Sage Notebook does not open properly when installed using Conda #21

ghost · 2018-07-10T02:04:18Z

Issue:

So it seems that when installing sage with conda through conda-forge, the dependencies for the sage notebook environment do not come along for the ride.

Typing : sage -n sagenb (to start the sage default notebook) yields the following error:

Please wait while the old SageNB Notebook server starts...
Traceback (most recent call last):
  File "/home/zeru/miniconda3/envs/sage/bin/sage-notebook", line 268, in <module>
    launcher(unknown)
  File "/home/zeru/miniconda3/envs/sage/bin/sage-notebook", line 69, in __init__
    from sagenb.notebook.notebook_object import notebook
ImportError: No module named sagenb.notebook.notebook_object

Additionally, in /miniconda3/envs/sage/bin there only seems to be a single py script, sage-notebook.py for the execution of the notebook.

An additional error that comes about when attempting to use other notebook back-ends. default and export yield 404 pages on local host and no other options. the IPython and Jupyter options work fine.

strangely enough, the same command integrate does not work for simple cases in either of the working notebooks, or of the shell, for simple integrals like integrate(x^2,x).
integralerror.txt

I am not a programmer of a high calibur, as I am a mere physicist, but i thought here would be the appropriate place to document this bug.

Let me know if i could help debug this nasty mess.

Environment (

``` alabaster 0.7.11 py_3 conda-forge appdirs 1.4.3 py_1 conda-forge arb 2.13.0 hb705a9b_1 conda-forge asn1crypto 0.24.0 py_1 conda-forge attrs 18.1.0 py_1 conda-forge automat 0.7.0 py27_0 conda-forge babel 2.6.0 py_1 conda-forge backports 1.0 py27_1 conda-forge backports.functools_lru_cache 1.5 py27_0 conda-forge backports.shutil_get_terminal_size 1.0.0 py_3 conda-forge backports_abc 0.5 py27_0 conda-forge bdw-gc 7.6.4 h2d50403_2 conda-forge blas 1.1 openblas conda-forge bleach 2.1.3 py_0 conda-forge boost-cpp 1.67.0 h3a22d5f_0 conda-forge brial 1.2.3 py_2 conda-forge bzip2 1.0.6 1 conda-forge ca-certificates 2018.4.16 0 conda-forge cairo 1.14.12 h77bcde2_0 cddlib 1!0.94i h16a7912_1 conda-forge certifi 2018.4.16 py27_0 conda-forge cffi 1.11.5 py27_0 conda-forge chardet 3.0.4 py_1 conda-forge cliquer 1.21 0 conda-forge configparser 3.5.0 py27_0 conda-forge constantly 15.1.0 py_0 conda-forge cryptography 2.2.1 py27hdffb7b8_1 conda-forge curl 7.60.0 0 conda-forge cvxopt 1.2.0 py27_blas_openblash9c03b7d_202 [blas_openblas] conda-forge cycler 0.10.0 py_1 conda-forge cypari2 1.1.4 py27h16a7912_2 conda-forge cysignals 1.7.1 py27h470a237_0 conda-forge cython 0.28.4 py27hfc679d8_0 conda-forge dbus 1.13.0 h3a4f0e9_0 conda-forge decorator 4.3.0 py_0 conda-forge docutils 0.14 py27_0 conda-forge dsdp 5.8 blas_openblash470a237_201 [blas_openblas] conda-forge ecl 16.1.3 h0b9cf6d_5 conda-forge eclib 20171219 h075c78f_1 conda-forge ecm 7.0.4 h16a7912_2 conda-forge entrypoints 0.2.3 py27_1 conda-forge enum34 1.1.6 py27_1 conda-forge expat 2.2.5 hfc679d8_1 conda-forge fastcache 1.0.2 py27_0 conda-forge fflas-ffpack 2.3.2 blas_openblashb06058e_1 [blas_openblas] conda-forge fftw 3.3.8 h470a237_0 conda-forge flintqs 1.0 0 conda-forge fontconfig 2.12.6 0 conda-forge fplll 5.2.0 h075c78f_1 conda-forge fpylll 0.3.0dev py27h075c78f_2 conda-forge freetype 2.8.1 0 conda-forge functools32 3.2.3.2 py27_2 conda-forge future 0.16.0 py27_0 conda-forge gap 4.8.6 hca56440_3 conda-forge gf2x 1.2 hfc679d8_2 conda-forge gfan 0.5 h0eace8b_1 conda-forge giac 1.4.9.57 