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2019-02-02 17:07:02 -0500 asked a question jsmol problem in Sagemath/Jupyter notebooks

Whenevr plotting 3d functions I get:

Interactive 3D plots using the default viewer do not work in SageNB, because JSmol cannot currently be packaged for Debian. See the README.source of the jmol package for more details on this situation. You have the following alternative options: View an interactive WebGL-based plot by giving the option viewer='threejs'. This should work out-of-the box on Firefox, but may require you to adjust some settings in Chromium - see chrome://flags for options and chrome://gpu for status. In both cases, the functionality also depends on your graphics hardware and drivers, but support should exist in most cases. View a less sophisticated interactive plot that does not require WebGL, by giving the option viewer='canvas3d'. View a non-interactive plot by giving the option viewer='tachyon'. Use the default viewer (Jmol) from the SageMath command-line interface, instead of the notebook.

I can use threejs for everything except plotting vector fields. Is there any way to get Jsmol working on a debian system? I've found nothing on google that would help.

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2016-05-29 21:22:59 -0500 asked a question More pyopenssl problems

I was able to get pyopenssl installed and compiled after a number of issues. I will post late on how I resolved these. However, now when I try to run a secure notebook I get more errors.

Any clue how to fix this?

OpenSSL.crypto.Error: [('PEM routines', 'PEM_read_bio', 'no start line')]

Failed to load application: [('PEM routines', 'PEM_read_bio', 'no start line')]

error Traceback (most recent call last) <ipython-input-3-3d6cf59ae321> in <module>() ----> 1 notebook(secure=True)

/usr/SageMath/src/sage/misc/lazy_import.pyx in sage.misc.lazy_import.LazyImport.__call__ (/usr/SageMath/src/build/cythonized/sage/misc/lazy_import.c:3560)() 384 True 385 """ --> 386 return self._get_object()(args, *kwds) 387 388 def __repr__(self):

/usr/SageMath/local/lib/python2.7/site-packages/sagenb-0.11.7-py2.7.egg/sagenb/notebook/notebook_object.pyc in __call__(self, args, *kwds) 237 """ 238 def __call__(self, args, *kwds): --> 239 return self.notebook(args, *kwds) 240 241 notebook = run_notebook.notebook_run

/usr/SageMath/local/lib/python2.7/site-packages/sagenb-0.11.7-py2.7.egg/sagenb/notebook/run_notebook.pyc in notebook_run(self, directory, port, interface, port_tries, secure, reset, accounts, openid, server_pool, ulimit, timeout, doc_timeout, upload, automatic_login, start_path, fork, quiet, server, profile, subnets, require_login, open_viewer, address) 638 os.chdir(cwd) 639 if e == 256: --> 640 raise socket.error 641 642 def get_admin_passwd():


2016-05-12 20:03:28 -0500 asked a question Has anyone successfully installed Sage with secure notebooks in ubuntu?

The default instructions on how to do this do not work. If someone has successfully installed Sage with ssl support in Ubuntu, can you please list the steps that were taken? My failed attempt was with the lastest sage version and a clean install of ubuntu. What pre steps were needed before running sage? (ie, apt-get install m4) Any help would be appreciated.

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2016-05-05 14:01:15 -0500 commented answer ./sage -i pyopenssl fails to compile

I tried to build from source, now I get a new error: line 14, in <module> from . import multiarray ImportError: cannot open shared object file: No such file or directory

Error building the Sage library

Please email sage-devel ( ( explaining the problem and including the relevant part of the log file /usr/SageMath/logs/pkgs/sage-7.1.log Describe your computer, operating system, etc.

Makefile:6: recipe for target 'sage' failed make[3]: * [sage] Error 1 make[3]: Leaving directory '/usr/SageMath/src'

2016-05-04 07:47:00 -0500 asked a question ./sage -i pyopenssl fails to compile

I've tried multiple times to get this to work. I've tried with a clean install of the latest version of sage and the latest version of ubuntu. I've run make install build essentials, make install m4. I've spent hours on google with no answers. This is the result ./sage -i pyopenssl (relevant output)

Using cached cffi-1.6.0.tar.gz Complete output from command python egg_info: /usr/SageMath/local/bin/pkg-config: line 16: /home/buildbot/slave/binary_pkg/build/tools/binary-pkg/bin/pkg-config: No such file or directory /usr/SageMath/local/bin/pkg-config: line 16: /home/buildbot/slave/binary_pkg/build/tools/binary-pkg/bin/pkg-config: No such file or directory /usr/SageMath/local/bin/pkg-config: line 16: /home/buildbot/slave/binary_pkg/build/tools/binary-pkg/bin/pkg-config: No such file or directory /usr/SageMath/local/bin/pkg-config: line 16: /home/buildbot/slave/binary_pkg/build/tools/binary-pkg/bin/pkg-config: No such file or directory /usr/SageMath/local/bin/pkg-config: line 16: /home/buildbot/slave/binary_pkg/build/tools/binary-pkg/bin/pkg-config: No such file or directory gcc: error: /usr/SageMath/local/lib/gcc/: Is a directory gcc: error: /usr/SageMath/local/lib/gcc/: Is a directory

    No working compiler found, or bogus compiler options
    passed to the compiler from Python's distutils module.
    See the error messages above.
    (If they are about -mno-fused-madd and you are on OS/X 10.8,


Command "python egg_info" failed with error code 1 in /tmp/pip-build-i0j969/cffi/ Makefile:2083: recipe for target 'pyopenssl' failed make[1]: * [pyopenssl] Error 1 make[1]: Leaving directory '/usr/SageMath/build/make'

real 0m10.091s user 0m7.088s sys 0m2.300s

Error building Sage.

The following package(s) may have failed to build (not necessarily during this run of 'make pyopenssl'):

  • package: openssl-1.0.2g log file: /usr/SageMath/logs/pkgs/openssl-1.0.2g.log build directory: /usr/SageMath/local/var/tmp/sage/build/openssl-1.0.2g

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.

Makefile:16: recipe for target 'pyopenssl' failed make: * [pyopenssl] Error 1

Does anyone have a clue how to fix this? I've run out of ideas, and have basically given up on making a secure sage server.