Re: [Ifeffit] Artemis crash on import
Hi Bruce, Thanks for you quick reply. Yes I can run gnuplot and plot functions with it. Also, I was able to open projects in Artemis with the previous version. The issue only appeared after I updated Demeter. Thanks, George On Thu, Oct 13, 2016 at 3:12 PM, Bruce Ravel wrote: > > That doesn't look like an artemis problem. It looks like a Mac problem. > Specifically it looks like gnuplot and or the windowing system is not > working correctly. > > Can you run gnuplot all by itself? > > B > > > > On 10/13/2016 04:02 PM, George Sterbinsky wrote: > >> Hello, >> >> I am using Demeter on Mac OS X 10.11.6. I recently updated Demeter to >> version 0.9.25 using the command "sudo port upgrade demeter". In >> Artemis, choosing the menu item "open project or data" causes Artemis to >> crash. I've pasted the information printed to the terminal below. This >> includes everything printed to the terminal from the point at which >> Artemis was started. Please let me know if any additional information >> would help in resolving this issue. >> >> Thank you, >> George >> >> >> $ Artemis >> 2016-10-13 14:51:18.097 perl5.24[20180:991862] CFPasteboardRef >> CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create >> global data >> >> gnuplot: unable to open display >> '/private/tmp/com.apple.launchd.U9mQNzlNS1/org.macosforge.xquartz:0' >> gnuplot: X11 aborted. >> 2016-10-13 14:51:22.884 perl5.24[20180:991862] CFPasteboardRef >> CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create >> global data >> 2016-10-13 14:51:22.885 perl5.24[20180:991862] CFPasteboardRef >> CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create >> global data >> 2016-10-13 14:51:22.885 perl5.24[20180:991862] CFPasteboardRef >> CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create >> global data >> 2016-10-13 14:51:22.885 perl5.24[20180:991862] CFPasteboardRef >> CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create >> global data >> 2016-10-13 14:51:23.096 perl5.24[20180:991862] CFPasteboardRef >> CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create >> global data >> 2016-10-13 14:51:23.097 perl5.24[20180:991862] CFPasteboardRef >> CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create >> global data >> 2016-10-13 14:51:23.443 perl5.24[20180:991862] CFPasteboardRef >> CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create >> global data >> 2016-10-13 14:51:23.443 perl5.24[20180:991862] CFPasteboardRefgnuplot: >> unable to open display '/private/tmp/com.apple.launch >> d.U9mQNzlNS1/org.macosforge.xquartz:0' >> > gnuplot: X11 aborted. > >> CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create >> >> global data >> 2016-10-13 14:51:25.277 perl5.24[20180:991862] CFPasteboardRef >> CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create >> global data >> 2016-10-13 14:51:25.278 perl5.24[20180:991862] CFPasteboardRef >> CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create >> global data >> 2016-10-13 14:51:26.809 perl5.24[20180:991862] CFPasteboardRef >> CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create >> global data >> 2016-10-13 14:51:26.809 perl5.24[20180:991862] CFPasteboardRef >> CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create >> global data >> 2016-10-13 14:51:27.278 perl5.24[20180:991862] CFPasteboardRef >> CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create >> global data >> 2016-10-13 14:51:27.278 perl5.24[20180:991862] CFPasteboardRef >> CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create >> global data >> 2016-10-13 14:51:28.221 perl5.24[20180:991862] CFPasteboardRef >> CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create >> global data >> 2016-10-13 14:51:28.221 perl5.24[20180:991862] CFPasteboardRef >> CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create >> global data >> 2016-10-13 14:51:28.555 perl5.24[20180:991862] CFPasteboardRef >> CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create >> global data >> 2016-10-13 14:51:28.555 perl5.24[20180:991862] CFPasteboardRef >> CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create >> global data >> 2016-10-13 14:51:34.322 perl5.24[20180:991862] CFPasteboardRef >> CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create >> global data >> 2016-10-13 14:51:34.322 perl5.24[20180:991862] CFPasteboardRef >> CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create >> global data >> 2016-10-13 14:52:30.445 perl5.24[20180:991862] CFPasteboardRef >> CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create >> global data >> 2016-10-13 14:52:30.446 perl5.24[20180:991862] CFPasteboardRef >> CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create >> global data >> 2016-10-13 14:52:32.009 perl5.24[20180:991862] CFPasteboardRef >> CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create >> global data >> 2016-10-13
[Ifeffit] General question
Hi All, I would like to ask, after a fit (in Artemis) which column in the output file gives the uncertainty for peaks position dR (R+/-dR i.e. 3+/-0.02 Angstroms) ? Is there additional information that could be extracted from wavelet transform ? Thank you. Dimitar ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] Installing Demeter on Mavericks
Hi, I had a similar experience although with many more uninstalled dependencies. The simple fix is to do "sudo port install pgplot +gcc48" Sincerely, Wayne On Thu, Oct 13, 2016 at 1:17 PM, Katy Evans wrote: > Dear All, > > Apologies – its another mac question! > > I went through the instruction on installing Demeter on Mac OSX, installed > Macports successfully. I then tried to install Demeter, and got an error > message. So I installed xorg server separately, no error message, and then > tried Demeter again, with the following command and response. I noticed > when installing xorg that the pgplot was pgplot +gcc49, not +gcc48, which > the Demeter installation seems to be looking for. Athena opens and does > stuff but no plot window. Has anyone experienced and resolved this? > > Thanks, cheers, Katy > > $sudo port install demeter-devel > > ---> Computing dependencies for ifeffit > > ---> Fetching distfiles for ifeffit > > Error: Install pgplot +gcc48 > > Error: org.macports.fetch for port ifeffit returned: pgplot +gcc48 not > installed > > Please see the log file for port ifeffit for details: > > /opt/local/var/macports/logs/_opt_local_var_macports_ > sources_rsync.macports.org_release_tarballs_ports_ > science_ifeffit/ifeffit/main.log > > Error: Unable to upgrade port: 1 > > Error: Unable to execute port: upgrade ifeffit failed > > > > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > -- Wayne Lukens Staff Scientist Lawrence Berkeley National Lab ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] Installing Demeter on Mavericks
