[sage-devel] Re: sage notebook with many Jmol viewers
Hi Jonathan, Thanks for your reply. I tried last night to figure out how to patch my notebook, and I ended up giving up after several hours. I also couldn't find any documentation for hg_sagenb.apply. After updating jmol to 1.1.5, I tried to follow the directions at http://www.sagemath.org/doc/developer/walk_through.html#reviewing-a-patch only replacing hg_sage.apply with hg_sagenb.apply, but things seem not to be as simple as described on that page. Running the command on a patch drops me into a vim editor that shows the text of the whole patch. Not knowing what to do, I press q and I am then asked to enter a commit message. No matter what I seem to do, when I try to quit vim it warns me that there was no write since last change, and if I quit with :q! then it seems I am back where I started. It doesn't help that I am next to clueless about vim, having been raised on emacs, but I really am beyond confused about why I am being dropped into the editor in the first place. Any pointers you could give me to get the new notebook up and running would be much appreciated. I'll be more than happy to test it. Thanks, Jon On Mar 31, 7:08 am, Jonathan gu...@uwosh.edu wrote: Jon, We are sorting this out. Ticket #9238 is the one you want. The .spkg you used is out-of-date. All the fixes are not in, but if you follow the patching instructions on #9238 you should get something that will work cleanly on MacOS + Chrome. FF has been inconsistent, so we are having trouble tracing the error and Safari appears to have a memory leak (the latest patches have a clunky work-around for this). If you want to see what is coming down the pike in the next few weeks, take a look at the published samples on my test server: http:///141.233.197.45:. I could really use some comments on how it works. Thanks, Jonathan On Mar 30, 12:02 am, jtyard jty...@gmail.com wrote: I am having issues with sage notebooks that contain more than five instances of the Jmol viewer. In short, if I create a notebook with more than 5 Jmol viewers, save, then reload it, I get an unresponsive script error in Firefox, Safari and Chrome. I've done some peeking around on the trac server and it seems that this is a well-documented problem for which a fix may exist, having to do with the tickets #9232 and #9238. So I apologize if this is not the correct place to ask about this, but I'm having trouble following what has been done on these tickets and, more importantly, what I would need to do in order to incorporate the fix to my sage distribution. I'm running sage 4.6.2 on osx 10.6.7, and I upgraded to Jmol_for_SageNoteBook-1.1.4.spkg so that I could use google Chrome. I'm sure that if I wait long enough this will all be incorporated into an upcoming release of sage, but I'd be very happy to resolve this issue asap so that I can use my notebooks without deleting all the 3d plots. I'm also more than happy to test the changes, but any pointer to how I can incorporate the new code would be helpful. Thanks, Jon -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
[sage-devel] Re: sage notebook with many Jmol viewers
Thanks guys. I was definitely using hg_sagenb.apply() and not hg_sagenb.commit(), so I am not sure why it was asking me to commit. The only difference from what you say Jonathan was that I was applying the patches from a local directory and not an http:, so I doubt that makes a difference. I will play with it some more tonight and see if I can get somewhere. Jon On Mar 31, 3:13 pm, Dr. David Kirkby david.kir...@onetel.net wrote: On 03/31/11 05:32 PM, jtyard wrote: Hi Jonathan, Thanks for your reply. I tried last night to figure out how to patch my notebook, and I ended up giving up after several hours. I also couldn't find any documentation for hg_sagenb.apply. After updating jmol to 1.1.5, I tried to follow the directions at http://www.sagemath.org/doc/developer/walk_through.html#reviewing-a-p... only replacing hg_sage.apply with hg_sagenb.apply, but things seem not to be as simple as described on that page. Running the command on a patch drops me into a vim editor that shows the text of the whole patch. Not knowing what to do, I press q and I am then asked to enter a commit message. No matter what I seem to do, when I try to quit vim it warns me that there was no write since last change, and if I quit with :q! then it seems I am back where I started. It doesn't help that I am next to clueless