Re: [ccp4bb] iMosflm in 6.1 under OS X
Dear Engin, Yep, I can reproduce this using a binary installation myself - that would be a bug. We (CCP4) will look into it and get a fix to you as soon as possible. Thanks for the report, Graeme CCP4 Support Team -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Engin Ozkan Sent: 18 December 2008 06:10 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] iMosflm in 6.1 under OS X Now that everything with coot and imosflm has been settled, how about sftools? I am getting errors when I try to open an sftools window with ccp4i, with 6.1.0. I get the same error with a fink-installed mac version, and a linux installation. Here is the error: bad window path name .main.canvas.contents.param_1.body bad window path name .main.canvas.contents.param_1.body while executing pack $wframe.body -side top -fill x (procedure update_folder_display line 23) invoked from within update_folder_display 1 sftools_PROJECT view invoked from within .w_sftools_PROJECT.main.canvas.contents.param_1.top.but invoke (command bound to event) Any ideas? Engin William G. Scott wrote: More specifically, issue fink selfupdate-cvs (or fink selfupdate-rsync) fink install itcl itk iwidgets tdom tkimg tktreectrl On Dec 17, 2008, at 7:56 AM, Andrzej Lyskowski wrote: Hi, I've just upgraded my fink distro and was wondering what else has to be done concerning configuration in order to make the iMosflm run on Mac OS. So far I'm getting the following error: Error in startup script: unknown namespace in import pattern itcl::* while executing namespace import itcl::* (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/src/imosflm.tcl line 91) invoked from within source $env(IMOSFLM) (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/imosflm.tcl line 111) Regards, Andrzej
Re: [ccp4bb] iMosflm in 6.1 under OS X
Strange ... I just updated to OS 10.5.6, and fully expected to have to reinstall X11 yet again, but I still have 2.3.1 on my machine after the update. Odd that it should be inconsistent from one machine to another. Randy Read On 17 Dec 2008, at 22:54, William G. Scott wrote: Please, we all need to mention this to the Apple people. This is totally unacceptable. On Dec 17, 2008, at 2:54 PM, Engin Ozkan wrote: Yep, this happened because of the latest Mac OS 10.5.6 update. With the update, my X11 version got downgraded from 2.3.1 to 2.1.5. Engin William G. Scott wrote: Hi Engin: What do you get in response to the command otool -L /usr/X11/lib/libXdamage.1.dylib | grep libXdamage.1.dylib You should see /usr/X11/lib/libXdamage.1.dylib (compatibility version 3.0.0, current version 3.0.0) If you don't, update X11 here (free) to at least 2.3.1: http://xquartz.macosforge.org/trac/wiki If you do see what I do, then I suspect you need to unset the evil $DYLD_LIBRARY_PATH variable Bill On Dec 17, 2008, at 1:53 PM, Engin Ozkan wrote: By the way, is anyone experiencing the following problem with fink-installed coot? dyld: Library not loaded: /usr/X11/lib/libXdamage.1.dylib Referenced from: /sw/bin/coot Reason: Incompatible library version: coot requires version 3.0.0 or later, but libXdamage.1.dylib provides version 2.0.0 [1]Trace/BPT trapcoot Engin William G. Scott wrote: More specifically, issue fink selfupdate-cvs (or fink selfupdate-rsync) fink install itcl itk iwidgets tdom tkimg tktreectrl On Dec 17, 2008, at 7:56 AM, Andrzej Lyskowski wrote: Hi, I've just upgraded my fink distro and was wondering what else has to be done concerning configuration in order to make the iMosflm run on Mac OS. So far I'm getting the following error: Error in startup script: unknown namespace in import pattern itcl::* while executing namespace import itcl::* (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/src/imosflm.tcl line 91) invoked from within source $env(IMOSFLM) (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/imosflm.tcl line 111) Regards, Andrzej -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www- structmed.cimr.cam.ac.uk
Re: [ccp4bb] iMosflm in 6.1 under OS X
This doesn't seem to be a general phenomenon. My xquartz is still 2.3.1 after installing the latest service pack (Leopard 6). Andreas William G. Scott wrote: Please, we all need to mention this to the Apple people. This is totally unacceptable. On Dec 17, 2008, at 2:54 PM, Engin Ozkan wrote: Yep, this happened because of the latest Mac OS 10.5.6 update. With the update, my X11 version got downgraded from 2.3.1 to 2.1.5. Engin
Re: [ccp4bb] iMosflm in 6.1 under OS X