Dear All, Apologies - its another mac question! I went through the instruction on installing Demeter on Mac OSX, installed Macports successfully. I then tried to install Demeter, and got an error message. So I installed xorg server separately, no error message, and then tried Demeter again, with the following command and response. I noticed when installing xorg that the pgplot was pgplot +gcc49, not +gcc48, which the Demeter installation seems to be looking for. Athena opens and does stuff but no plot window. Has anyone experienced and resolved this? Thanks, cheers, Katy $sudo port install demeter-devel ---> Computing dependencies for ifeffit ---> Fetching distfiles for ifeffit Error: Install pgplot +gcc48 Error: org.macports.fetch for port ifeffit returned: pgplot +gcc48 not installed Please see the log file for port ifeffit for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_ifeffit/ifeffit/main.log Error: Unable to upgrade port: 1 Error: Unable to execute port: upgrade ifeffit failed ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] Artemis crash on import
That doesn't look like an artemis problem. It looks like a Mac problem. Specifically it looks like gnuplot and or the windowing system is not working correctly. Can you run gnuplot all by itself? B On 10/13/2016 04:02 PM, George Sterbinsky wrote: Hello, I am using Demeter on Mac OS X 10.11.6. I recently updated Demeter to version 0.9.25 using the command "sudo port upgrade demeter". In Artemis, choosing the menu item "open project or data" causes Artemis to crash. I've pasted the information printed to the terminal below. This includes everything printed to the terminal from the point at which Artemis was started. Please let me know if any additional information would help in resolving this issue. Thank you, George $ Artemis 2016-10-13 14:51:18.097 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data gnuplot: unable to open display '/private/tmp/com.apple.launchd.U9mQNzlNS1/org.macosforge.xquartz:0' gnuplot: X11 aborted. 2016-10-13 14:51:22.884 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:22.885 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:22.885 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:22.885 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:23.096 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:23.097 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:23.443 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:23.443 perl5.24[20180:991862] CFPasteboardRefgnuplot: unable to open display '/private/tmp/com.apple.launchd.U9mQNzlNS1/org.macosforge.xquartz:0' gnuplot: X11 aborted. CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:25.277 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:25.278 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:26.809 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:26.809 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:27.278 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:27.278 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:28.221 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:28.221 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:28.555 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:28.555 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:34.322 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:34.322 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:30.445 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:30.446 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:32.009 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:32.009 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:34.926 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:34.926 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:35.148 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:35.14
[Ifeffit] Artemis crash on import
Hello, I am using Demeter on Mac OS X 10.11.6. I recently updated Demeter to version 0.9.25 using the command "sudo port upgrade demeter". In Artemis, choosing the menu item "open project or data" causes Artemis to crash. I've pasted the information printed to the terminal below. This includes everything printed to the terminal from the point at which Artemis was started. Please let me know if any additional information would help in resolving this issue. Thank you, George $ Artemis 2016-10-13 14:51:18.097 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data gnuplot: unable to open display '/private/tmp/com.apple.launchd.U9mQNzlNS1/org.macosforge.xquartz:0' gnuplot: X11 aborted. 2016-10-13 14:51:22.884 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:22.885 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:22.885 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:22.885 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:23.096 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:23.097 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:23.443 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:23.443 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:25.277 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:25.278 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:26.809 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:26.809 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:27.278 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:27.278 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:28.221 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:28.221 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:28.555 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:28.555 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:34.322 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:34.322 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:30.445 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:30.446 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:32.009 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:32.009 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:34.926 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:34.926 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:35.148 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:35.148 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:38.016 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:38.017 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to
