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Re: [nmrpipe] nmrPipe, XQuartz and Apple's Software Update

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  • Ryan McKay
    So running Mac OSX 10.6.5 (latest) with XQuartz 2.5.3 (latest) and NMRPipe 5.5 rev2010.302.14.25 (latest) No bus error. No problems. Can be launched from
    Message 1 of 13 , Nov 19, 2010
    • 0 Attachment
      So running Mac OSX 10.6.5 (latest) with XQuartz 2.5.3 (latest) and NMRPipe 5.5 rev2010.302.14.25 (latest)


      No bus error.  No problems.  Can be launched from Apples "Terminal" and it auto switches over to XQuartz (the X11 for Snow Leopard Mac OSX 10.6.x).

      Running it directly from XQuartz works fine also.

      Running it from the default X11 that comes with Mac OSX (remember it's still there beside XQuartz) does NOT work and causes the bus error problem.

      Not to mention it's slower than stink.

      I also checked all the sub-menus and they're working fine.





      Now one problem I have, which may be my mouse, is that the scroll wheel only works as a button in NMRPipe but works in everything else I've tested in the X11 windowing environment.

      specific e.g. When trying to select a directory my scroll wheel doesn't scroll the list.

      Anyone else?





      On 2010-11-17, at 11:22 AM, Ryan McKay wrote:

      Interestingly I've got NMRPipe working without the bus error but my mouse scroll wheel has stopped working in the selected menus of NMRDraw.  e.g. file/select I can't scroll down the window list of files.

      Perplexing.

      R



      On 2010-11-15, at 3:45 PM, Adams, Kristie (NIH/NCI) [F] wrote:

       

      Don't forget that after you do Apple Software Update and re-install XQuartz 2.5.3, you have to log out and log in. Simply closing and re-starting X11 isn't enough! Restart if you have to, but the log out/log in worked for me.

      Try this and see if it works.

      Kristie

      On 11/15/10 4:43 PM, "Ryan McKay" <ryan@...> wrote:

      Interestingly I didn't have the problem, but after re-installing 2.5.3 I now get the bus error.

      I'm going to try re-re-installing X11 Quartz.

      R

      On 2010-11-15, at 2:27 PM, Ryan McKay wrote:

      Awesome! Thanks for the heads up.
      Ryan

      On 2010-11-12, at 12:05 PM, kristie_1213 wrote:

      Hi all,

      I thought I would pass along recent experience with nmrPipe (latest, Version 5.5 Rev 2010.302.14.25), XQuartz 2.5.3 and Mac OS X 10.6.5, and a mysterious 'bus error' upon installation of 10.6.5.

      I previously had Mac OS 10.6.4 (Apple just pushed 10.6.5 last evening/this morning) and I installed 10.6.5 today. After installing (and rebooting, of course), I received a 'bus error' upon attempting to open nmrDraw. After some research, I discovered that (even though it's not documented) Apple still pushes parts of X11 code with their software updates, and this code supersedes that installed with XQuartz. Thus, it is necessary to re-install XQuartz 2.5.3 AFTER installing the 10.6.5 update. After doing this and logging out/in, all works fine with nmrPipe and nmrDraw.

      This issue is mentioned on the XQuartz sourceforge page as a problem primarily occurring with Leopard, but the suggested fix (reinstall of XQuartz 2.5.3) restored my functionality perfectly.

      Thanks!
      Kristie

      *****************************
      Kristie M. Adams, Ph.D.
      CRTA Postdoctoral Fellow
      Chemical Biology Laboratory
      National Cancer Institute-Frederick
      376 Boyles St, Room 117
      National Institutes of Health
      Frederick, MD 21702
      USA
      Phone: 301-846-5962
      Fax: 301-846-6033
      *****************************

      ----------------------------------------------------------
      Ryan T. McKay, Ph.D. - Scientific Director
      NANUC - Canada's National High Field NMR Centre
      Room 105 Email: ryan@...
      NANUC Bld. Phone: (780) 492-2700
      University of Alberta Fax: (780) 492-9174
      Edmonton, Alberta Cell: (780) 920-8871
      Canada T6G 2E1 AIM: ryanmckaynmr
      http://www.nanuc.ca <http://www.nanuc.ca/>

      <NANUC2001_small.jpg>

      ----------------------------------------------------------

      Ryan T. McKay, Ph.D. - Scientific Director

      NANUC - Canada's National High Field NMR Centre

      Room 105 Email: ryan@...