blas_openblashb294cb5_3 [blas_openblas] conda-forge giflib 5.1.4 h470a237_0 conda-forge givaro 4.0.4 h0eace8b_1 conda-forge glib 2.53.6 h5d9569c_2 glpk 4.65 h16a7912_1 conda-forge gmp 6.1.2 hfc679d8_0 conda-forge gmpy2 2.0.8 py27_0 conda-forge graphite2 1.3.11 hfc679d8_0 conda-forge gsl 2.2.1 blas_openblas_4 [blas_openblas] conda-forge gst-plugins-base 1.12.4 h33fb286_0 gstreamer 1.12.4 hb53b477_0 harfbuzz 1.7.6 hc5b324e_0 html5lib 1.0.1 py_0 conda-forge hyperlink 17.3.1 py_0 conda-forge icu 58.2 hfc679d8_0 conda-forge idna 2.7 py_1 conda-forge imagesize 1.0.0 py_1 conda-forge iml 1.0.5 blas_openblash905a843_1 [blas_openblas] conda-forge incremental 17.5.0 py_0 conda-forge ipaddress 1.0.22 py_1 conda-forge ipykernel 4.8.2 py27_0 conda-forge ipython 5.7.0 py27_0 conda-forge ipython_genutils 0.2.0 py_1 conda-forge ipywidgets 7.2.1 py27_1 conda-forge jinja2 2.10 py27_0 conda-forge jmol 14.29.15 1 conda-forge jpeg 9c h470a237_0 conda-forge jsonschema 2.6.0 py27_1 conda-forge jupyter_client 5.2.3 py_1 conda-forge jupyter_core 4.4.0 py_0 conda-forge kiwisolver 1.0.1 py27_1 conda-forge krb5 1.14.6 0 conda-forge lcalc 1.23 heb735ee_1 conda-forge libbrial 1.2.3 hafa9fcd_2 conda-forge libffi 3.2.1 3 conda-forge libflint 2.5.2 heb735ee_2 conda-forge libgap 4.8.6 hb705a9b_1 conda-forge libgcc 7.2.0 h69d50b8_2 libgcc-ng 7.2.0 hdf63c60_3 libgd 2.2.5 3 conda-forge libgfortran 3.0.0 1 libiconv 1.15 h470a237_1 conda-forge libpng 1.6.34 ha92aebf_1 conda-forge libsodium 1.0.16 0 conda-forge libssh2 1.8.0 h5b517e9_2 conda-forge libstdcxx-ng 7.2.0 hdf63c60_3 libtiff 4.0.9 he6b73bb_1 conda-forge libwebp 0.5.2 7 conda-forge libxcb 1.13 h470a237_1 conda-forge libxml2 2.9.8 h422b904_2 conda-forge linbox 1.5.2 hb3e9661_2 conda-forge lrcalc 1.2 0 conda-forge m4ri 20140914 0 conda-forge m4rie 20150908 0 conda-forge markupsafe 1.0 py27_0 conda-forge matplotlib 2.2.2 py27_1 conda-forge maxima 5.39.0 h0b9cf6d_3 conda-forge metis 5.1.0 3 conda-forge mistune 0.8.3 py27_1 conda-forge mpc 1.1.0 hb705a9b_6 conda-forge mpfi 1.5.3 hb705a9b_1 conda-forge mpfr 4.0.1 h16a7912_0 conda-forge mpmath 1.0.0 py_0 conda-forge nauty 2.6r7 0 conda-forge nbconvert 5.3.1 py_1 conda-forge nbformat 4.4.0 py27_0 conda-forge ncurses 5.9 10 conda-forge networkx 1.11 py27_0 conda-forge notebook 5.5.0 py27_0 conda-forge ntl 10.3.0 1 conda-forge numpy 1.14.5 py27_blas_openblashd3ea46f_201 [blas_openblas] conda-forge olefile 0.45.1 py_1 conda-forge openblas 0.2.20 8 conda-forge openjdk 8.0.144 zulu8.23.0.3_1 conda-forge openssl 1.0.2o 0 conda-forge packaging 17.1 py_0 conda-forge palp 2.1 0 conda-forge pandoc 2.2.1 0 conda-forge pandocfilters 1.4.2 py27_0 conda-forge pango 1.40.14 0 conda-forge pari 2.9.5 pl526h787e8ac_1 conda-forge path.py 11.0.1 py_0 conda-forge pathlib2 2.3.2 py27_0 conda-forge pcre 8.39 0 conda-forge perl 5.26.2 h470a237_0 conda-forge pexpect 4.6.0 py27_0 conda-forge pickleshare 0.7.4 py27_0 conda-forge pillow 4.3.0 py27_2 conda-forge pip 9.0.3 py27_0 conda-forge pixman 0.34.0 2 conda-forge pkg-config 0.29.2 1 conda-forge pkgconfig 1.3.1 py27_0 conda-forge planarity 3.0.0.5 0 conda-forge ppl 1.2 0 conda-forge prompt_toolkit 1.0.15 py27_0 conda-forge psutil 5.4.6 py27_0 conda-forge pthread-stubs 0.4 h470a237_1 conda-forge ptyprocess 0.6.0 py27_0 conda-forge pyasn1 0.4.3 py_0 conda-forge pyasn1-modules 0.2.1 py_0 conda-forge pycparser 2.18 py27_0 conda-forge pycrypto 2.6.1 py27_1 conda-forge pygments 2.2.0 py_1 conda-forge pyhamcrest 1.9.0 py27_1 conda-forge pynac 0.7.17 py27h075c78f_1 conda-forge pyopenssl 18.0.0 py27_0 conda-forge pyparsing 2.2.0 