Installing on yet another computer today. Same basic deal: everything builds except dochtml. This time I did check the logs before running ./sage -i jmol, and can confirm that no file with a name of the form $SAGE_ROOT/logs/pkgs/jmol-*.log was written on the initial build.
On Sunday, June 26, 2016 at 3:05:36 PM UTC-4, Joseph Hundley wrote: > > Ah. Then I think we can say with reasonable certainty that there was > nothing in > $SAGE_ROOT/logs/pkgs/jmol-*.log > before today, because when I looked the first time today, there was only > > > Found local metadata for jmol-14.2.11_2015.01.20 > > Attempting to download package jmol-14.2.11_2015.01.20.tar.bz2 from mirrors > > Downloading the Sage mirror list > > Searching fastest mirror > > 227ms: http://echidna.maths.usyd.edu.au/sage/ > > <snip... list of mirrors> > > 178ms: http://www.mirrorservice.org/sites/www.sagemath.org/ > > Fastest mirror: http://ftp.ntua.gr/pub/sagemath/ > > > http://ftp.ntua.gr/pub/sagemath/spkg/upstream/jmol/jmol-14.2.11_2015.01.20.tar.$ > > [................ > > > On Sunday, June 26, 2016 at 2:13:53 PM UTC-4, leif wrote: >> >> Joseph Hundley wrote: >> > Running ./sage -i jmol fixes the problem of "point3d((0,0,0))" >> producing >> > a message about a Jmol viewer being launched but no actual Jmol >> > viewer. And fixing jmol fixes the problem with building dochtml. >> > >> > Thanks! >> > >> > I went to check $SAGE_ROOT/logs/pkgs/jmol-*.log after issuing the >> > ./sage -i jmol command, unfortunately. So, all I found there was the >> log >> > file being written >> > at that time. >> >> Sage doesn't overwrite existing logs, so the log should contain the >> output from both attempts. >> >> >> -leif >> >> > Interestingly enough, my first run of "make" on my other machine >> > (running elementary OS) produced a nearly identical dochtml problem. I >> > presumed I'd have to fix jmol on that one too. But A second run of >> > "make" just now failed to replicated the problem and Jmol works over >> there. >> > >> > Sorry for not better documenting the bug. >> > >> > Best, >> > >> > JH >> > >> > On Sunday, June 26, 2016 at 3:30:09 AM UTC-4, Dima Pasechnik wrote: >> > >> > >> > >> > On Sunday, June 26, 2016 at 8:21:16 AM UTC+1, Dima Pasechnik wrote: >> > >> > >> > >> > On Sunday, June 26, 2016 at 2:48:26 AM UTC+1, Joseph Hundley >> wrote: >> > >> > Was this ever resolved? >> > I seem to be having the same problem trying to build on >> both >> > a Mac and a recent install of elementary OS. >> > >> > Certainly there is recent Java on this machine. Other Java >> > programs run fine. >> > >> > The error message appears to say that sage (or Jmol called >> > by sage?) is looking for JmolData.jar in >> > local/share/jmol/. >> > >> > >> > local/share/jmol/ is meant to be $SAGE_ROOT/local/share/jmol/ >> > and these files are meant to be installed there during Sage >> > installation. >> > >> > What do you see in >> > $SAGE_ROOT/logs/pkgs/jmol-14.2.11_2015.01.20.log ? >> > (or perhaps in $SAGE_ROOT/logs/pkgs/jmol-<someoterversion>.log) >> > >> > >> > >> > >> > I decided to try downloading Jmol >> > from >> https://sourceforge.net/projects/jmol/?source=typ_redirect >> > <https://sourceforge.net/projects/jmol/?source=typ_redirect> >> >> > One of the files is indeed JmolData.jar. Instead of moving >> > just that file into a directory called /local/share/jmol >> > what I did is move/rename the whole folder it is in into >> > local/share/jmol. This had an interesting effect. >> > The first time I tried point3d((0,0,0)) in sage after >> making >> > these changes I got a new, pretty long error message >> > which I regrettably neglected to save. The second time >> > (different Sage session) I got "Launched jmol viewer >> > for Graphics3d Object." >> > >> > >> > anyhow, you should reinstall jmol package, by doing >> > ./sage -i jmol >> > (or ./sage -f jmol) >> > >> > >> > >> > >> > >> > Best, >> > JH >> > >> > On Sunday, May 29, 2016 at 1:17:46 AM UTC-4, Eric Larson >> wrote: >> > >> > Hi all, >> > >> > Yes, sage mostly works --- except I cannot create a 3D >> > graphics