      NANUC Bld. Phone: (780) 492-2700

      University of Alberta Fax: (780) 492-9174

      Edmonton, Alberta Cell: (780) 920-8871

      Canada T6G 2E1 AIM: ryanmckaynmr

      http://www.nanuc.ca

      [cid:3372687931_3883337]



      ------------------------------------------------------------------------------------
      Ryan T. McKay, Ph.D. -     Scientific Director
      NANUC - Canada's National High Field NMR Centre
      Room 105                           Email:  ryan@...
      NANUC Bld.                        Phone: (780) 492-2700
      University of Alberta            Fax:     (780) 492-9174
      Edmonton, Alberta              Cell:     (780) 920-8871
      Canada T6G 2E1                AIM:     ryanmckaynmr
                           http://www.nanuc.ca

      <NANUC2001_small.jpg>



      ------------------------------------------------------------------------------------

      Ryan T. McKay, Ph.D. -     Scientific Director

      NANUC - Canada's National High Field NMR Centre

      Room 105                           Email:  ryan@...

      NANUC Bld.                        Phone: (780) 492-2700

      University of Alberta            Fax:     (780) 492-9174

      Edmonton, Alberta              Cell:     (780) 920-8871

      Canada T6G 2E1

    • Stefano Luciano Ciurli
      Hello everybody, I have a MacBookPro running 10.6.6. I have installed the latest version of nmrPipe and I got into the bus error mentioned in this thread.
      Message 2 of 13 , Mar 17 9:16 AM
      • 0 Attachment
        Hello everybody,

        I have a MacBookPro running 10.6.6. I have installed the latest version of nmrPipe and I got into the bus error mentioned in this thread.

        Thus, I followed the suggestions given here: I downloaded and installed XQuartz 2.5.3, upgraded it to 2.6.0, and the PROBLEM DISAPPEARS IF I CALL nmrDraw form the XQuartz X11 window.

        However, I checked that if I call the command from the old X11 window, the bus error appears again. Also, and most importantly for me, if I call the command form the iTerm window (I use iTerm because it nicely can open windows directly from the Finder window where my files opportunely reside), the bus error reappears, because, apparently, iTerm calls the old X11.

        So I have the following questions:
        1) can I remove the old X11 completely, using, let's say, CleanMyMac?
        2) is there a way to convince iTerm to call the new XQuartz X11 rather than the old one?

        Regards
        Stefano Ciurli

        On Nov 15, 2010, at 11:45 PM, Adams, Kristie (NIH/NCI) [F] wrote:



        Don't forget that after you do Apple Software Update and re-install XQuartz 2.5.3, you have to log out and log in. Simply closing and re-starting X11 isn't enough! Restart if you have to, but the log out/log in worked for me.

        Try this and see if it works.

        Kristie

        On 11/15/10 4:43 PM, "Ryan McKay" <ryan@...<mailto:ryan%40nanuc.ca>> wrote:

        Interestingly I didn't have the problem, but after re-installing 2.5.3 I now get the bus error.

        I'm going to try re-re-installing X11 Quartz.

        R

        On 2010-11-15, at 2:27 PM, Ryan McKay wrote:

        Awesome! Thanks for the heads up.
        Ryan

        On 2010-11-12, at 12:05 PM, kristie_1213 wrote:

        Hi all,

        I thought I would pass along recent experience with nmrPipe (latest, Version 5.5 Rev 2010.302.14.25), XQuartz 2.5.3 and Mac OS X 10.6.5, and a mysterious 'bus error' upon installation of 10.6.5.

        I previously had Mac OS 10.6.4 (Apple just pushed 10.6.5 last evening/this morning) and I installed 10.6.5 today. After installing (and rebooting, of course), I received a 'bus error' upon attempting to open nmrDraw. After some research, I discovered that (even though it's not documented) Apple still pushes parts of X11 code with their software updates, and this code supersedes that installed with XQuartz. Thus, it is necessary to re-install XQuartz 2.5.3 AFTER installing the 10.6.5 update. After doing this and logging out/in, all works fine with nmrPipe and nmrDraw.

        This issue is mentioned on the XQuartz sourceforge page as a problem primarily occurring with Leopard, but the suggested fix (reinstall of XQuartz 2.5.3) restored my functionality perfectly.

        Thanks!
        Kristie

        *****************************
        Kristie M. Adams, Ph.D.
        CRTA Postdoctoral Fellow
        Chemical Biology Laboratory
        National Cancer Institute-Frederick
        376 Boyles St, Room 117
        National Institutes of Health
        Frederick, MD 21702
        USA
        Phone: 301-846-5962
        Fax: 301-846-6033
        *****************************

        ----------------------------------------------------------
        Ryan T. McKay, Ph.D. - Scientific Director
        NANUC - Canada's National High Field NMR Centre
        Room 105 Email: ryan@...<mailto:ryan%40nanuc.ca>
        NANUC Bld. Phone: (780) 492-2700
        University of Alberta Fax: (780) 492-9174
        Edmonton, Alberta Cell: (780) 920-8871
        Canada T6G 2E1 AIM: ryanmckaynmr
        http://www.nanuc.ca<http://www.nanuc.ca/> <http://www.nanuc.ca/>