py_1 conda-forge pyqt 5.6.0 py27h8210e8a_6 conda-forge pysocks 1.6.8 py27_1 conda-forge python 2.7.14 ha6fc286_23 python-dateutil 2.7.3 py_0 conda-forge pytz 2018.5 py_0 conda-forge pyzmq 17.0.0 py27_4 conda-forge qd 2.3.17 h26a2512_2 conda-forge qt 5.6.2 hd25b39d_14 r-base 3.4.1 4 conda-forge ratpoints 2.1.3 h16a7912_2 conda-forge readline 7.0 0 conda-forge requests 2.19.1 py_1 conda-forge rpy2 2.8.5 py27r3.4.1_0 conda-forge rubiks 20070912 0 conda-forge rw 0.7 1 conda-forge sage 8.2 py27_2 conda-forge sagelib 8.2 py27_blas_openblash4416362_3 [blas_openblas] conda-forge sagemath-db-combinatorial-designs 20140630 0 conda-forge sagemath-db-conway-polynomials 0.5.p0 py27_0 conda-forge sagemath-db-elliptic-curves 0.8 1 conda-forge sagemath-db-graphs 20161026 0 conda-forge sagemath-db-polytopes 20170220 0 conda-forge scandir 1.7 py27_0 conda-forge scipy 1.1.0 py27_blas_openblas_200 [blas_openblas] conda-forge send2trash 1.5.0 py_0 conda-forge service_identity 17.0.0 py_0 conda-forge setuptools 40.0.0 py27_0 conda-forge simplegeneric 0.8.1 py_1 conda-forge singledispatch 3.4.0.3 py27_0 conda-forge singular 4.1.0.p3 h1e9d69d_2 conda-forge sip 4.18 py27_1 conda-forge six 1.11.0 py27_1 conda-forge snowballstemmer 1.2.1 py_1 conda-forge sphinx 1.7.5 py27_0 conda-forge sphinxcontrib-websupport 1.0.1 py27_0 conda-forge sqlite 3.23.1 h2d50403_0 conda-forge ssl_match_hostname 3.5.0.1 py27_1 conda-forge subprocess32 3.5.2 py27_0 conda-forge suitesparse 4.5.6 blas_openblas_200 [blas_openblas] conda-forge symmetrica 2.0 0 conda-forge sympow 1.018.1 h470a237_2 conda-forge sympy 1.1.1 py27_0 conda-forge tachyon 0.99b6 0 conda-forge tbb 2018_20171205 0 conda-forge terminado 0.8.1 py27_0 conda-forge testpath 0.3.1 py27_0 conda-forge tk 8.6.7 0 conda-forge tornado 4.5.3 py27_0 conda-forge traitlets 4.3.2 py27_0 conda-forge twisted 18.4.0 py27h470a237_0 conda-forge typing 3.6.4 py27_2 conda-forge urllib3 1.23 py27_0 conda-forge wcwidth 0.1.7 py_1 conda-forge webencodings 0.5 py27_0 conda-forge wheel 0.31.1 py27_0 conda-forge widgetsnbextension 3.2.1 py27_0 conda-forge xorg-libxau 1.0.8 h470a237_5 conda-forge xorg-libxdmcp 1.1.2 h470a237_6 conda-forge xz 5.2.3 0 conda-forge zeromq 4.2.5 hfc679d8_3 conda-forge zlib 1.2.11 h470a237_3 conda-forge zn_poly 0.9 h16a7912_2 conda-forge zope.interface 4.5.0 py27h470a237_0 conda-forge ``` ):

Details about conda and system ( conda info ):

     active environment : sage
    active env location : /home/zeru/miniconda3/envs/sage
            shell level : 1
       user config file : /home/zeru/.condarc
 populated config files : /home/zeru/.condarc
          conda version : 4.5.6
    conda-build version : not installed
         python version : 3.6.5.final.0
       base environment : /home/zeru/miniconda3  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/pro/linux-64
                          https://repo.anaconda.com/pkgs/pro/noarch
          package cache : /home/zeru/miniconda3/pkgs
                          /home/zeru/.conda/pkgs
       envs directories : /home/zeru/miniconda3/envs
                          /home/zeru/.conda/envs
               platform : linux-64
             user-agent : conda/4.5.6 requests/2.19.1 CPython/3.6.5 Linux/4.15.0-23-generic ubuntu/18.04 glibc/2.27
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

The text was updated successfully, but these errors were encountered:

isuruf · 2018-07-10T02:25:38Z

For the sagenb error, install sagenb conda package. It was packaged recently and will be installed by default with sage conda package in the future.