Hi Randy and Andreas, I wouldn't rely on the reported XQuartz version after updating to 10.5.6, but rather re-install the most recent version of Xquartz again, to be on the safe side. Best regards, Dirk. P.S.: This version allows to overwrite the X11 resolution with the command defaults write org.x.X11 dpi -int 72 as an example. You can check the assumed resolution with xdpyinfo | grep resolution Am 18.12.2008 um 11:25 schrieb Andreas Förster: This doesn't seem to be a general phenomenon. My xquartz is still 2.3.1 after installing the latest service pack (Leopard 6). Andreas William G. Scott wrote: Please, we all need to mention this to the Apple people. This is totally unacceptable. On Dec 17, 2008, at 2:54 PM, Engin Ozkan wrote: Yep, this happened because of the latest Mac OS 10.5.6 update. With the update, my X11 version got downgraded from 2.3.1 to 2.1.5. Engin *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@lmb.uni-muenchen.de ***
Re: [ccp4bb] iMosflm in 6.1 under OS X
I have a theory. Automated software updates did not update many computers correctly, macs in our lab hung at configuring installation and had to be restarted. This phenomenon is observed by many, and consider yourself lucky, if you haven't (Apple might have fixed it by now). http://discussions.apple.com/thread.jspa?threadID=1827638tstart=0 http://www.pcmag.com/article2/0,2817,2337045,00.asp So, many had to download a software update from Apple's webpage for manual installation: if you have incidentally downloaded the combo update, that probably downgrades your X11. That's my theory. Engin Randy Read wrote: Strange ... I just updated to OS 10.5.6, and fully expected to have to reinstall X11 yet again, but I still have 2.3.1 on my machine after the update. Odd that it should be inconsistent from one machine to another. Randy Read On 17 Dec 2008, at 22:54, William G. Scott wrote: Please, we all need to mention this to the Apple people. This is totally unacceptable. On Dec 17, 2008, at 2:54 PM, Engin Ozkan wrote: Yep, this happened because of the latest Mac OS 10.5.6 update. With the update, my X11 version got downgraded from 2.3.1 to 2.1.5. Engin William G. Scott wrote: Hi Engin: What do you get in response to the command otool -L /usr/X11/lib/libXdamage.1.dylib | grep libXdamage.1.dylib You should see /usr/X11/lib/libXdamage.1.dylib (compatibility version 3.0.0, current version 3.0.0) If you don't, update X11 here (free) to at least 2.3.1: http://xquartz.macosforge.org/trac/wiki If you do see what I do, then I suspect you need to unset the evil $DYLD_LIBRARY_PATH variable Bill On Dec 17, 2008, at 1:53 PM, Engin Ozkan wrote: By the way, is anyone experiencing the following problem with fink-installed coot? dyld: Library not loaded: /usr/X11/lib/libXdamage.1.dylib Referenced from: /sw/bin/coot Reason: Incompatible library version: coot requires version 3.0.0 or later, but libXdamage.1.dylib provides version 2.0.0 [1]Trace/BPT trapcoot Engin William G. Scott wrote: More specifically, issue fink selfupdate-cvs (or fink selfupdate-rsync) fink install itcl itk iwidgets tdom tkimg tktreectrl On Dec 17, 2008, at 7:56 AM, Andrzej Lyskowski wrote: Hi, I've just upgraded my fink distro and was wondering what else has to be done concerning configuration in order to make the iMosflm run on Mac OS. So far I'm getting the following error: Error in startup script: unknown namespace in import pattern itcl::* while executing namespace import itcl::* (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/src/imosflm.tcl line 91) invoked from within source $env(IMOSFLM) (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/imosflm.tcl line 111) Regards, Andrzej -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
Re: [ccp4bb] iMosflm in 6.1 under OS X
I've just now added these as fink packages (cvs unstable). Sorry for the delay. I dropped the ball. Steffen Schmidt did the hard work, so many thanks to Seffen!!! Bill On Dec 17, 2008, at 7:56 AM, Andrzej Lyskowski wrote: Hi, I've just upgraded my fink distro and was wondering what else has to be done concerning configuration in order to make the iMosflm run on Mac OS. So far I'm getting the following error: Error in startup script: unknown namespace in import pattern itcl::* while executing namespace import itcl::* (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/src/imosflm.tcl line 91) invoked from within source $env(IMOSFLM) (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/imosflm.tcl line 111) Regards, Andrzej
Re: [ccp4bb] iMosflm in 6.1 under OS X