        <NANUC2001_small.jpg>

        ----------------------------------------------------------

        Ryan T. McKay, Ph.D. - Scientific Director

        NANUC - Canada's National High Field NMR Centre

        Room 105 Email: ryan@...<mailto:ryan%40nanuc.ca>

        NANUC Bld. Phone: (780) 492-2700

        University of Alberta Fax: (780) 492-9174

        Edmonton, Alberta Cell: (780) 920-8871

        Canada T6G 2E1 AIM: ryanmckaynmr

        http://www.nanuc.ca<http://www.nanuc.ca/>

        [cid:3372687931_3883337]
      • Ryan McKay
        Good morning, I would not remove the old X11. My impression is that the new 2.6.0 Quartz X11 installs in an isolated directory for Mac OSX 10.6, but I have no
        Message 3 of 13 , Mar 17 10:21 AM
        • 0 Attachment
          Good morning,

          I would not remove the old X11.  My impression is that the new 2.6.0 Quartz X11 installs in an isolated directory for Mac OSX 10.6, but I have no idea the consequences of removing the old X11 manually from the system.  The size is small and the inconvenience may not be worth the risk.  Make sure you have a backup if you do decide to try it.

          I believe if you set up your environmental variables correctly there is a way to get iTerm/Terminal to work.  However it's a fair bit of hunting, trial and error.  I used to have my Terminal (Mac OS application) working but it broke with the latest NMRPipe/X11 update to 2.6.  I basically just launch it from the new Xquartz X11 window and haven't bothered with figuring out why Terminal doesn't work.

          If you do figure it out let me know please.

          Best wishes,
          Ryan

          ps anyone know a way to get nmrDraw to open on only one screen in a dual display set up?



          On 2011-03-17, at 10:16 AM, Stefano Luciano Ciurli wrote:

          Hello everybody,

          I have a MacBookPro running 10.6.6. I have installed the latest version of nmrPipe and I got into the bus error mentioned in this thread.

          Thus, I followed the suggestions given here: I downloaded and installed XQuartz 2.5.3, upgraded it to 2.6.0, and the PROBLEM DISAPPEARS IF I CALL nmrDraw form the XQuartz X11 window.

          However, I checked that if I call the command from the old X11 window, the bus error appears again. Also, and most importantly for me, if I call the command form the iTerm window (I use iTerm because it nicely can open windows directly from the Finder window where my files opportunely reside), the bus error reappears, because, apparently, iTerm calls the old X11.

          So I have the following questions:
          1) can I remove the old X11 completely, using, let's say, CleanMyMac?
          2) is there a way to convince iTerm to call the new XQuartz X11 rather than the old one?

          Regards
          Stefano Ciurli

          On Nov 15, 2010, at 11:45 PM, Adams, Kristie (NIH/NCI) [F] wrote:



          Don't forget that after you do Apple Software Update and re-install XQuartz 2.5.3, you have to log out and log in. Simply closing and re-starting X11 isn't enough! Restart if you have to, but the log out/log in worked for me.

          Try this and see if it works.

          Kristie

          On 11/15/10 4:43 PM, "Ryan McKay" <ryan@...<mailto:ryan%40nanuc.ca>> wrote:

          Interestingly I didn't have the problem, but after re-installing 2.5.3 I now get the bus error.

          I'm going to try re-re-installing X11 Quartz.

          R

          On 2010-11-15, at 2:27 PM, Ryan McKay wrote:

          Awesome! Thanks for the heads up.
          Ryan

          On 2010-11-12, at 12:05 PM, kristie_1213 wrote:

          Hi all,

          I thought I would pass along recent experience with nmrPipe (latest, Version 5.5 Rev 2010.302.14.25), XQuartz 2.5.3 and Mac OS X 10.6.5, and a mysterious 'bus error' upon installation of 10.6.5.

          I previously had Mac OS 10.6.4 (Apple just pushed 10.6.5 last evening/this morning) and I installed 10.6.5 today. After installing (and rebooting, of course), I received a 'bus error' upon attempting to open nmrDraw. After some research, I discovered that (even though it's not documented) Apple still pushes parts of X11 code with their software updates, and this code supersedes that installed with XQuartz. Thus, it is necessary to re-install XQuartz 2.5.3 AFTER installing the 10.6.5 update. After doing this and logging out/in, all works fine with nmrPipe and nmrDraw.

          This issue is mentioned on the XQuartz sourceforge page as a problem primarily occurring with Leopard, but the suggested fix (reinstall of XQuartz 2.5.3) restored my functionality perfectly.