For the integrate error, did you try running it in python shell instead of sage shell?

ghost · 2018-07-10T13:09:28Z

installing sagenb fixed the first problem. for sagenb notebook backend. default and export still give a 404 page for jupyter notebook.

what do you mean in python shell? do you mean with sympy? otherwise python does not have symbolic integration

isuruf · 2018-07-10T13:11:48Z

what do you mean in python shell? do you mean with sympy? otherwise python does not have symbolic integration

sage can be used as a normal python library. Can you try the following?

import sage.all as sage
sage.var('x')
sage.integrate(x^2, x)

ghost · 2018-07-10T13:14:49Z

The return seems to be the same:

Python 2.7.14 |Anaconda, Inc.| (default, Nov  8 2017, 22:44:41) 
[GCC 7.2.0] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import sage.all as sage
>>> sage.var('x')
x
>>> sage.integrate('x')
/home/zeru/miniconda3/envs/sage/lib/python2.7/site-packages/sage/symbolic/integration/integral.py:812: DeprecationWarning: Variable of integration should be specified explicitly.
See http://trac.sagemath.org/12438 for details.
  expression, v, a, b = _normalize_integral_input(expression, v, a, b)
------------------------------------------------------------------------
/home/zeru/miniconda3/envs/sage/lib/python2.7/site-packages/cysignals/signals.so(+0x6e45)[0x7f126fa93e45]
/home/zeru/miniconda3/envs/sage/lib/python2.7/site-packages/cysignals/signals.so(+0x6eef)[0x7f126fa93eef]
/home/zeru/miniconda3/envs/sage/lib/python2.7/site-packages/cysignals/signals.so(+0xa815)[0x7f126fa97815]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x12890)[0x7f1273133890]
/home/zeru/miniconda3/envs/sage/lib/python2.7/site-packages/sage/libs/mpmath/ext_impl.so(initext_impl+0x456)[0x7f11965e2f10]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(_PyImport_LoadDynamicModule+0x9e)[0x7f1273436f5e]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xf50f3)[0x7f12734350f3]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xf5348)[0x7f1273435348]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0xfc)[0x7f1273435c9c]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xd8aa6)[0x7f1273418aa6]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7f1273388773]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0x4885c)[0x7f127338885c]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyObject_CallFunction+0x92)[0x7f1273388952]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyImport_Import+0xf8)[0x7f12734367d8]
/home/zeru/miniconda3/envs/sage/lib/python2.7/site-packages/sage/libs/mpmath/ext_libmp.so(+0x4e86)[0x7f1196800e86]
/home/zeru/miniconda3/envs/sage/lib/python2.7/site-packages/sage/libs/mpmath/ext_libmp.so(initext_libmp+0x325)[0x7f119680a26b]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(_PyImport_LoadDynamicModule+0x9e)[0x7f1273436f5e]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xf50f3)[0x7f12734350f3]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xf5348)[0x7f1273435348]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0xfc)[0x7f1273435c9c]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xd8aa6)[0x7f1273418aa6]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7f1273388773]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x48)[0x7f127341a6d8]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x54fd)[0x7f127342012d]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9)[0x7f12734244e9]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCode+0x1a)[0x7f127342470a]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0xae)[0x7f12734341ee]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xf446d)[0x7f127343446d]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xf50f3)[0x7f12734350f3]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xf5348)[0x7f1273435348]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0xbc)[0x7f1273435c5c]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xd8aa6)[0x7f1273418aa6]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7f1273388773]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x48)[0x7f127341a6d8]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x54fd)[0x7f127342012d]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9)[0x7f12734244e9]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCode+0x1a)[0x7f127342470a]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0xae)[0x7f12734341ee]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xf446d)[0x7f127343446d]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xf58ef)[0x7f12734358ef]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xf50f3)[0x7f12734350f3]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xf5348)[0x7f1273435348]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0xbc)[0x7f1273435c5c]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xd8aa6)[0x7f1273418aa6]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7f1273388773]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x48)[0x7f127341a6d8]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x54fd)[0x7f127342012d]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9)[0x7f12734244e9]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCode+0x1a)[0x7f127342470a]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0xae)[0x7f12734341ee]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xf446d)[0x7f127343446d]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xf50f3)[0x7f12734350f3]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xf5348)[0x7f1273435348]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0xbc)[0x7f1273435c5c]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xd8aa6)[0x7f1273418aa6]
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/home/zeru/miniconda3/envs/sage/lib/python2.7/site-packages/sage/symbolic/expression.so(+0x26c10)[0x7f11aefc1c10]
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/home/zeru/miniconda3/envs/sage/lib/python2.7/site-packages/sage/structure/sage_object.so(+0xb34d)[0x7f12672bf34d]
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/home/zeru/miniconda3/envs/sage/lib/python2.7/site-packages/sage/libs/pynac/../../../../../libpynac.so.17(_ZN5GiNaC2ex20construct_from_basicERKNS_5basicE+0x76)[0x7f11af38bb96]
/home/zeru/miniconda3/envs/sage/lib/python2.7/site-packages/sage/symbolic/function.so(_Z16g_function_eval2jRKN5GiNaC2exES2_b+0xb0)[0x7f11ae4b6120]
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/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6852)[0x7f1273421482]
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/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xfd93d)[0x7f127343d93d]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyRun_InteractiveOneFlags+0x15e)[0x7f127343f97e]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyRun_InteractiveLoopFlags+0x5f)[0x7f127343fb1f]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyRun_AnyFileExFlags+0x40)[0x7f1273440160]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(Py_Main+0xbac)[0x7f1273451d3c]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7f12725acb97]
python(+0x87f)[0x5559a607f87f]
------------------------------------------------------------------------
Attaching gdb to process id 29522.