about vim, having been raised on emacs, but I really am beyond confused about why I am being dropped into the editor in the first place. Any pointers you could give me to get the new notebook up and running would be much appreciated. I'll be more than happy to test it. Thanks, Jon If you make changes to the code and try to commit them, then you must give a message why. I must admit I can't see why that should be so with you applying a patch though. I personally never use the hg commands in Sage, but use a version of hg on my system, so I can't really say too much about your issues. If set this: EDITOR=emacs export EDITOR then instead of firing up vim, you will get emacs. (I had the almost the opposite problem to you - my system kept firing up the GUI editor gedit, but I wanted vi!) I believe there's a variable you can use that selects the editor for Mercurial (i.e. hg) only. I'm not sure what it is, but Google would find it. But I just use EDITOR as I use vi for everything anyway. I must admit though, I'm still puzzled why you are asked to supply a commit message. Dave -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
[sage-devel] Re: sage notebook with many Jmol viewers
So I just made a fresh build of sage and the patching went smoothly. Not sure what was causing the problem. So far, everything works great! I also noticed that it did seem to take a long time for the applets to load, and somehow it seems that the image resolution is not as good as it was before I did the update. Presumably this is to save memory, but it would be nice if this could be a global option somehow. Thanks! Jon On Mar 31, 4:05 pm, jtyard jty...@gmail.com wrote: Thanks guys. I was definitely using hg_sagenb.apply() and not hg_sagenb.commit(), so I am not sure why it was asking me to commit. The only difference from what you say Jonathan was that I was applying the patches from a local directory and not an http:, so I doubt that makes a difference. I will play with it some more tonight and see if I can get somewhere. Jon On Mar 31, 3:13 pm, Dr. David Kirkby david.kir...@onetel.net wrote: On 03/31/11 05:32 PM, jtyard wrote: Hi Jonathan, Thanks for your reply. I tried last night to figure out how to patch my notebook, and I ended up giving up after several hours. I also couldn't find any documentation for hg_sagenb.apply. After updating jmol to 1.1.5, I tried to follow the directions at http://www.sagemath.org/doc/developer/walk_through.html#reviewing-a-p... only replacing hg_sage.apply with hg_sagenb.apply, but things seem not to be as simple as described on that page. Running the command on a patch drops me into a vim editor that shows the text of the whole patch. Not knowing what to do, I press q and I am then asked to enter a commit message. No matter what I seem to do, when I try to quit vim it warns me that there was no write since last change, and if I quit with :q! then it seems I am back where I started. It doesn't help that I am next to clueless about vim, having been raised on emacs, but I really am beyond confused about why I am being dropped into the editor in the first place. Any pointers you could give me to get the new notebook up and running would be much appreciated. I'll be more than happy to test it. Thanks, Jon If you make changes to the code and try to commit them, then you must give a message why. I must admit I can't see why that should be so with you applying a patch though. I personally never use the hg commands in Sage, but use a version of hg on my system, so I can't really say too much about your issues. If set this: EDITOR=emacs export EDITOR then instead of firing up vim, you will get emacs. (I had the almost the opposite problem to you - my system kept firing up the GUI editor gedit, but I wanted vi!) I believe there's a variable you can use that selects the editor for Mercurial (i.e. hg) only. I'm not sure what it is, but Google would find it. But I just use EDITOR as I use vi for everything anyway. I must admit though, I'm still puzzled why you are asked to supply a commit message. Dave -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
[sage-devel] sage notebook with many Jmol viewers