          Thanks!
          Kristie

          *****************************
          Kristie M. Adams, Ph.D.
          CRTA Postdoctoral Fellow
          Chemical Biology Laboratory
          National Cancer Institute-Frederick
          376 Boyles St, Room 117
          National Institutes of Health
          Frederick, MD 21702
          USA
          Phone: 301-846-5962
          Fax: 301-846-6033
          *****************************

          ----------------------------------------------------------
          Ryan T. McKay, Ph.D. - Scientific Director
          NANUC - Canada's National High Field NMR Centre
          Room 105 Email: ryan@...<mailto:ryan%40nanuc.ca>
          NANUC Bld. Phone: (780) 492-2700
          University of Alberta Fax: (780) 492-9174
          Edmonton, Alberta Cell: (780) 920-8871
          Canada T6G 2E1 AIM: ryanmckaynmr
          http://www.nanuc.ca<http://www.nanuc.ca/> <http://www.nanuc.ca/>

          <NANUC2001_small.jpg>

          ----------------------------------------------------------

          Ryan T. McKay, Ph.D. - Scientific Director

          NANUC - Canada's National High Field NMR Centre

          Room 105 Email: ryan@...<mailto:ryan%40nanuc.ca>

          NANUC Bld. Phone: (780) 492-2700

          University of Alberta Fax: (780) 492-9174

          Edmonton, Alberta Cell: (780) 920-8871

          Canada T6G 2E1 AIM: ryanmckaynmr

          http://www.nanuc.ca<http://www.nanuc.ca/>

          [cid:3372687931_3883337]






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          ------------------------------------------------------------------------------------

          Ryan T. McKay, Ph.D. -     Scientific Director

          NANUC - Canada's National High Field NMR Centre

          Room 105                           Email:  ryan@...

          NANUC Bld.                        Phone: (780) 492-2700

          University of Alberta            Fax:     (780) 492-9174

          Edmonton, Alberta

          Canada T6G 2E1

                               http://www.nanuc.ca



        • Stefano Luciano Ciurli
          Hi Ryan, thanks a lot for not letting me feel alone having this problem :-) I will adapt to launching nmrDraw from the new XQuartz X11 window until the iTerm
          Message 4 of 13 , Mar 17 11:08 AM
          • 0 Attachment
            Hi Ryan,
            thanks a lot for not letting me feel alone having this problem :-)
            I will adapt to launching nmrDraw from the new XQuartz X11 window until the iTerm people will figure it out themselves.
            Regards
            Stefano

            On Mar 17, 2011, at 6:21 PM, Ryan McKay wrote:

            Good morning,

            I would not remove the old X11. My impression is that the new 2.6.0 Quartz X11 installs in an isolated directory for Mac OSX 10.6, but I have no idea the consequences of removing the old X11 manually from the system. The size is small and the inconvenience may not be worth the risk. Make sure you have a backup if you do decide to try it.

            I believe if you set up your environmental variables correctly there is a way to get iTerm/Terminal to work. However it's a fair bit of hunting, trial and error. I used to have my Terminal (Mac OS application) working but it broke with the latest NMRPipe/X11 update to 2.6. I basically just launch it from the new Xquartz X11 window and haven't bothered with figuring out why Terminal doesn't work.

            If you do figure it out let me know please.

            Best wishes,
            Ryan

            ps anyone know a way to get nmrDraw to open on only one screen in a dual display set up?



            On 2011-03-17, at 10:16 AM, Stefano Luciano Ciurli wrote:

            Hello everybody,

            I have a MacBookPro running 10.6.6. I have installed the latest version of nmrPipe and I got into the bus error mentioned in this thread.

            Thus, I followed the suggestions given here: I downloaded and installed XQuartz 2.5.3, upgraded it to 2.6.0, and the PROBLEM DISAPPEARS IF I CALL nmrDraw form the XQuartz X11 window.

            However, I checked that if I call the command from the old X11 window, the bus error appears again. Also, and most importantly for me, if I call the command form the iTerm window (I use iTerm because it nicely can open windows directly from the Finder window where my files opportunely reside), the bus error reappears, because, apparently, iTerm calls the old X11.

            So I have the following questions:
            1) can I remove the old X11 completely, using, let's say, CleanMyMac?
            2) is there a way to convince iTerm to call the new XQuartz X11 rather than the old one?

            Regards
            Stefano Ciurli

            On Nov 15, 2010, at 11:45 PM, Adams, Kristie (NIH/NCI) [F] wrote:



            Don't forget that after you do Apple Software Update and re-install XQuartz 2.5.3, you have to log out and log in. Simply closing and re-starting X11 isn't enough! Restart if you have to, but the log out/log in worked for me.

            Try this and see if it works.