GNU gdb (Ubuntu 8.1-0ubuntu3) 8.1.0.20180409-git
Copyright (C) 2018 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-linux-gnu".
Type "show configuration" for configuration details.
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>.
Find the GDB manual and other documentation resources online at:
<http://www.gnu.org/software/gdb/documentation/>.
For help, type "help".
Type "apropos word" to search for commands related to "word".

Stack backtrace
---------------
Could not attach to process.  If your uid matches the uid of the target
process, check the setting of /proc/sys/kernel/yama/ptrace_scope, or try
again as the root user.  For more details, see /etc/sysctl.d/10-ptrace.conf
ptrace: Operation not permitted.
No stack.
Traceback (most recent call last):
  File "<string>", line 25, in <module>
ModuleNotFoundError: No module named 'Cython'
Error while executing Python code.
warning: Inferior ID 1 is not running.
Saved trace to /home/zeru/Desktop/cysignals_crash_logs/crash_GyCeP_.log
------------------------------------------------------------------------
Unhandled SIGFPE: An unhandled floating point exception occurred.
This probably occurred because a *compiled* module has a bug
in it and is not properly wrapped with sig_on(), sig_off().
Python will now terminate.
------------------------------------------------------------------------
Floating point exception (core dumped)

isuruf · 2018-07-10T13:20:09Z

Thanks for the info. Can you do conda update sagelib and run again?

ghost · 2018-07-10T14:06:43Z

I updated sagelib:


(sage) zeru@ZOS-MATE:~/Desktop$ conda update sagelib
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.5.6
  latest version: 4.5.7

Please update conda by running

    $ conda update -n base conda



## Package Plan ##

  environment location: /home/zeru/miniconda3/envs/sage

  added / updated specs: 
    - sagelib


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    arb-2.12.0                 |       hb705a9b_0         1.9 MB  conda-forge
    twisted-17.5.0             |           py27_0         4.4 MB
    sagelib-8.2                |py27_blas_openblash4416362_5       169.1 MB  conda-forge
    pynac-0.7.16               |   py27h075c78f_1        21.5 MB  conda-forge
    ------------------------------------------------------------
                                           Total:       196.8 MB

The following packages will be REMOVED:

    sage:    8.2-py27_2                       conda-forge

The following packages will be UPDATED:

    sagelib: 8.2-py27_blas_openblash4416362_3 conda-forge [blas_openblas] --> 8.2-py27_blas_openblash4416362_5 conda-forge [blas_openblas]

The following packages will be DOWNGRADED:

    arb:     2.13.0-hb705a9b_1                conda-forge --> 2.12.0-hb705a9b_0                conda-forge
    pynac:   0.7.17-py27h075c78f_1            conda-forge --> 0.7.16-py27h075c78f_1            conda-forge
    twisted: 18.4.0-py27h470a237_0            conda-forge --> 17.5.0-py27_0                               

Proceed ([y]/n)? y


Downloading and Extracting Packages
arb-2.12.0           |  1.9 MB | ############################################################### | 100% 
twisted-17.5.0       |  4.4 MB | ############################################################### | 100% 
sagelib-8.2          | 169.1 MB | ############################################################## | 100% 
pynac-0.7.16         | 21.5 MB | ########################################################################################################################################################################## | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

and then i tried to integrate again, it did not work:

┌────────────────────────────────────────────────────────────────────┐
│ SageMath version 8.2, Release Date: 2018-05-05                     │
│ Type "notebook()" for the browser-based notebook interface.        │
│ Type "help()" for help.                                            │
└────────────────────────────────────────────────────────────────────┘

sage: 
sage: var('x')
x
sage: integrate(x^2,x)
------------------------------------------------------------------------