I am having issues with sage notebooks that contain more than five instances of the Jmol viewer. In short, if I create a notebook with more than 5 Jmol viewers, save, then reload it, I get an unresponsive script error in Firefox, Safari and Chrome. I've done some peeking around on the trac server and it seems that this is a well-documented problem for which a fix may exist, having to do with the tickets #9232 and #9238. So I apologize if this is not the correct place to ask about this, but I'm having trouble following what has been done on these tickets and, more importantly, what I would need to do in order to incorporate the fix to my sage distribution. I'm running sage 4.6.2 on osx 10.6.7, and I upgraded to Jmol_for_SageNoteBook-1.1.4.spkg so that I could use google Chrome. I'm sure that if I wait long enough this will all be incorporated into an upcoming release of sage, but I'd be very happy to resolve this issue asap so that I can use my notebooks without deleting all the 3d plots. I'm also more than happy to test the changes, but any pointer to how I can incorporate the new code would be helpful. Thanks, Jon -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
[sage-devel] Re: Problem building sage from source
I fixed the problem. It turns out that while sage is not on a network- mounted volume, my .sage directory was. After moving the .sage to the local volume, everything works fine now. I'm still not entirely sure what went wrong, since it was working that way for a while. Thanks, Jon On Mar 23, 1:14 am, Dima Pasechnik dimp...@gmail.com wrote: Hi, could it be that you use a network-mounted volume, and got a data corruption (or permissions?) issue due to this? What is 10.6.7 ? It seems that the latest is 10.6.6, no? And finally, which version of Xcode are you using? Dmitrii On Mar 23, 7:07 am, jtyard jty...@gmail.com wrote: Hi, I'm unable to successfully build sage 4.6.2 from source on OS X 10.6.7. Everything in the build seems to work fine until the very end. Here is where the build starts complaining: Sage build/upgrade complete! spkg/pipestatus ./sage -docbuild all html 21 tee -a dochtml.log sphinx-build -b html -d /Volumes/Extra/jtyard/sage-4.6.2/devel/sage/ doc/output/doctrees/en/a_tour_of_sage /Volumes/Extra/jtyard/ sage-4.6.2/devel/sage/doc/en/a_tour_of_sage /Volumes/Extra/jtyard/ sage-4.6.2/devel/sage/doc/output/html/en/a_tour_of_sage Traceback (most recent call last): File /Volumes/Extra/jtyard/sage-4.6.2/local/bin/sphinx-build, line 6, in module import sage.all File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python2.6/site- packages/sage/all.py, line 319, in module sage.misc.lazy_import.save_cache_file() File lazy_import.pyx, line 779, in sage.misc.lazy_import.save_cache_file (sage/misc/lazy_import.c:4185) File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.py, line 264, in move copy2(src, real_dst) File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.py, line 100, in copy2 copystat(src, dst) File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.py, line 77, in copystat os.chflags(dst, st.st_flags) OSError: [Errno 45] Operation not supported: '/nh/nest/u/jtyard/.sage/ _Volumes_Extra_jtyard_sage-4.6.2_devel_sage-main- lazy_import_cache.pickle' Build finished. The built documents can be found in /Volumes/Extra/ jtyard/sage-4.6.2/devel/sage/doc/output/html/en/a_tour_of_sage sphinx-build -b html -d /Volumes/Extra/jtyard/sage-4.6.2/devel/sage/ doc/output/doctrees/en/bordeaux_2008 /Volumes/Extra/jtyard/ sage-4.6.2/devel/sage/doc/en/bordeaux_2008 /Volumes/Extra/jtyard/ sage-4.6.2/devel/sage/doc/output/html/en/bordeaux_2008 Traceback (most recent call last): File /Volumes/Extra/jtyard/sage-4.6.2/local/bin/sphinx-build, line 6, in module import sage.all File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python2.6/site- packages/sage/all.py, line 319, in module sage.misc.lazy_import.save_cache_file() File lazy_import.pyx, line 779, in sage.misc.lazy_import.save_cache_file (sage/misc/lazy_import.c:4185) File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.py, line 264, in move copy2(src, real_dst) File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.py, line 100, in copy2 copystat(src, dst) File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.py, line 77, in copystat os.chflags(dst, st.st_flags) OSError: [Errno 45] Operation not supported: '/nh/nest/u/jtyard/.sage/ _Volumes_Extra_jtyard_sage-4.6.2_devel_sage-main- lazy_import_cache.pickle' Build finished. The built documents can be found in /Volumes/Extra/ jtyard/sage-4.6.2/devel/sage/doc/output/html/en/bordeaux_2008 sphinx-build -b html -d /Volumes/Extra/jtyard/sage-4.6.2/devel/sage/ doc/output/doctrees/en/constructions /Volumes/Extra/jtyard/ sage-4.6.2/devel/sage/doc/en/constructions /Volumes/Extra/jtyard/ sage-4.6.2/devel/sage/doc/output/html/en/constructions Traceback (most recent call last): File /Volumes/Extra/jtyard/sage-4.6.2/local/bin/sphinx-build, line 6, in module import sage.all File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python2.6/site- packages/sage/all.py, line 319, in module sage.misc.lazy_import.save_cache_file() File lazy_import.pyx, line 779, in sage.misc.lazy_import.save_cache_file (sage/misc/lazy_import.c:4185) File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.py, line 264, in move copy2(src, real_dst) File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.py, line 100, in copy2 copystat(src, dst) File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.py, line 77, in copystat os.chflags(dst, st.st_flags) OSError: [Errno 45] Operation not supported: '/nh/nest/u/jtyard/.sage/ _Volumes_Extra_jtyard_sage-4.6.2_devel_sage-main- lazy_import_cache.pickle' Build finished. The built documents can be found in /Volumes/Extra/ jtyard/sage-4.6.2/devel/sage/doc/output/html/en/constructions sphinx-build -b html -d /Volumes/Extra/jtyard/sage-4.6.2/devel/sage/ doc
[sage-devel] Re: Problem building sage from source
No, I cannot. It spits out a bunch of error information: -- | Sage Version 4.6.2, Release Date: 2011-02-25 | | Type notebook() for the GUI, and license() for information.| -- --- OSError Traceback (most recent call last) /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python2.6/site-packages/ IPython/ipmaker.pyc in force_import(modname) 64 reload(sys.modules[modname]) 65 else: --- 66 __import__(modname) 67 68 /Volumes/Extra/jtyard/sage-4.6.2/local/bin/ipy_profile_sage.py in module() 5 preparser(True) 6 7 import sage.all_cmdline 8 sage.all_cmdline._init_cmdline(globals()) 9 /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python2.6/site-packages/ sage/all_cmdline.py in module() 12 try: 13 --- 14 from sage.all import * 15 from sage.calculus.predefined import x 16 preparser(on=True) /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python2.6/site-packages/ sage/all.py in module() 317 # Cache the contents of star imports. 318 import sage.misc.lazy_import -- 319 sage.misc.lazy_import.save_cache_file() 320 321 /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python2.6/site-packages/ sage/misc/lazy_import.so in sage.misc.lazy_import.save_cache_file (sage/misc/lazy_import.c:4185)() /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.pyc in move(src, dst) 262 rmtree(src) 263 else: -- 264 copy2(src, real_dst) 265 os.unlink(src) 266 /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.pyc in copy2(src, dst) 98 dst = os.path.join(dst, os.path.basename(src)) 99 copyfile(src, dst) -- 100 copystat(src, dst) 101 102 def ignore_patterns(*patterns): /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.pyc in copystat(src, dst) 75 os.chmod(dst, mode) 76 if hasattr(os, 'chflags') and hasattr(st, 'st_flags'): --- 77 os.chflags(dst, st.st_flags) 78 79 OSError: [Errno 45] Operation not supported: '/nh/nest/u/jtyard/.sage/ _Volumes_Extra_jtyard_sage-4.6.2_devel_sage-main- lazy_import_cache.pickle' Error importing ipy_profile_sage - perhaps you should run %upgrade? WARNING: Loading of ipy_profile_sage failed. On Mar 22, 9:43 pm, mhampton hampto...@gmail.com wrote: I don't really understand those error messages, but they look like they are only coming from the documentation builds. Can you start up Sage itself (i.e. do ./sage from the top-level sage directory)? -M. Hampton On Mar 22, 6:07 pm, jtyard jty...@gmail.com wrote: Hi, I'm unable to successfully build sage 4.6.2 from source on OS X 10.6.7. Everything in the build seems to work fine until the very end. Here is where the build starts complaining: Sage build/upgrade complete! spkg/pipestatus ./sage -docbuild all html 21 tee -a dochtml.log sphinx-build -b html -d /Volumes/Extra/jtyard/sage-4.6.2/devel/sage/ doc/output/doctrees/en/a_tour_of_sage /Volumes/Extra/jtyard/ sage-4.6.2/devel/sage/doc/en/a_tour_of_sage /Volumes/Extra/jtyard/ sage-4.6.2/devel/sage/doc/output/html/en/a_tour_of_sage Traceback (most recent call last): File /Volumes/Extra/jtyard/sage-4.6.2/local/bin/sphinx-build, line 6, in module import sage.all File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python2.6/site- packages/sage/all.py, line 319, in module sage.misc.lazy_import.save_cache_file() File lazy_import.pyx, line 779, in sage.misc.lazy_import.save_cache_file (sage/misc/lazy_import.c:4185) File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.py, line 264, in move copy2(src, real_dst) File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.py, line 100, in copy2 copystat(src, dst) File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.py, line 77, in copystat os.chflags(dst, st.st_flags) OSError: [Errno 45] Operation not supported: '/nh/nest/u/jtyard/.sage/ _Volumes_Extra_jtyard_sage-4.6.2_devel_sage-main- lazy_import_cache.pickle' Build finished. The built documents can be found in /Volumes/Extra/ jtyard/sage-4.6.2/devel/sage/doc/output/html/en/a_tour_of_sage sphinx-build -b html -d /Volumes/Extra/jtyard/sage-4.6.2/devel/sage/ doc/output/doctrees/en/bordeaux_2008 /Volumes/Extra/jtyard/ sage-4.6.2/devel/sage/doc/en/bordeaux_2008 /Volumes/Extra/jtyard/ sage-4.6.2/devel/sage/doc/output/html/en/bordeaux_2008 Traceback (most recent call last): File /Volumes/Extra/jtyard/sage-4.6.2/local/bin/sphinx-build, line 6, in module import sage.all File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python2.6/site- packages
[sage-devel] Re: Problem building sage from source
Sage is not on a network-mounted volume. The latest mac os is actually 10.6.7. It was released on 3/21/11. I am using Xcode 3.2.6 (1761). On Mar 23, 1:14 am, Dima Pasechnik dimp...@gmail.com wrote: Hi, could it be that you use a network-mounted volume, and got a data corruption (or permissions?) issue due to this? What is 10.6.7 ? It seems that the latest is 10.6.6, no? And finally, which version of Xcode are you using? Dmitrii On Mar 23, 7:07 am, jtyard jty...@gmail.com wrote: Hi, I'm unable to successfully build sage 4.6.2 from source on OS X 10.6.7. Everything in the build seems to work fine until the very end. Here is where the build starts complaining: Sage build/upgrade complete! spkg/pipestatus ./sage -docbuild all html 21 tee -a dochtml.log sphinx-build -b html -d /Volumes/Extra/jtyard/sage-4.6.2/devel/sage/ doc/output/doctrees/en/a_tour_of_sage /Volumes/Extra/jtyard/ sage-4.6.2/devel/sage/doc/en/a_tour_of_sage /Volumes/Extra/jtyard/ sage-4.6.2/devel/sage/doc/output/html/en/a_tour_of_sage Traceback (most recent call last): File /Volumes/Extra/jtyard/sage-4.6.2/local/bin/sphinx-build, line 6, in module import sage.all File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python2.6/site- packages/sage/all.py, line 319, in module sage.misc.lazy_import.save_cache_file() File lazy_import.pyx, line 779, in sage.misc.lazy_import.save_cache_file (sage/misc/lazy_import.c:4185) File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.py, line 264, in move copy2(src, real_dst) File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.py, line 100, in copy2 copystat(src, dst) File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.py, line 77, in copystat os.chflags(dst, st.st_flags) OSError: [Errno 45] Operation not supported: '/nh/nest/u/jtyard/.sage/ _Volumes_Extra_jtyard_sage-4.6.2_devel_sage-main- lazy_import_cache.pickle' Build finished. The built documents can be found in /Volumes/Extra/ jtyard/sage-4.6.2/devel/sage/doc/output/html/en/a_tour_of_sage sphinx-build -b html -d /Volumes/Extra/jtyard/sage-4.6.2/devel/sage/ doc/output/doctrees/en/bordeaux_2008 /Volumes/Extra/jtyard/ sage-4.6.2/devel/sage/doc/en/bordeaux_2008 /Volumes/Extra/jtyard/ sage-4.6.2/devel/sage/doc/output/html/en/bordeaux_2008 Traceback (most recent call last): File /Volumes/Extra/jtyard/sage-4.6.2/local/bin/sphinx-build, line 6, in module import sage.all File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python2.6/site- packages/sage/all.py, line 319, in module sage.misc.lazy_import.save_cache_file() File lazy_import.pyx, line 779, in sage.misc.lazy_import.save_cache_file (sage/misc/lazy_import.c:4185) File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.py, line 264, in move copy2(src, real_dst) File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.py, line 100, in copy2 copystat(src, dst) File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.py, line 77, in copystat os.chflags(dst, st.st_flags) OSError: [Errno 45] Operation not supported: '/nh/nest/u/jtyard/.sage/ _Volumes_Extra_jtyard_sage-4.6.2_devel_sage-main- lazy_import_cache.pickle' Build finished. The built documents can be found in /Volumes/Extra/ jtyard/sage-4.6.2/devel/sage/doc/output/html/en/bordeaux_2008 sphinx-build -b html -d /Volumes/Extra/jtyard/sage-4.6.2/devel/sage/ doc/output/doctrees/en/constructions /Volumes/Extra/jtyard/ sage-4.6.2/devel/sage/doc/en/constructions /Volumes/Extra/jtyard/ sage-4.6.2/devel/sage/doc/output/html/en/constructions Traceback (most recent call last): File /Volumes/Extra/jtyard/sage-4.6.2/local/bin/sphinx-build, line 6, in module import sage.all File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python2.6/site- packages/sage/all.py, line 319, in module sage.misc.lazy_import.save_cache_file() File lazy_import.pyx, line 779, in sage.misc.lazy_import.save_cache_file (sage/misc/lazy_import.c:4185) File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.py, line 264, in move copy2(src, real_dst) File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.py, line 100, in copy2 copystat(src, dst) File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.py, line 77, in copystat os.chflags(dst, st.st_flags) OSError: [Errno 45] Operation not supported: '/nh/nest/u/jtyard/.sage/ _Volumes_Extra_jtyard_sage-4.6.2_devel_sage-main- lazy_import_cache.pickle' Build finished. The built documents can be found in /Volumes/Extra/ jtyard/sage-4.6.2/devel/sage/doc/output/html/en/constructions sphinx-build -b html -d /Volumes/Extra/jtyard/sage-4.6.2/devel/sage/ doc/output/doctrees/en/developer /Volumes/Extra/jtyard/sage-4.6.2/ devel/sage/doc/en/developer /Volumes/Extra/jtyard/sage-4.6.2/devel/ sage/doc
[sage-devel] Problem building sage from source
Hi, I'm unable to successfully build sage 4.6.2 from source on OS X 10.6.7. Everything in the build seems to work fine until the very end. Here is where the build starts complaining: Sage build/upgrade complete! spkg/pipestatus ./sage -docbuild all html 21 tee -a dochtml.log sphinx-build -b html -d /Volumes/Extra/jtyard/sage-4.6.2/devel/sage/ doc/output/doctrees/en/a_tour_of_sage/Volumes/Extra/jtyard/ sage-4.6.2/devel/sage/doc/en/a_tour_of_sage /Volumes/Extra/jtyard/ sage-4.6.2/devel/sage/doc/output/html/en/a_tour_of_sage Traceback (most recent call last): File /Volumes/Extra/jtyard/sage-4.6.2/local/bin/sphinx-build, line 6, in module import sage.all File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python2.6/site- packages/sage/all.py, line 319, in module sage.misc.lazy_import.save_cache_file() File lazy_import.pyx, line 779, in sage.misc.lazy_import.save_cache_file (sage/misc/lazy_import.c:4185) File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.py, line 264, in move copy2(src, real_dst) File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.py, line 100, in copy2 copystat(src, dst) File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.py, line 77, in copystat os.chflags(dst, st.st_flags) OSError: [Errno 45] Operation not supported: '/nh/nest/u/jtyard/.sage/ _Volumes_Extra_jtyard_sage-4.6.2_devel_sage-main- lazy_import_cache.pickle' Build finished. The built documents can be found in /Volumes/Extra/ jtyard/sage-4.6.2/devel/sage/doc/output/html/en/a_tour_of_sage sphinx-build -b html -d /Volumes/Extra/jtyard/sage-4.6.2/devel/sage/ doc/output/doctrees/en/bordeaux_2008/Volumes/Extra/jtyard/ sage-4.6.2/devel/sage/doc/en/bordeaux_2008 /Volumes/Extra/jtyard/ sage-4.6.2/devel/sage/doc/output/html/en/bordeaux_2008 Traceback (most recent call last): File /Volumes/Extra/jtyard/sage-4.6.2/local/bin/sphinx-build, line 6, in module import sage.all File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python2.6/site- packages/sage/all.py, line 319, in module sage.misc.lazy_import.save_cache_file() File lazy_import.pyx, line 779, in sage.misc.lazy_import.save_cache_file (sage/misc/lazy_import.c:4185) File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.py, line 264, in move copy2(src, real_dst) File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.py, line 100, in copy2 copystat(src, dst) File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.py, line 77, in copystat os.chflags(dst, st.st_flags) OSError: [Errno 45] Operation not supported: '/nh/nest/u/jtyard/.sage/ _Volumes_Extra_jtyard_sage-4.6.2_devel_sage-main- lazy_import_cache.pickle' Build finished. The built documents can be found in /Volumes/Extra/ jtyard/sage-4.6.2/devel/sage/doc/output/html/en/bordeaux_2008 sphinx-build -b html -d /Volumes/Extra/jtyard/sage-4.6.2/devel/sage/ doc/output/doctrees/en/constructions/Volumes/Extra/jtyard/ sage-4.6.2/devel/sage/doc/en/constructions /Volumes/Extra/jtyard/ sage-4.6.2/devel/sage/doc/output/html/en/constructions Traceback (most recent call last): File /Volumes/Extra/jtyard/sage-4.6.2/local/bin/sphinx-build, line 6, in module import sage.all