More specifically, issue fink selfupdate-cvs (or fink selfupdate-rsync) fink install itcl itk iwidgets tdom tkimg tktreectrl On Dec 17, 2008, at 7:56 AM, Andrzej Lyskowski wrote: Hi, I've just upgraded my fink distro and was wondering what else has to be done concerning configuration in order to make the iMosflm run on Mac OS. So far I'm getting the following error: Error in startup script: unknown namespace in import pattern itcl::* while executing namespace import itcl::* (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/src/imosflm.tcl line 91) invoked from within source $env(IMOSFLM) (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/imosflm.tcl line 111) Regards, Andrzej
Re: [ccp4bb] iMosflm in 6.1 under OS X
Hi I should say, while this subject has been brought up, that Luke and I are working hard to remove many of these dependencies, so iMosflm should work with a more plain vanilla version of TclTk (but you will still need iTcl and iTk. On 17 Dec 2008, at 16:34, William G. Scott wrote: More specifically, issue fink selfupdate-cvs (or fink selfupdate-rsync) fink install itcl itk iwidgets tdom tkimg tktreectrl On Dec 17, 2008, at 7:56 AM, Andrzej Lyskowski wrote: Hi, I've just upgraded my fink distro and was wondering what else has to be done concerning configuration in order to make the iMosflm run on Mac OS. So far I'm getting the following error: Error in startup script: unknown namespace in import pattern itcl::* while executing namespace import itcl::* (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/src/imosflm.tcl line 91) invoked from within source $env(IMOSFLM) (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/imosflm.tcl line 111) Regards, Andrzej Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] iMosflm in 6.1 under OS X
By the way, is anyone experiencing the following problem with fink-installed coot? dyld: Library not loaded: /usr/X11/lib/libXdamage.1.dylib Referenced from: /sw/bin/coot Reason: Incompatible library version: coot requires version 3.0.0 or later, but libXdamage.1.dylib provides version 2.0.0 [1]Trace/BPT trapcoot Engin William G. Scott wrote: More specifically, issue fink selfupdate-cvs (or fink selfupdate-rsync) fink install itcl itk iwidgets tdom tkimg tktreectrl On Dec 17, 2008, at 7:56 AM, Andrzej Lyskowski wrote: Hi, I've just upgraded my fink distro and was wondering what else has to be done concerning configuration in order to make the iMosflm run on Mac OS. So far I'm getting the following error: Error in startup script: unknown namespace in import pattern itcl::* while executing namespace import itcl::* (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/src/imosflm.tcl line 91) invoked from within source $env(IMOSFLM) (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/imosflm.tcl line 111) Regards, Andrzej
Re: [ccp4bb] iMosflm in 6.1 under OS X
Yep, this happened because of the latest Mac OS 10.5.6 update. With the update, my X11 version got downgraded from 2.3.1 to 2.1.5. Engin William G. Scott wrote: Hi Engin: What do you get in response to the command otool -L /usr/X11/lib/libXdamage.1.dylib | grep libXdamage.1.dylib You should see /usr/X11/lib/libXdamage.1.dylib (compatibility version 3.0.0, current version 3.0.0) If you don't, update X11 here (free) to at least 2.3.1: http://xquartz.macosforge.org/trac/wiki If you do see what I do, then I suspect you need to unset the evil $DYLD_LIBRARY_PATH variable Bill On Dec 17, 2008, at 1:53 PM, Engin Ozkan wrote: By the way, is anyone experiencing the following problem with fink-installed coot? dyld: Library not loaded: /usr/X11/lib/libXdamage.1.dylib Referenced from: /sw/bin/coot Reason: Incompatible library version: coot requires version 3.0.0 or later, but libXdamage.1.dylib provides version 2.0.0 [1]Trace/BPT trapcoot Engin William G. Scott wrote: More specifically, issue fink selfupdate-cvs (or fink selfupdate-rsync) fink install itcl itk iwidgets tdom tkimg tktreectrl On Dec 17, 2008, at 7:56 AM, Andrzej Lyskowski wrote: Hi, I've just upgraded my fink distro and was wondering what else has to be done concerning configuration in order to make the iMosflm run on Mac OS. So far I'm getting the following error: Error in startup script: unknown namespace in import pattern itcl::* while executing namespace import itcl::* (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/src/imosflm.tcl line 91) invoked from within source $env(IMOSFLM) (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/imosflm.tcl line 111) Regards, Andrzej
Re: [ccp4bb] iMosflm in 6.1 under OS X