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/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0x6cfda)[0x7f68f8b5afda]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7f68f8b36773]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0x5750d)[0x7f68f8b4550d]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7f68f8b36773]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xa1574)[0x7f68f8b8f574]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7f68f8b36773]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x190b)[0x7f68f8bca53b]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9)[0x7f68f8bd24e9]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6852)[0x7f68f8bcf482]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9)[0x7f68f8bd24e9]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6852)[0x7f68f8bcf482]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9)[0x7f68f8bd24e9]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6852)[0x7f68f8bcf482]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9)[0x7f68f8bd24e9]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6852)[0x7f68f8bcf482]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9)[0x7f68f8bd24e9]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0x6cfda)[0x7f68f8b5afda]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7f68f8b36773]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0x5750d)[0x7f68f8b4550d]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7f68f8b36773]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0x4885c)[0x7f68f8b3685c]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyObject_CallMethod+0xb0)[0x7f68f8b36bb0]
/home/zeru/miniconda3/envs/sage/lib/python2.7/site-packages/sage/libs/pynac/../../../../../libpynac.so.17(_ZNK5GiNaC8function4evalEi+0x283)[0x7f682ec5c893]
/home/zeru/miniconda3/envs/sage/lib/python2.7/site-packages/sage/libs/pynac/../../../../../libpynac.so.17(_ZN5GiNaC2ex20construct_from_basicERKNS_5basicE+0x76)[0x7f682ec462c6]
/home/zeru/miniconda3/envs/sage/lib/python2.7/site-packages/sage/symbolic/function.so(_Z16g_function_eval2jRKN5GiNaC2exES2_b+0xb0)[0x7f682ddb80f0]
/home/zeru/miniconda3/envs/sage/lib/python2.7/site-packages/sage/symbolic/function.so(+0x34177)[0x7f682ddba177]
/home/zeru/miniconda3/envs/sage/lib/python2.7/site-packages/sage/symbolic/function.so(+0xa8c2)[0x7f682dd908c2]
/home/zeru/miniconda3/envs/sage/lib/python2.7/site-packages/sage/symbolic/function.so(+0x2f828)[0x7f682ddb5828]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7f68f8b36773]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x190b)[0x7f68f8bca53b]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9)[0x7f68f8bd24e9]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0x6d0c7)[0x7f68f8b5b0c7]
/home/zeru/miniconda3/envs/sage/lib/python2.7/site-packages/sage/symbolic/expression.so(+0x83a55)[0x7f682e8e0a55]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6d60)[0x7f68f8bcf990]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9)[0x7f68f8bd24e9]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6852)[0x7f68f8bcf482]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9)[0x7f68f8bd24e9]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCode+0x1a)[0x7f68f8bd270a]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6490)[0x7f68f8bcf0c0]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9)[0x7f68f8bd24e9]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6852)[0x7f68f8bcf482]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9)[0x7f68f8bd24e9]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6852)[0x7f68f8bcf482]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9)[0x7f68f8bd24e9]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6852)[0x7f68f8bcf482]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9)[0x7f68f8bd24e9]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6852)[0x7f68f8bcf482]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9)[0x7f68f8bd24e9]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6852)[0x7f68f8bcf482]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9)[0x7f68f8bd24e9]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6852)[0x7f68f8bcf482]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9)[0x7f68f8bd24e9]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCode+0x1a)[0x7f68f8bd270a]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xfd93d)[0x7f68f8beb93d]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyRun_FileExFlags+0x78)[0x7f68f8becab8]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyRun_SimpleFileExFlags+0xe8)[0x7f68f8bedcd8]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(Py_Main+0xbac)[0x7f68f8bffd3c]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7f68f7d5ab97]
sage-python23(+0x87f)[0x561f40bdd87f]
------------------------------------------------------------------------
Attaching gdb to process id 30461.
GNU gdb (Ubuntu 8.1-0ubuntu3) 8.1.0.20180409-git
Copyright (C) 2018 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-linux-gnu".
Type "show configuration" for configuration details.
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>.
Find the GDB manual and other documentation resources online at:
<http://www.gnu.org/software/gdb/documentation/>.
For help, type "help".
Type "apropos word" to search for commands related to "word".

Stack backtrace
---------------
Could not attach to process.  If your uid matches the uid of the target
process, check the setting of /proc/sys/kernel/yama/ptrace_scope, or try
again as the root user.  For more details, see /etc/sysctl.d/10-ptrace.conf
ptrace: Operation not permitted.
No stack.