File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python2.6/site- packages/sage/all.py, line 319, in module sage.misc.lazy_import.save_cache_file() File lazy_import.pyx, line 779, in sage.misc.lazy_import.save_cache_file (sage/misc/lazy_import.c:4185) File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.py, line 264, in move copy2(src, real_dst) File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.py, line 100, in copy2 copystat(src, dst) File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.py, line 77, in copystat os.chflags(dst, st.st_flags) OSError: [Errno 45] Operation not supported: '/nh/nest/u/jtyard/.sage/ _Volumes_Extra_jtyard_sage-4.6.2_devel_sage-main- lazy_import_cache.pickle' Build finished. The built documents can be found in /Volumes/Extra/ jtyard/sage-4.6.2/devel/sage/doc/output/html/en/constructions sphinx-build -b html -d /Volumes/Extra/jtyard/sage-4.6.2/devel/sage/ doc/output/doctrees/en/developer/Volumes/Extra/jtyard/sage-4.6.2/ devel/sage/doc/en/developer /Volumes/Extra/jtyard/sage-4.6.2/devel/ sage/doc/output/html/en/developer Traceback (most recent call last): File /Volumes/Extra/jtyard/sage-4.6.2/local/bin/sphinx-build, line 6, in module import sage.all File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python2.6/site- packages/sage/all.py, line 319, in module sage.misc.lazy_import.save_cache_file() File lazy_import.pyx, line 779, in sage.misc.lazy_import.save_cache_file (sage/misc/lazy_import.c:4185) File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.py, line 264, in move copy2(src, real_dst) File /Volumes/Extra/jtyard/sage-4.6.2/local/lib/python/shutil.py, line 100, in copy2 copystat(src, dst) File /Volumes/Extra/jtyard/sage-4.6.2/local
[sage-devel] mpmath and plot incompatibility
Hi, I'm running sage 4.6.1 and cannot use plot after loading mpmath. Namely, running from mpmath import * plot(lambda t: sin(2*pi*t), [1, 4]) produces no output in the notebook. I'm loading mpmath because I need to make plots of theta functions, and the page http://mpmath.googlecode.com/svn/trunk/doc/build/functions/elliptic.html#jacobi-theta-functions tells me to first run from mpmath import * to gain access to jtheta. Presumably this is a bug? Jon -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
[sage-devel] Re: build error for sage 4.6.1 on OS X 10.5.8
Thanks Georg, Before I posted my question, I had tried an earlier build with SAGE64=yes, but (of course) that didn't work and I received the same error that I posted. Then I had set SAGE64=no, tried again and got the same error. I then ran make clean and got the same error. I even rebooted and tried the build again without setting SAGE64. This still gave me the error. After seeing your response, I just deleted the entire install, untarred a fresh copy of the source, and ran make on that. This succeeded in building the 32 bit version. This behavior is a little unexpected, since nowhere was SAGE64 getting reset, and yet somehow make thought that I still wanted to build the 64 bit version even after make clean. So maybe this counts as a bug? At this point, however, I'm just going to install 10.6 so that I can compile with 64-bit. Just thought I'd point out what was going on. Jon On Jan 29, 8:27 am, Georg S. Weber georgswe...@googlemail.com wrote: Hmm, the important information seem to be: a) You try to build Sage on Mac OS X 10.5 (Leopard). b) There's a -m64 in the third line of your output, i.e. the build system tries to build a 64-bit library. (Then it seems that qdCocoa.o is only a 32-bit object file, hence rejected, hence later some symbols are missing, boom.) From my experience, building Sage works on OS X 10.4 and OS X 10.5 in 32-bit, and only on OS X 10.6 in 64-bit. I don't know whether anybody has successfully built Sage on OS X 10.5 in 64-bit. I wonder, in your build run on OS X 10.5, where and how the -m64 creeps in, that simply shouldn't be --- I myself did build Sage-4.6.1 on OS X 10.4, and it worked fine. Maybe in your build environment the SAGE64 environment variable was set somehow? Cheers, Georg -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
[sage-devel] Re: build error for sage 4.6.1 on OS X 10.5.8
Dima,
It looks like it is getting set pretty early, so I'm just posting here
the beginning of the install.log, rather than the whole huge file.
But it sounds to me that somehow the problem is that make clean
leaves too much behind. For instance, it seems to want to start
building r right away, even though I would think it would start with a