object: >> > >> > sage: point3d((0, 0, 0)) >> > >> /home/eric/sage-src/local/lib/python2.7/site-packages/sage/repl/rich_output/display_manager.py:590: >> >> >> > RichReprWarning: Exception in _rich_repr_ while >> > displaying object: Jmol failed to create file >> > >> '/home/eric/.sage/temp/serre/4032/dir_Kn6nvZ/preview.png', >> > see '/home/eric/.sage/temp/serre/4032/tmp_UBdIvW.txt' >> > for details >> > RichReprWarning, >> > Graphics3d Object >> > sage: >> > >> > The file >> /home/eric/.sage/temp/serre/4032/tmp_UBdIvW.txt >> > disappears after exiting sage; but while sage is still >> > running, I can view it, and it contains the following >> text: >> > >> > Error: Unable to access jarfile >> > /home/eric/sage-src/local/share/jmol/JmolData.jar >> > >> > The directory /home/eric/sage-src/local/share/jmol/ >> does >> > not exist: >> > >> > eric@serre:~$ cd /home/eric/sage-src/local/share/jmol/ >> > bash: cd: /home/eric/sage-src/local/share/jmol/: No >> such >> > file or directory >> > eric@serre:~$ cd /home/eric/sage-src/local/share/ >> > eric@serre:~/sage-src/local/share$ ls >> > aclocal doc iml lrcalc maxima >> > singular >> > cliquer gc info man pari >> > tabset >> > conway_polynomials gcc-4.9.3 jupyter mathjax sage >> > terminfo >> > eric@serre:~/sage-src/local/share$ >> > >> > Best, >> > -Eric >> > >> > On Saturday, May 28, 2016 at 8:04:37 PM UTC-4, >> > vdelecroix wrote: >> > >> > The error occurred during the documentation build. >> > You should be able to >> > start Sage without any problem. >> > >> > If it works, try to create some 3d plots and see >> > them (via jmol). >> > >> > On 28/05/16 17:35, Eric Larson wrote: >> > > ...But I can attach a google drive link to the >> file: >> > > >> > > install.log >> > > >> > < >> https://drive.google.com/file/d/0BzxearNxPfAuTGZ3YVFvS0dHN1U/view?usp=drive_web >> >> > < >> https://drive.google.com/file/d/0BzxearNxPfAuTGZ3YVFvS0dHN1U/view?usp=drive_web>> >> >> >> > >> > > >> > > >> > > On Sat, May 28, 2016 at 6:29 PM, Eric Larson >> > <elar...@gmail.com> wrote: >> > > >> > >> Hi Dima, >> > >> >> > >> Hm... I think most of the issue was that my >> fresh >> > install of debian 8 was >> > >> from the initial release CD, which included a >> > buggy compiler? Because when >> > >> I ran system updates, I noticed that one of the >> > things updated was gcc, and >> > >> figured I should try recompilation. This time I >> > get a *different* error >> > >> --- sage itself builds fine, and appears to run >> > fine, unlike last time, but >> > >> it was unable to build the documentation: >> > >> >> > >> [plot3d ] RuntimeError: Jmol failed to create >> file >> > >> >> > >> '/home/eric/.sage/temp/serre/31647/dir_gUwtRI/preview..png', >> > see >> > >> >> > '/home/eric/.sage/temp/serre/31647/tmp_xSBzt6.txt' >> > for details >> > >> Error building the documentation. >> > >> Traceback (most recent call last): >> > >> File >> > "/home/eric/sage-src/local/lib/python/runpy.py", >> > line 162, in >> > >> _run_module_as_main >> > >> "__main__", fname, loader, pkg_name) >> > >> File >> > "/home/eric/sage-src/local/lib/python/runpy.py", >> > line 72, in >> > >> _run_code >> > >> exec code in run_globals >> > >> File >> > >> >> > >> "/home/eric/sage-src/local/lib/python2.7/site-packages/sage_setup/docbuild/__main__.py", >> >> >> > >> > >> line 2, in <module> >> > >> main() >> > >> File >> > >> >> > >> "/home/eric/sage-src/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py", >> >> >> > >> > >> line 1629, in main >> > >> builder() >> > >> File >> > >> >> > >> "/home/eric/sage-src/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py", >> >> >> > >> > >> line 284, in _wrapper >> > >> getattr(get_builder(document), >> > 'inventory')(*args, **kwds) >> > >> File >> > >> >> > >> "/home/eric/sage-src/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py", >> >> >> > >> > >> line 495, in _wrapper >> > >> x.get(99999) >> > >> File >> > >> "/home/eric/sage-src/local/lib/python/multiprocessing/pool.py", >> > >> > >> line 567, in get >> > >> raise self._value >> > >> OSError: [plot3d ] >> > >> >> > >> /home/eric/sage-src/local/lib/python2.7/site-packages/sage/plot/plot3d/platonic.py:docstring >> >> >> > >> > >> of sage.plot.plot3d.platonic:10: WARNING: >> > Exception occurred in plotting >> > >> platonic-1 >> > >> >> > >> Makefile:1003: recipe for target 'doc-html' >> failed >> > >> make[2]: *** [doc-html] Error 1 >> > >> make[2]: Leaving directory >> > '/home/eric/sage-src/build/make' >> > >> Makefile:826: recipe for target 'all' failed >> > >> make[1]: *** [all] Error 2 >> > >> make[1]: Leaving directory >> > '/home/eric/sage-src/build/make' >> > >> >> > >> real 314m1.704s >> > >> user 286m3.212s >> > >> sys 12m12.704s >> > >> >> > >> *************************************************************** >> > >> > >> Error building Sage. >> > >> >> > >> The following package(s) may have failed to >> build >> > (not necessarily >> > >> during this run of 'make all'): >> > >> >> > >> * documentation: dochtml >> > >> log file: >> > /home/eric/sage-src/logs/pkgs/../dochtml.log >> > >> >> > >> The build directory may contain configuration >> > files and other potentially >> > >> helpful information. WARNING: if you now run >> > 'make' again, the build >> > >> directory will, by default, be deleted. Set the >> > environment variable >> > >> SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this. >> > >> >> > >> >> > >> >> > >> I can't find either file mentioned >> > >> (/home/eric/sage-src/logs/pkgs/../dochtml.log OR >> > >> >> /home/eric/.sage/temp/serre/31647/tmp_xSBzt6.txt) >> > --- I'm not sure how to >> > >> expand the former file into a full path (what's >> > the /../?); and the later >> > >> file doesn't exist on my system. >> > >> >> > >> Also when I try to upload a file here I get an >> > "upload error"... >> > >> >> > >> Best, >> > >> -Eric >> > >> >> > >> On Friday, May 27, 2016 at 6:31:59 PM UTC-4, >> Eric >> > Larson wrote: >> > >>> >> > >>> Any suggestions? From >> > /home/eric/sage/logs/pkgs/sagelib-7.2.log (full log >> > >>> file attached): >> > >>> >> > >>> make[3]: Entering directory >> '/home/eric/sage/src' >> > >>> python -u setup.py install >> > >>> >> > >> ************************************************************************ >> > >> > >>> Traceback (most recent call last): >> > >>> File "setup.py", line 67, in <module> >> > >>> include_dirs = >> > sage_include_directories(use_sources=True) >> > >>> File "/home/eric/sage/src/sage/env.py", line >> > 172, in >> > >>> sage_include_directories >> > >>> import os, numpy >> > >>> File >> > >>> >> > >> "/home/eric/sage/local/lib/python2.7/site-packages/numpy-1.11.0-py2.7-linux-x86_64.egg/numpy/__init__.py", >> >> >> > >> > >>> line 180, in <module> >> > >>> from . import add_newdocs >> > >>> File >> > >>> >> > >> "/home/eric/sage/local/lib/python2.7/site-packages/numpy-1.11.0-py2.7-linux-x86_64.egg/numpy/add_newdocs.py", >> >> >> > >> > >>> line 13, in <module> >> > >>> from numpy.lib import add_newdoc >> > >>> File >> > >>> >> > >> "/home/eric/sage/local/lib/python2.7/site-packages/numpy-1.11.0-py2.7-linux-x86_64.egg/numpy/lib/__init__.py", >> >> >> > >> > >>> line 8, in <module> >> > >>> from .type_check import * >> > >>> File >> > >>> >> > >> "/home/eric/sage/local/lib/python2.7/site-packages/numpy-1.11.0-py2.7-linux-x86_64.egg/numpy/lib/type_check.py", >> >> >> > >> > >>> line 11, in <module> >> > >>> import numpy.core.numeric as _nx >> > >>> File >> > >>> >> > >> "/home/eric/sage/local/lib/python2.7/site-packages/numpy-1.11.0-py2.7-linux-x86_64.egg/numpy/core/__init__.py", >> >> >> > >> > >>> line 14, in <module> >> > >>> from . import multiarray >> > >>> ImportError: libatlas.so.3: cannot open shared >> > object file: No such file >> > >>> or directory >> > >>> >> > >> ************************************************************************ >> > >> > >>> Error building the Sage library >> > >>> >> > >> ************************************************************************ >> >> >> -- You received this message because you are subscribed to the Google Groups "sage-devel" group. 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