Traceback (most recent call last):
  File "<string>", line 25, in <module>
ModuleNotFoundError: No module named 'Cython'
Error while executing Python code.
warning: Inferior ID 1 is not running.
Saved trace to /home/zeru/.sage/crash_logs/crash_7UU3dX.log
------------------------------------------------------------------------
Unhandled SIGFPE: An unhandled floating point exception occurred.
This probably occurred because a *compiled* module has a bug
in it and is not properly wrapped with sig_on(), sig_off().
Python will now terminate.
------------------------------------------------------------------------
Floating point exception (core dumped)

what was most strange was that it removed the sage package in the conda download, but sage still worked... idk what that means.

saraedum · 2018-07-10T14:10:32Z

I can reproduce these errors. I think it's the same floating point exceptions that we see in conda-forge/sagelib-feedstock#19.

isuruf · 2018-07-13T13:56:37Z

@saraedum, can you do conda remove gmpy2 --force and check?

ghost · 2018-07-17T21:56:47Z

@isuruf

i have done as you bid, and here is the result:

>>> import sage.all as sage

>>> sage.var('x')
x
>>> sage.integrate(x^2, x)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "sage/structure/element.pyx", line 953, in sage.structure.element.Element.__xor__ (build/cythonized/sage/structure/element.c:8982)
RuntimeError: Use ** for exponentiation, not '^', which means xor
in Python, and has the wrong precedence.
>>> sage.integrate(x**2, x)
------------------------------------------------------------------------
/home/zeru/miniconda3/envs/sage/lib/python2.7/site-packages/cysignals/signals.so(+0x6e45)[0x7f2cafd49e45]
/home/zeru/miniconda3/envs/sage/lib/python2.7/site-packages/cysignals/signals.so(+0x6eef)[0x7f2cafd49eef]
/home/zeru/miniconda3/envs/sage/lib/python2.7/site-packages/cysignals/signals.so(+0xa815)[0x7f2cafd4d815]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x12890)[0x7f2cb33e9890]
/home/zeru/miniconda3/envs/sage/lib/python2.7/site-packages/sage/libs/mpmath/ext_impl.so(initext_impl+0x456)[0x7f2bd688bf10]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(_PyImport_LoadDynamicModule+0x9e)[0x7f2cb36ecf5e]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xf50f3)[0x7f2cb36eb0f3]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xf5348)[0x7f2cb36eb348]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0xfc)[0x7f2cb36ebc9c]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xd8aa6)[0x7f2cb36ceaa6]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7f2cb363e773]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0x4885c)[0x7f2cb363e85c]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyObject_CallFunction+0x92)[0x7f2cb363e952]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyImport_Import+0xf8)[0x7f2cb36ec7d8]
/home/zeru/miniconda3/envs/sage/lib/python2.7/site-packages/sage/libs/mpmath/ext_libmp.so(+0x4e86)[0x7f2bd6aa9e86]
/home/zeru/miniconda3/envs/sage/lib/python2.7/site-packages/sage/libs/mpmath/ext_libmp.so(initext_libmp+0x325)[0x7f2bd6ab326b]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(_PyImport_LoadDynamicModule+0x9e)[0x7f2cb36ecf5e]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xf50f3)[0x7f2cb36eb0f3]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xf5348)[0x7f2cb36eb348]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0xfc)[0x7f2cb36ebc9c]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xd8aa6)[0x7f2cb36ceaa6]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7f2cb363e773]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x48)[0x7f2cb36d06d8]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x54fd)[0x7f2cb36d612d]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9)[0x7f2cb36da4e9]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCode+0x1a)[0x7f2cb36da70a]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0xae)[0x7f2cb36ea1ee]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xf446d)[0x7f2cb36ea46d]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xf50f3)[0x7f2cb36eb0f3]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xf5348)[0x7f2cb36eb348]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0xbc)[0x7f2cb36ebc5c]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xd8aa6)[0x7f2cb36ceaa6]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7f2cb363e773]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x48)[0x7f2cb36d06d8]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x54fd)[0x7f2cb36d612d]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9)[0x7f2cb36da4e9]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCode+0x1a)[0x7f2cb36da70a]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0xae)[0x7f2cb36ea1ee]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xf446d)[0x7f2cb36ea46d]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xf58ef)[0x7f2cb36eb8ef]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xf50f3)[0x7f2cb36eb0f3]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xf5348)[0x7f2cb36eb348]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0xbc)[0x7f2cb36ebc5c]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xd8aa6)[0x7f2cb36ceaa6]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7f2cb363e773]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x48)[0x7f2cb36d06d8]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x54fd)[0x7f2cb36d612d]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9)[0x7f2cb36da4e9]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCode+0x1a)[0x7f2cb36da70a]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0xae)[0x7f2cb36ea1ee]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