fresh compile.
Jon
*** ALL ENVIRONMENT VARIABLES BEFORE BUILD: ***
SAGENB=sagenb-0.8.10
GD=gd-2.0.35.p5
CONWAY=conway_polynomials-0.2
CLIQUER=cliquer-1.2.p7
MANPATH=/usr/share/man:/usr/local/share/man:/Library/TeX/
Distributions/.DefaultT
eX/Contents/Man:/usr/X11/man
READLINE=readline-6.1
JINJA2=jinja2-2.5.5
SAGE_LOGS=/Users/jtyard/test/sage-4.6.1/spkg/logs
PEXPECT=pexpect-2.0.p4
F2C=f2c-20070816.p2
TERM_PROGRAM=Apple_Terminal
MATPLOTLIB=matplotlib-1.0.0.p0
G2RED=genus2reduction-0.3.p8
LIBM4RI=libm4ri-20100701.p1
SAGE_BZIP2=bzip2-1.0.5
TERM=xterm-color
SHELL=/bin/bash
CYTHON=cython-0.13.p1
MAKEFLAGS=
TMPDIR=/var/folders/5g/5gZAKtBmGPW3YZx94BmD3TM/-Tmp-/
SQLALCHEMY=sqlalchemy-0.5.8
DOCUTILS=docutils-0.5.p0
Apple_PubSub_Socket_Render=/tmp/launch-GGQ5RD/Render
ZNPOLY=zn_poly-0.9.p5
WEAVE=weave-0.4.9.p0
SYMMETRICA=symmetrica-2.0.p5
GIVARO=givaro-3.2.13rc2.p2
TERM_PROGRAM_VERSION=240.2
SAGETEX=sagetex-2.2.5
MPFR=mpfr-2.4.2
SYMPY=sympy-0.6.4.p0
POLYTOPES_DB=polytopes_db-20100210
OLDPWD=/Users/jtyard/test/sage-4.6.1
EXAMPLES=examples-4.6.1
ATLAS=atlas-3.8.3.p16
PREREQ=prereq-0.7
DIR=dir-0.1
TACHYON=tachyon-0.98beta.p11
SCIPY_SANDBOX=scipy_sandbox-20071020.p7
MPFI=mpfi-1.3.4-cvs20071125.p8
MERCURIAL=mercurial-1.6.4.p0
CDDLIB=cddlib-094f.p8
DOT_SAGE=/Users/jtyard/.sage
ECLIB=eclib-20100711
USER=jtyard
R=r-2.10.1.p4
SPHINX=sphinx-1.0.4.p5
COMMAND_MODE=unix2003
LIBGCRYPT=libgcrypt-1.4.4.p3
CVXOPT=cvxopt-1.1.3
BOEHM_GC=boehm_gc-7.1.p6
TERMCAP=termcap-1.3.1.p1
MPIR=mpir-1.2.2.p2
SSH_AUTH_SOCK=/tmp/launch-Cq1ACl/Listeners
ZODB=zodb3-3.7.0.p4
GRAPHS=graphs-20070722.p1
ICONV=iconv-1.13.1.p3
__CF_USER_TEXT_ENCODING=0x1F6:0:0
ECL=ecl-10.4.1
CEPHES=cephes-2.8
SAGE_LOCAL=/Users/jtyard/test/sage-4.6.1/local
MAKELEVEL=1
SAGE_SCRIPTS=sage_scripts-4.6.1
ECM=ecm-6.2.1.p2
TWISTED=twisted-9.0.p2
RUBIKS=rubiks-20070912.p12
FREETYPE=freetype-2.3.5.p3
MFLAGS=
PYGMENTS=pygments-1.3.1.p0
GAP=gap-4.4.12.p4
PATH=/Users/jtyard/test/sage-4.6.1:/Users/jtyard/test/sage-4.6.1/local/
bin:/User
s/jtyard/sage-4.6:/usr/bin:/bin:/usr/sbin:/sbin:/Users/jtyard:/usr/
local/bin:/us
r/texbin:/usr/X11/bin
IML=iml-1.0.1.p13
LAPACK=lapack-20071123.p2
EXTCODE=extcode-4.6.1
BLAS=blas-20070724
ZLIB=zlib-1.2.5
SINGULAR=singular-3-1-1-4.p3
GNUTLS=gnutls-2.2.1.p5
POLYBORI=polybori-0.6.4.p6
LIBGPG_ERROR=libgpg_error-1.6.p3
PWD=/Users/jtyard/test/sage-4.6.1/spkg
LCALC=lcalc-20100428-1.23.p5
SCONS=scons-1.2.0
LINBOX=linbox-1.1.6.p3
OPENCDK=opencdk-0.6.6.p5
LANG=en_US.UTF-8
FLINTQS=flintqs-20070817.p5
GDMODULE=gdmodule-0.56.p7
SCIPY=scipy-0.8
GFAN=gfan-0.4plus.p1
SAGE_ROOT=/Users/jtyard/test/sage-4.6.1
SAGE=sage-4.6.1
RATPOINTS=ratpoints-2.1.3.p1
NUMPY=numpy-1.5.0
FIDUCIAL_DIRECTORY=/Users/jtyard/fiducials
PARI=pari-2.4.3.alpha.p0
PATCH=patch-2.5.9
GLPK=glpk-4.44
PALP=palp-1.1.p3
SHLVL=4
HOME=/Users/jtyard
PYCRYPTO=pycrypto-2.1.0
GSL=gsl-1.14
PYTHON_GNUTLS=python_gnutls-1.1.4.p7
DROPBOX=/Users/meagenharriman/Dropbox
IPYTHON=ipython-0.9.1.p0
FLINT=flint-1.5.0.p5
PYTHONPATH=/Users/jtyard/test/sage-4.6.1/local
LOGNAME=jtyard
SQLITE=sqlite-3.6.22
MPMATH=mpmath-0.15
NTL=ntl-5.4.2.p12
FORTRAN=fortran-20100629
PIL=pil-1.1.6.p4
SYMPOW=sympow-1.018.1.p8
PYNAC=pynac-0.2.1
MAXIMA=maxima-5.22.1
FPLLL=libfplll-3.0.12.p1
DISPLAY=/tmp/launch-FaNKeD/:0
SETUPTOOLS=setuptools-0.6c9.p0
MOIN=moin-1.9.1.p1
ELLIPTIC_CURVES=elliptic_curves-0.1
BOOST_CROPPED=boost-cropped-1.34.1
SECURITYSESSIONID=26c06c0
PYTHON=python-2.6.4.p9
NETWORKX=networkx-1.2.p1
LIBPNG=libpng-1.2.35.p2
_=/usr/bin/env
***
/Users/jtyard/test/sage-4.6.1/spkg/pipestatus sage-spkg $
{SAGE_SPKG_OPTS} r-2.1
0.1.p4 21 tee -a /Users/jtyard/test/sage-4.6.1/spkg/logs/
r-2.10.1.p4.log
Warning: Attempted to overwrite SAGE_ROOT environment variable
Detected SAGE64 flag
Building Sage on OS X in 64-bit mode
r-2.10.1.p4
Machine:
Darwin Megatron.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15
16:55:01 PDT
2009; root:xnu-1228.15.4~1/RELEASE_I386 i386
Deleting directories from past builds of previous/current versions of
r-2.10.1.p
4
Extracting package /Users/jtyard/test/sage-4.6.1/spkg/standard/
r-2.10.1.p4.spkg
...
-rw-r--r--@ 1 jtyard staff 17013408 Sep 25 16:30 /Users/jtyard/test/
sage-4.6.1
/spkg/standard/r-2.10.1.p4.spkg
Finished extraction
Host system
uname -a:
Darwin Megatron.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15
16:55:01 PDT
2009; root:xnu-1228.15.4~1/RELEASE_I386 i386
CC Version
gcc -v
Using built-in specs.
Target: i686-apple-darwin9
Configured with: /var/tmp/gcc