Hi Engin: What do you get in response to the command otool -L /usr/X11/lib/libXdamage.1.dylib | grep libXdamage.1.dylib You should see /usr/X11/lib/libXdamage.1.dylib (compatibility version 3.0.0, current version 3.0.0) If you don't, update X11 here (free) to at least 2.3.1: http://xquartz.macosforge.org/trac/wiki If you do see what I do, then I suspect you need to unset the evil $DYLD_LIBRARY_PATH variable Bill On Dec 17, 2008, at 1:53 PM, Engin Ozkan wrote: By the way, is anyone experiencing the following problem with fink- installed coot? dyld: Library not loaded: /usr/X11/lib/libXdamage.1.dylib Referenced from: /sw/bin/coot Reason: Incompatible library version: coot requires version 3.0.0 or later, but libXdamage.1.dylib provides version 2.0.0 [1]Trace/BPT trapcoot Engin William G. Scott wrote: More specifically, issue fink selfupdate-cvs (or fink selfupdate-rsync) fink install itcl itk iwidgets tdom tkimg tktreectrl On Dec 17, 2008, at 7:56 AM, Andrzej Lyskowski wrote: Hi, I've just upgraded my fink distro and was wondering what else has to be done concerning configuration in order to make the iMosflm run on Mac OS. So far I'm getting the following error: Error in startup script: unknown namespace in import pattern itcl::* while executing namespace import itcl::* (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/src/imosflm.tcl line 91) invoked from within source $env(IMOSFLM) (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/imosflm.tcl line 111) Regards, Andrzej
Re: [ccp4bb] iMosflm in 6.1 under OS X
Yes, William I do agree with you, and in the same line of doubt, I have one more thing to ask you. Where is this .cvspass resides. I have problem in updating my fink , with fink selfupdate-cvs. thanks S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany. On Wed, Dec 17, 2008 at 11:54 PM, William G. Scott wgsc...@chemistry.ucsc.edu wrote: Please, we all need to mention this to the Apple people. This is totally unacceptable. On Dec 17, 2008, at 2:54 PM, Engin Ozkan wrote: Yep, this happened because of the latest Mac OS 10.5.6 update. With the update, my X11 version got downgraded from 2.3.1 to 2.1.5. Engin William G. Scott wrote: Hi Engin: What do you get in response to the command otool -L /usr/X11/lib/libXdamage.1.dylib | grep libXdamage.1.dylib You should see /usr/X11/lib/libXdamage.1.dylib (compatibility version 3.0.0, current version 3.0.0) If you don't, update X11 here (free) to at least 2.3.1: http://xquartz.macosforge.org/trac/wiki If you do see what I do, then I suspect you need to unset the evil $DYLD_LIBRARY_PATH variable Bill On Dec 17, 2008, at 1:53 PM, Engin Ozkan wrote: By the way, is anyone experiencing the following problem with fink-installed coot? dyld: Library not loaded: /usr/X11/lib/libXdamage.1.dylib Referenced from: /sw/bin/coot Reason: Incompatible library version: coot requires version 3.0.0 or later, but libXdamage.1.dylib provides version 2.0.0 [1]Trace/BPT trapcoot Engin William G. Scott wrote: More specifically, issue fink selfupdate-cvs (or fink selfupdate-rsync) fink install itcl itk iwidgets tdom tkimg tktreectrl On Dec 17, 2008, at 7:56 AM, Andrzej Lyskowski wrote: Hi, I've just upgraded my fink distro and was wondering what else has to be done concerning configuration in order to make the iMosflm run on Mac OS. So far I'm getting the following error: Error in startup script: unknown namespace in import pattern itcl::* while executing namespace import itcl::* (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/src/imosflm.tcl line 91) invoked from within source $env(IMOSFLM) (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/imosflm.tcl line 111) Regards, Andrzej
Re: [ccp4bb] iMosflm in 6.1 under OS X
Now that everything with coot and imosflm has been settled, how about sftools? I am getting errors when I try to open an sftools window with ccp4i, with 6.1.0. I get the same error with a fink-installed mac version, and a linux installation. Here is the error: bad window path name .main.canvas.contents.param_1.body bad window path name .main.canvas.contents.param_1.body while executing pack $wframe.body -side top -fill x (procedure update_folder_display line 23) invoked from within update_folder_display 1 sftools_PROJECT view invoked from within .w_sftools_PROJECT.main.canvas.contents.param_1.top.but invoke (command bound to event) Any ideas? Engin William G. Scott wrote: More specifically, issue fink selfupdate-cvs (or fink selfupdate-rsync) fink install itcl itk iwidgets tdom tkimg tktreectrl On Dec 17, 2008, at 7:56 AM, Andrzej Lyskowski wrote: Hi, I've just upgraded my fink distro and was wondering what else has to be done concerning configuration in order to make the iMosflm run on Mac OS. So far I'm getting the following error: Error in startup script: unknown namespace in import pattern itcl::* while executing namespace import itcl::* (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/src/imosflm.tcl line 91) invoked from within source $env(IMOSFLM) (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/imosflm.tcl line 111) Regards, Andrzej
