Re: [ccp4bb] CCP4 update 6.3.0 006
Hi Ben, Applications launched from Finder and Spotlight get environment variables from ~/.MacOSX/environment.plist (before 10.8) their own Info.plist (10.8) and launchd (system-wide) and not .tcshrc etc. Sounds like to get the updater to work from Finder for all users you have to set your $CCP4 in launchd.conf Not sure if it's worth the effort. The environment is probably set correctly (somewhere) on the machine that was used to install CCP4... http://apple.stackexchange.com/questions/57385/where-are-system-environment-variables-set-in-mountain-lion http://www.dowdandassociates.com/content/howto-set-environment-variable-mac-os-x-etclaunchdconf Dmitry On 2012-10-12, at 3:46 PM, Ben Eisenbraun wrote: On Mon, Oct 08, 2012 at 06:20:59PM +, Ronan Keegan wrote: Dear CCP4 Users, A CCP4 update has just been released, consisting of the following changes: Hi Ronan et al, The update client on OS X doesn't seem to like our installation and dies with: Can't make class cfol of alias programs:i386-mac:ccp4:6.3.0:lib_exec:Update.app: into type Unicode text But I found an odd workaround. If I double-click the Update.app in Finder, I get the administrator password prompt, enter the credentials, and then the updater tells me that $CCP4 is unset, etc. I can then run 'open Update.app' from the shell, and it inherits $CCP4 and runs correctly. Any ideas? The workaround works, but since I don't really know why, I don't feel particularly good about it. Also, my installation is on NFS and is not owned by root, so it doesn't require administrator privileges to update. It would be nice if the application checked for write privileges before assuming it needs to be run with escalated privileges. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |
Re: [ccp4bb] CCP4 update 6.3.0 006
On Mon, Oct 08, 2012 at 06:20:59PM +, Ronan Keegan wrote: Dear CCP4 Users, A CCP4 update has just been released, consisting of the following changes: Hi Ronan et al, The update client on OS X doesn't seem to like our installation and dies with: Can't make class cfol of alias programs:i386-mac:ccp4:6.3.0:lib_exec:Update.app: into type Unicode text But I found an odd workaround. If I double-click the Update.app in Finder, I get the administrator password prompt, enter the credentials, and then the updater tells me that $CCP4 is unset, etc. I can then run 'open Update.app' from the shell, and it inherits $CCP4 and runs correctly. Any ideas? The workaround works, but since I don't really know why, I don't feel particularly good about it. Also, my installation is on NFS and is not owned by root, so it doesn't require administrator privileges to update. It would be nice if the application checked for write privileges before assuming it needs to be run with escalated privileges. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |
Re: [ccp4bb] CCP4 update 6.3.0 006
Dear Ronan et al: I apologize if I have missed it, but is there a simple way to obtain the corresponding changes in the source code for those of us who compile ccp4 ourselves? I looked on the web site and the ftp site but can't seem to find it. Many thanks in advance. Bill On Oct 8, 2012, at 11:20 AM, ronan.kee...@stfc.ac.uk wrote: Dear CCP4 Users, A CCP4 update has just been released, consisting of the following changes: * MrBUMP: model building options added * PISA: new QT interface * AMPLE: bug fixes and expanded interface (Linux and MAC only) * tlsextract: correction of output format which broke parsing of output * DiffractionImage: corrections to reading of pilatus mini-cbf * ccp4i: New AMPLE (Linux and Mac) and MrBUMP interfaces, QT-PISA launcher and bug fixes * crank: bug fix (Windows only) The easiest way to obtain the update is to install the CCP4 update client, if you have not done so already. Note that auto-updates will work correctly only with CCP4 release 6.3.0, therefore upgrade if necessary. Report bugs to c...@stfc.ac.uk. Many thanks for using CCP4, -- Ronan Keegan -- Scanned by iCritical.