            Kristie

            On 11/15/10 4:43 PM, "Ryan McKay" <ryan@...<mailto:ryan%40nanuc.ca>> wrote:

            Interestingly I didn't have the problem, but after re-installing 2.5.3 I now get the bus error.

            I'm going to try re-re-installing X11 Quartz.

            R

            On 2010-11-15, at 2:27 PM, Ryan McKay wrote:

            Awesome! Thanks for the heads up.
            Ryan

            On 2010-11-12, at 12:05 PM, kristie_1213 wrote:

            Hi all,

            I thought I would pass along recent experience with nmrPipe (latest, Version 5.5 Rev 2010.302.14.25), XQuartz 2.5.3 and Mac OS X 10.6.5, and a mysterious 'bus error' upon installation of 10.6.5.

            I previously had Mac OS 10.6.4 (Apple just pushed 10.6.5 last evening/this morning) and I installed 10.6.5 today. After installing (and rebooting, of course), I received a 'bus error' upon attempting to open nmrDraw. After some research, I discovered that (even though it's not documented) Apple still pushes parts of X11 code with their software updates, and this code supersedes that installed with XQuartz. Thus, it is necessary to re-install XQuartz 2.5.3 AFTER installing the 10.6.5 update. After doing this and logging out/in, all works fine with nmrPipe and nmrDraw.

            This issue is mentioned on the XQuartz sourceforge page as a problem primarily occurring with Leopard, but the suggested fix (reinstall of XQuartz 2.5.3) restored my functionality perfectly.

            Thanks!
            Kristie

            *****************************
            Kristie M. Adams, Ph.D.
            CRTA Postdoctoral Fellow
            Chemical Biology Laboratory
            National Cancer Institute-Frederick
            376 Boyles St, Room 117
            National Institutes of Health
            Frederick, MD 21702
            USA
            Phone: 301-846-5962
            Fax: 301-846-6033
            *****************************

            ----------------------------------------------------------
            Ryan T. McKay, Ph.D. - Scientific Director
            NANUC - Canada's National High Field NMR Centre
            Room 105 Email: ryan@...<mailto:ryan%40nanuc.ca>
            NANUC Bld. Phone: (780) 492-2700
            University of Alberta Fax: (780) 492-9174
            Edmonton, Alberta Cell: (780) 920-8871
            Canada T6G 2E1 AIM: ryanmckaynmr
            http://www.nanuc.ca<http://www.nanuc.ca/> <http://www.nanuc.ca/>

            <NANUC2001_small.jpg>

            ----------------------------------------------------------

            Ryan T. McKay, Ph.D. - Scientific Director

            NANUC - Canada's National High Field NMR Centre

            Room 105 Email: ryan@...<mailto:ryan%40nanuc.ca>

            NANUC Bld. Phone: (780) 492-2700

            University of Alberta Fax: (780) 492-9174

            Edmonton, Alberta Cell: (780) 920-8871

            Canada T6G 2E1 AIM: ryanmckaynmr

            http://www.nanuc.ca<http://www.nanuc.ca/>

            [cid:3372687931_3883337]






            ------------------------------------

            Yahoo! Groups Links





            ------------------------------------------------------------------------------------
            Ryan T. McKay, Ph.D. - Scientific Director
            NANUC - Canada's National High Field NMR Centre
            Room 105 Email: ryan@...<mailto:ryan@...>
            NANUC Bld. Phone: (780) 492-2700
            University of Alberta Fax: (780) 492-9174
            Edmonton, Alberta
            Canada T6G 2E1
            http://www.nanuc.ca<http://www.nanuc.ca/>

            <NANUC2001_small.jpg>
          • Ryan McKay
            Awesome! Thank you for the hint. Ryan On 2011-03-17, at 12:51 PM, sameer.wahid wrote: Hi Ryan, I had the same problem with my mulitmonitor setup. You can edit
            Message 5 of 13 , Mar 17 1:12 PM
            • 0 Attachment
              Awesome! Thank you for the hint.
              Ryan

              On 2011-03-17, at 12:51 PM, sameer.wahid wrote:

              Hi Ryan,

              I had the same problem with my mulitmonitor setup.  You can edit the ~/NMRPipe/nmrbin.mac/nmrDraw file, near the bottom, from:

              nmrdraw.app \
                -default scrollbar.repeatDelay 999 -position 0 0 -Wfsdb               \

              to:

              nmrdraw.app \
                -geometry 1680x1050  \
                -default scrollbar.repeatDelay 999 -position 0 0 -Wfsdb               \


              where you can change the -geometry argument to suit your needs.  In a multimonitor setup, this will open nmrDraw at (0x0) on the main display, with a width of 1680px and height of 1050px.  No idea on how to make it open on the "secondary" display.

