtained from. I downloaded it from there. But, still I havent been able to start sparky. Has any one experienced similar problems? Does anyone know how to deal with it? Any help regarding this will be highly appreciated.
Thanks,
Kalyan





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Andrew P. Hinck, Ph.D.
Professor of Biochemistry
Director UTHSCSA Biomolecular NMR Core
Director CTRC Macromolecular Structure Core
Department of Biochemistry, MC 7760
University of Texas Health Science Center at San Antonio
San Antonio, TX 78229-3900
office phone: 210-567-8780
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email:hinck@...