xf446d)[0x7f2cb36ea46d]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xf50f3)[0x7f2cb36eb0f3]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xf5348)[0x7f2cb36eb348]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0xbc)[0x7f2cb36ebc5c]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xd8aa6)[0x7f2cb36ceaa6]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7f2cb363e773]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x48)[0x7f2cb36d06d8]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x54fd)[0x7f2cb36d612d]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9)[0x7f2cb36da4e9]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCode+0x1a)[0x7f2cb36da70a]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0xae)[0x7f2cb36ea1ee]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xf446d)[0x7f2cb36ea46d]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xf50f3)[0x7f2cb36eb0f3]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xf5348)[0x7f2cb36eb348]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0xbc)[0x7f2cb36ebc5c]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(+0xd8aa6)[0x7f2cb36ceaa6]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7f2cb363e773]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x48)[0x7f2cb36d06d8]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x54fd)[0x7f2cb36d612d]
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/home/zeru/miniconda3/envs/sage/lib/python2.7/site-packages/sage/libs/pynac/../../../../../libpynac.so.17(_ZN5GiNaC2ex20construct_from_basicERKNS_5basicE+0x76)[0x7f2bef62d2c6]
/home/zeru/miniconda3/envs/sage/lib/python2.7/site-packages/sage/symbolic/function.so(_Z16g_function_eval2jRKN5GiNaC2exES2_b+0xb0)[0x7f2bee75f0f0]
/home/zeru/miniconda3/envs/sage/lib/python2.7/site-packages/sage/symbolic/function.so(+0x34177)[0x7f2bee761177]
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/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyRun_InteractiveOneFlags+0x15e)[0x7f2cb36f597e]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyRun_InteractiveLoopFlags+0x5f)[0x7f2cb36f5b1f]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(PyRun_AnyFileExFlags+0x40)[0x7f2cb36f6160]
/home/zeru/miniconda3/envs/sage/bin/../lib/libpython2.7.so.1.0(Py_Main+0xbac)[0x7f2cb3707d3c]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7f2cb2862b97]
python(+0x87f)[0x55b5a614f87f]
------------------------------------------------------------------------
Attaching gdb to process id 28807.
GNU gdb (Ubuntu 8.1-0ubuntu3) 8.1.0.20180409-git
Copyright (C) 2018 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-linux-gnu".
Type "show configuration" for configuration details.
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>.
Find the GDB manual and other documentation resources online at:
<http://www.gnu.org/software/gdb/documentation/>.
For help, type "help".
Type "apropos word" to search for commands related to "word".

Stack backtrace
---------------
Could not attach to process.  If your uid matches the uid of the target
process, check the setting of /proc/sys/kernel/yama/ptrace_scope, or try
again as the root user.  For more details, see /etc/sysctl.d/10-ptrace.conf
ptrace: Operation not permitted.
No stack.
Traceback (most recent call last):
  File "<string>", line 25, in <module>
ModuleNotFoundError: No module named 'Cython'
Error while executing Python code.
warning: Inferior ID 1 is not running.
Saved trace to /home/zeru/.sage/crash_logs/crash_NoRYOK.log
------------------------------------------------------------------------
Unhandled SIGFPE: An unhandled floating point exception occurred.
This probably occurred because a *compiled* module has a bug
in it and is not properly wrapped with sig_on(), sig_off().
Python will now terminate.
------------------------------------------------------------------------
Floating point exception (core dumped)

clearly, it does not seem to solve the problem, but perhaps there is something in cysignals which is causing the error cascade?

ghost · 2018-08-23T00:01:26Z

So uh, an update on this issue, since i have been playing around with sage for the first time in a while

The problem is solved by plotting something first, then going about any integral business one may have afterward. By doing:

plot(x)
then following up with an integral the function seems to work fine.
I have absolutely no idea what causes this
This is both a sage shell and notebook issue

isuruf · 2018-08-23T00:02:53Z

Can you try doing conda install conda-forge::python?

MohamedAbdulHameed · 2018-10-28T01:18:47Z

I have the same issue. I decided to remove sage from conda and install is independently. So any advice on how to remove it from conda?

ickc · 2018-11-17T06:23:27Z

So any advice on how to remove it from conda?

This really depends on how you install it in the first place. Did you create a new conda environment just for sage? Or did you install it in-place of another environment?

# remove an entire environment
conda remove --name SAGE_ENVIRONMENT_NAME_HERE --all
# remove sage from an existing environment
conda remove --name NAME sage

ghost closed this as completed Jan 30, 2019

This issue was closed.

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Sage Notebook does not open properly when installed using Conda #21

Sage Notebook does not open properly when installed using Conda #21

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ickc commented Nov 17, 2018

Sage Notebook does not open properly when installed using Conda #21

Sage Notebook does not open properly when installed using Conda #21

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