              Cheers,
              Sameer

              --
              Sameer Al-Abdul-Wahid, Ph.D. Candidate
              Lab of Dr. R. S. Prosser, Department of Chemical and Physical Sciences
              University of Toronto Mississauga
              3359 Mississauga Rd, Mississauga ON, L5L 1C6






              --- In nmrpipe@yahoogroups.com, Ryan McKay <ryan@...> wrote:

              Good morning,

              I would not remove the old X11.  My impression is that the new 2.6.0 Quartz X11 installs in an isolated directory for Mac OSX 10.6, but I have no idea the consequences of removing the old X11 manually from the system.  The size is small and the inconvenience may not be worth the risk.  Make sure you have a backup if you do decide to try it.

              I believe if you set up your environmental variables correctly there is a way to get iTerm/Terminal to work.  However it's a fair bit of hunting, trial and error.  I used to have my Terminal (Mac OS application) working but it broke with the latest NMRPipe/X11 update to 2.6.  I basically just launch it from the new Xquartz X11 window and haven't bothered with figuring out why Terminal doesn't work.

              If you do figure it out let me know please.

              Best wishes,
              Ryan

              ps anyone know a way to get nmrDraw to open on only one screen in a dual display set up?



              On 2011-03-17, at 10:16 AM, Stefano Luciano Ciurli wrote:

              Hello everybody,

              I have a MacBookPro running 10.6.6. I have installed the latest version of nmrPipe and I got into the bus error mentioned in this thread.

              Thus, I followed the suggestions given here: I downloaded and installed XQuartz 2.5.3, upgraded it to 2.6.0, and the PROBLEM DISAPPEARS IF I CALL nmrDraw form the XQuartz X11 window.

              However, I checked that if I call the command from the old X11 window, the bus error appears again. Also, and most importantly for me, if I call the command form the iTerm window (I use iTerm because it nicely can open windows directly from the Finder window where my files opportunely reside), the bus error reappears, because, apparently, iTerm calls the old X11.

              So I have the following questions:
              1) can I remove the old X11 completely, using, let's say, CleanMyMac?
              2) is there a way to convince iTerm to call the new XQuartz X11 rather than the old one?

              Regards
              Stefano Ciurli

              On Nov 15, 2010, at 11:45 PM, Adams, Kristie (NIH/NCI) [F] wrote:



              Don't forget that after you do Apple Software Update and re-install XQuartz 2.5.3, you have to log out and log in. Simply closing and re-starting X11 isn't enough! Restart if you have to, but the log out/log in worked for me.

              Try this and see if it works.

              Kristie

              On 11/15/10 4:43 PM, "Ryan McKay" <ryan@...<mailto:ryan%40nanuc.ca>> wrote:

              Interestingly I didn't have the problem, but after re-installing 2.5.3 I now get the bus error.

              I'm going to try re-re-installing X11 Quartz.

              R

              On 2010-11-15, at 2:27 PM, Ryan McKay wrote:

              Awesome! Thanks for the heads up.
              Ryan

              On 2010-11-12, at 12:05 PM, kristie_1213 wrote:

              Hi all,

              I thought I would pass along recent experience with nmrPipe (latest, Version 5.5 Rev 2010.302.14.25), XQuartz 2.5.3 and Mac OS X 10.6.5, and a mysterious 'bus error' upon installation of 10.6.5.

              I previously had Mac OS 10.6.4 (Apple just pushed 10.6.5 last evening/this morning) and I installed 10.6.5 today. After installing (and rebooting, of course), I received a 'bus error' upon attempting to open nmrDraw. After some research, I discovered that (even though it's not documented) Apple still pushes parts of X11 code with their software updates, and this code supersedes that installed with XQuartz. Thus, it is necessary to re-install XQuartz 2.5.3 AFTER installing the 10.6.5 update. After doing this and logging out/in, all works fine with nmrPipe and nmrDraw.

              This issue is mentioned on the XQuartz sourceforge page as a problem primarily occurring with Leopard, but the suggested fix (reinstall of XQuartz 2.5.3) restored my functionality perfectly.

              Thanks!
              Kristie

              *****************************
              Kristie M. Adams, Ph.D.
              CRTA Postdoctoral Fellow
              Chemical Biology Laboratory
              National Cancer Institute-Frederick
              376 Boyles St, Room 117
              National Institutes of Health
              Frederick, MD 21702
              USA
              Phone: 301-846-5962
              Fax: 301-846-6033
              *****************************

              ----------------------------------------------------------
              Ryan T. McKay, Ph.D. - Scientific Director
              NANUC - Canada's National High Field NMR Centre
              Room 105 Email: ryan@...<mailto:ryan%40nanuc.ca>
              NANUC Bld. Phone: (780) 492-2700
              University of Alberta Fax: (780) 492-9174
              Edmonton, Alberta Cell: (780) 920-8871
              Canada T6G 2E1 AIM: ryanmckaynmr
              http://www.nanuc.ca<http://www.nanuc.ca/> <http://www.nanuc.ca/>