Re: [ccp4bb] CCP4 update 6.3.0 006
On 09/10/12 15:09, William G. Scott wrote: Dear Ronan et al: I apologize if I have missed it, but is there a simple way to obtain the corresponding changes in the source code for those of us who compile ccp4 ourselves? I looked on the web site and the ftp site but can't seem to find it. Can I second that as well. Thanks Andrew Many thanks in advance. Bill On Oct 8, 2012, at 11:20 AM, ronan.kee...@stfc.ac.uk wrote: Dear CCP4 Users, A CCP4 update has just been released, consisting of the following changes: * MrBUMP: model building options added * PISA: new QT interface * AMPLE: bug fixes and expanded interface (Linux and MAC only) * tlsextract: correction of output format which broke parsing of output * DiffractionImage: corrections to reading of pilatus mini-cbf * ccp4i: New AMPLE (Linux and Mac) and MrBUMP interfaces, QT-PISA launcher and bug fixes * crank: bug fix (Windows only) The easiest way to obtain the update is to install the CCP4 update client, if you have not done so already. Note that auto-updates will work correctly only with CCP4 release 6.3.0, therefore upgrade if necessary. Report bugs to c...@stfc.ac.uk. Many thanks for using CCP4, -- Ronan Keegan -- Scanned by iCritical. -- -- *Dr. Andrew J. Sharff D.Phil** *Research Scientist / Software Developer Global Phasing Ltd Sheraton House Castle Park Cambridge CB3 0AX UK Tel: +(0)1223 353033 Fax: +(0)1223 366889
Re: [ccp4bb] CCP4 update 6.3.0 006
Dear Bill, You have not missed anything, we do not have a mechanism for delivering source code *updates* in automatic fashion as yet. Our statistics shows that source code distributions make only 2-3% of binary downloads, therefore, I hope that you would understand that we have to prioritise our efforts. CCP4 is currently in transitional state regarding its repository system and build mechanism, so that not everything is in due shape, and I apologise for any inconvenience this is causing to you. Current source codes are available from FusionForge at http://fg.oisin.rc-harwell.ac.uk just choose Project-Project List-Project Name (e.g. sfcheck) - SCM and a checkout command will be on the screen. These are our new repositories, but we have not finished migration to them yet. Codes that you do not see on FusionForge, are still available from CVS: http://www.ccp4.ac.uk/cvs We do realise that checking out sources and building them on client's side may be a non-trivial task to do. In order to help that, we are developing a completely new build system, which allows one to automatically check out CCP4 components and build them individually or all at once with a single command. This is meant to be our build system for next release (hopefully), and, in fact, Windows part of 6.3.0 was actually built with it. I would like to encourage you to have a look at http://devtools.fg.oisin.rc-harwell.ac.uk which is a not-so-long instruction on how to use the new system. It can be used right away to build current source codes, so that you do not have to browse the repositories. We would be highly appreciative if you give it a try and communicate your feedback to us. As I mentioned, things are currently being shaped, and we are prepared to have any suggestions. Please do not put it away if it does not work for you for any reason, and speak to us instead. Responsible people, who are to be contacted for feedback/clarification/help: New build system: Marcin Wojdyr at marcin.woj...@stfc.ac.uk New repositories: Charles Ballard at charles.ball...@stfc.ac.uk and/or Ville Uski at ville.u...@stfc.ac.uk I hope that this clarifies the issue, but let me know if it does not. Best regards, Eugene On 9 Oct 2012, at 15:09, William G. Scott wrote: Dear Ronan et al: I apologize if I have missed it, but is there a simple way to obtain the corresponding changes in the source code for those of us who compile ccp4 ourselves? I looked on the web site and the ftp site but can't seem to find it. Many thanks in advance. Bill On Oct 8, 2012, at 11:20 AM, ronan.kee...@stfc.ac.uk wrote: Dear CCP4 Users, A CCP4 update has just been released, consisting of the following changes: *MrBUMP: model building options added *PISA: new QT interface *AMPLE: bug fixes and expanded interface (Linux and MAC only) *tlsextract: correction of output format which broke parsing of output *DiffractionImage: corrections to reading of pilatus mini-cbf *ccp4i: New AMPLE (Linux and Mac) and MrBUMP interfaces, QT-PISA launcher and bug fixes *crank: bug fix (Windows only) The easiest way to obtain the update is to install the CCP4 update client, if you have not done so already. Note that auto-updates will work correctly only with CCP4 release 6.3.0, therefore upgrade if necessary. Report bugs to c...@stfc.ac.uk. Many thanks for using CCP4, -- Ronan Keegan -- Scanned by iCritical. -- Scanned by iCritical.
[ccp4bb] CCP4 update 6.3.0 006
Dear CCP4 Users, A CCP4 update has just been released, consisting of the following changes: * MrBUMP: model building options added * PISA: new QT interface * AMPLE: bug fixes and expanded interface (Linux and MAC only) * tlsextract: correction of output format which broke parsing of output * DiffractionImage: corrections to reading of pilatus mini-cbf * ccp4i: New AMPLE (Linux and Mac) and MrBUMP interfaces, QT-PISA launcher and bug fixes * crank: bug fix (Windows only) The easiest way to obtain the update is to install the CCP4 update client, if you have not done so already. Note that auto-updates will work correctly only with CCP4 release 6.3.0, therefore upgrade if necessary. Report bugs to c...@stfc.ac.uk. Many thanks for using CCP4, -- Ronan Keegan -- Scanned by iCritical.