              <NANUC2001_small.jpg>

              ----------------------------------------------------------

              Ryan T. McKay, Ph.D. - Scientific Director

              NANUC - Canada's National High Field NMR Centre

              Room 105 Email: ryan@...<mailto:ryan%40nanuc.ca>

              NANUC Bld. Phone: (780) 492-2700

              University of Alberta Fax: (780) 492-9174

              Edmonton, Alberta Cell: (780) 920-8871

              Canada T6G 2E1 AIM: ryanmckaynmr

              http://www.nanuc.ca<http://www.nanuc.ca/>

              [cid:3372687931_3883337]






              ------------------------------------

              Yahoo! Groups Links





              ------------------------------------------------------------------------------------
              Ryan T. McKay, Ph.D. -     Scientific Director
              NANUC - Canada's National High Field NMR Centre
              Room 105                           Email:  ryan@...
              NANUC Bld.                        Phone: (780) 492-2700
              University of Alberta            Fax:     (780) 492-9174
              Edmonton, Alberta
              Canada T6G 2E1
                                  http://www.nanuc.ca





              ------------------------------------------------------------------------------------

              Ryan T. McKay, Ph.D. -     Scientific Director

              NANUC - Canada's National High Field NMR Centre

              Room 105                           Email:  ryan@...

              NANUC Bld.                        Phone: (780) 492-2700

              University of Alberta            Fax:     (780) 492-9174

              Edmonton, Alberta

              Canada T6G 2E1

                                   http://www.nanuc.ca



            • michellelynngill
              Greetings, Yes, XQuartz (as installed from MacOSForge) installs in a different directory from the stock X11 included on the Max OS X install disk. This has
              Message 6 of 13 , Mar 21 8:03 AM
              • 0 Attachment
                Greetings,

                Yes, XQuartz (as installed from MacOSForge) installs in a different directory from the stock X11 included on the Max OS X install disk. This has been the case for sometime now. You can verify the difference by launching X11.app and XQuartz.app (both located in /Applications/Utilities). On my computer, selecting "About X11" in XQuartz shows XQuartz 2.6.1 with xorg-server 1.9.5, whereas the same window in X11 shows XQuartz 2.3.6 with xorg-server 1.4.2-apple56.

                I spent a good deal of time tinkering with this last fall when I was trying to help Frank troubleshoot this issue and while NMRDraw launches fine for me from the terminal application, I could never get it to launch from iTerm. I went through my environment variables with a fine tooth comb and tried to make everything as identical as I could. Just my experience, though.

                Regards,
                Michelle Gill

                ---------------------------------------------
                Michelle L. Gill, Ph.D.
                NIH Postdoctoral Research Fellow
                Palmer Laboratory
                Columbia University Medical Center
                Department of Biochemistry & Molecular Biophysics
                Black Building, Room 511
                650 West 168th Street
                New York, NY 10032
                Email: mg2917@..., michelle.lynn.gill@...
                Phone: (212) 305-0257
                Fax: (212) 305-6949

                --- In nmrpipe@yahoogroups.com, Ryan McKay <ryan@...> wrote:
                >
                > Good morning,
                >
                > I would not remove the old X11. My impression is that the new 2.6.0 Quartz X11 installs in an isolated directory for Mac OSX 10.6, but I have no idea the consequences of removing the old X11 manually from the system. The size is small and the inconvenience may not be worth the risk. Make sure you have a backup if you do decide to try it.
                >
                > I believe if you set up your environmental variables correctly there is a way to get iTerm/Terminal to work. However it's a fair bit of hunting, trial and error. I used to have my Terminal (Mac OS application) working but it broke with the latest NMRPipe/X11 update to 2.6. I basically just launch it from the new Xquartz X11 window and haven't bothered with figuring out why Terminal doesn't work.
                >
                > If you do figure it out let me know please.
                >
                > Best wishes,
                > Ryan
                >
                > ps anyone know a way to get nmrDraw to open on only one screen in a dual display set up?
                >
                >
                >
                > On 2011-03-17, at 10:16 AM, Stefano Luciano Ciurli wrote:
                >
                > Hello everybody,
                >
                > I have a MacBookPro running 10.6.6. I have installed the latest version of nmrPipe and I got into the bus error mentioned in this thread.
                >
                > Thus, I followed the suggestions given here: I downloaded and installed XQuartz 2.5.3, upgraded it to 2.6.0, and the PROBLEM DISAPPEARS IF I CALL nmrDraw form the XQuartz X11 window.
                >
                > However, I checked that if I call the command from the old X11 window, the bus error appears again. Also, and most importantly for me, if I call the command form the iTerm window (I use iTerm because it nicely can open windows directly from the Finder window where my files opportunely reside), the bus error reappears, because, apparently, iTerm calls the old X11.
                >
                > So I have the following questions:
                > 1) can I remove the old X11 completely, using, let's say, CleanMyMac?
                > 2) is there a way to convince iTerm to call the new XQuartz X11 rather than the old one?
                >
                > Regards
                > Stefano Ciurli
                >
                > On Nov 15, 2010, at 11:45 PM, Adams, Kristie (NIH/NCI) [F] wrote:
                >
                >
                >
                > Don't forget that after you do Apple Software Update and re-install XQuartz 2.5.3, you have to log out and log in. Simply closing and re-starting X11 isn't enough! Restart if you have to, but the log out/log in worked for me.
                >
                > Try this and see if it works.
                >
                > Kristie
                >
                > On 11/15/10 4:43 PM, "Ryan McKay" <ryan@...<mailto:ryan%40nanuc.ca>> wrote:
                >
                > Interestingly I didn't have the problem, but after re-installing 2.5.3 I now get the bus error.
                >
                > I'm going to try re-re-installing X11 Quartz.
                >
                > R
                >
                > On 2010-11-15, at 2:27 PM, Ryan McKay wrote:
                >
                > Awesome! Thanks for the heads up.
                > Ryan
                >
                > On 2010-11-12, at 12:05 PM, kristie_1213 wrote:
                >
                > Hi all,
                >
                > I thought I would pass along recent experience with nmrPipe (latest, Version 5.5 Rev 2010.302.14.25), XQuartz 2.5.3 and Mac OS X 10.6.5, and a mysterious 'bus error' upon installation of 10.6.5.
                >
                > I previously had Mac OS 10.6.4 (Apple just pushed 10.6.5 last evening/this morning) and I installed 10.6.5 today. After installing (and rebooting, of course), I received a 'bus error' upon attempting to open nmrDraw. After some research, I discovered that (even though it's not documented) Apple still pushes parts of X11 code with their software updates, and this code supersedes that installed with XQuartz. Thus, it is necessary to re-install XQuartz 2.5.3 AFTER installing the 10.6.5 update. After doing this and logging out/in, all works fine with nmrPipe and nmrDraw.
                >
                > This issue is mentioned on the XQuartz sourceforge page as a problem primarily occurring with Leopard, but the suggested fix (reinstall of XQuartz 2.5.3) restored my functionality perfectly.
                >
                > Thanks!
                > Kristie
                >
                > *****************************
                > Kristie M. Adams, Ph.D.
                > CRTA Postdoctoral Fellow
                > Chemical Biology Laboratory
                > National Cancer Institute-Frederick
                > 376 Boyles St, Room 117
                > National Institutes of Health
                > Frederick, MD 21702
                > USA
                > Phone: 301-846-5962
                > Fax: 301-846-6033
                > *****************************
                >
                > ----------------------------------------------------------
                > Ryan T. McKay, Ph.D. - Scientific Director
                > NANUC - Canada's National High Field NMR Centre
                > Room 105 Email: ryan@...<mailto:ryan%40nanuc.ca>
                > NANUC Bld. Phone: (780) 492-2700
                > University of Alberta Fax: (780) 492-9174
                > Edmonton, Alberta Cell: (780) 920-8871
                > Canada T6G 2E1 AIM: ryanmckaynmr
                > http://www.nanuc.ca<http://www.nanuc.ca/> <http://www.nanuc.ca/>
                >
                > <NANUC2001_small.jpg>
                >
                > ----------------------------------------------------------
                >
                > Ryan T. McKay, Ph.D. - Scientific Director
                >
                > NANUC - Canada's National High Field NMR Centre
                >
                > Room 105 Email: ryan@...<mailto:ryan%40nanuc.ca>
                >
                > NANUC Bld. Phone: (780) 492-2700
                >
                > University of Alberta Fax: (780) 492-9174
                >
                > Edmonton, Alberta Cell: (780) 920-8871
                >
                > Canada T6G 2E1 AIM: ryanmckaynmr
                >
                > http://www.nanuc.ca<http://www.nanuc.ca/>
                >
                > [cid:3372687931_3883337]
                >
                >
                >
                >
                >
                >
                > ------------------------------------
                >
                > Yahoo! Groups Links
                >
                >
                >
                >
                >
                > ------------------------------------------------------------------------------------
                > Ryan T. McKay, Ph.D. - Scientific Director
                > NANUC - Canada's National High Field NMR Centre
                > Room 105 Email: ryan@...
                > NANUC Bld. Phone: (780) 492-2700
                > University of Alberta Fax: (780) 492-9174
                > Edmonton, Alberta
                > Canada T6G 2E1
                > http://www.nanuc.ca
                >
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