Sage Crash Report: Missing symbols in conda build for macOS?

[Michael Boyle]

I followed the installation instructions for conda with both
python=3.6 (the most recent version that could install sage without
conflicts) and then python=2.7 (the one specifically cited in the
instructions) on macOS 10.13.6, using miniconda3.7.  Both complete
installation happily, but sage immediately dies in both environment.s
I have never used Sage before, so I have no Sage configuration, and I had
no input history during the session because I literally just typed `sage`

on the command line and it failed.  I use conda frequently, and don't usually

have problems, so I doubt that it's anything very specific to my setup.

Both 3.6 and 2.7 fail in the same way: there's a missing symbol from some
dylib.  The symbol is

    __ZNSt3__16vectorIN5GiNaC2exENS_9allocatorIS2_EEE10deallocateEv

which demangles to

    std::__1::vector<GiNaC::ex, std::__1::allocator<GiNaC::ex> >::deallocate()

So I guess that's not getting included in lib, somehow.  The full report
for 2.7 is attached — though the 3.6 report is essentially identical.

I've searched through every dylib that conda installs in envs/sage/lib, and
the only similar symbol I find is

    __ZNSt3__16vectorIN5GiNaC2exENS_9allocatorIS2_EEE13__vdeallocateEv

which is in libpynac.dylib -> libpynac.18.dylib, and demangles to

    std::__1::vector<GiNaC::ex, std::__1::allocator<GiNaC::ex> >::__vdeallocate()

I wonder if it's related to https://github.com/pynac/pynac/issues/239.

I appreciate any help you can give me.  Thanks!

[Julian Rüth]

Hi Micheal,

could you share the output of `conda list` for that environment?

Feel free to open an issue for this at https://github.com/conda-forge/sage-feedstock/issues as well.

julian

[Michael Boyle]

Sure.  Here it is:

> conda list
# packages in environment at /Users/myusername/.continuum/miniconda3.7/envs/sage27:
#
# Name                    Version                   Build  Channel
_r-mutex                  1.0.1               anacondar_1    conda-forge
alabaster                 0.7.12                     py_0    conda-forge
appdirs                   1.4.3                      py_1    conda-forge
appnope                   0.1.0                 py27_1000    conda-forge
arb                       2.16.0            h3aece09_1000    conda-forge
attrs                     19.3.0                     py_0    conda-forge
automat                   0.8.0                      py_0    conda-forge
babel                     2.7.0                      py_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.1                      py_0    conda-forge
backports.os              0.1.1                 py27_1001    conda-forge
backports.shutil_get_terminal_size 1.0.0                      py_3    conda-forge
backports_abc             0.5                        py_1    conda-forge
bdw-gc                    8.0.4                ha1b3eb9_0    conda-forge
bleach                    3.1.0                      py_0    conda-forge
brial                     1.2.5                      py_1    conda-forge
bwidget                   1.9.13                        0    conda-forge
bzip2                     1.0.8                h01d97ff_1    conda-forge
ca-certificates           2019.9.11            hecc5488_0    conda-forge
cairo                     1.16.0            he1c11cd_1002    conda-forge
cctools                   921                  h5ba7a2e_4    conda-forge
cddlib                    1!0.94j           h65ac59c_1001    conda-forge
certifi                   2019.9.11                py27_0    conda-forge
cffi                      1.13.2           py27h33e799b_0    conda-forge
chardet                   3.0.4                 py27_1003    conda-forge
clang                     9.0.0           default_hf57f61e_4    conda-forge
clang_osx-64              9.0.0                h22b1bf0_3    conda-forge
clangxx                   9.0.0           default_hf57f61e_4    conda-forge
clangxx_osx-64            9.0.0                h22b1bf0_3    conda-forge
click                     7.0                        py_0    conda-forge
cliquer                   1.21              h1de35cc_1000    conda-forge
compiler-rt               9.0.0                h2b4a0d1_1    conda-forge
configparser              3.7.3                    py27_1    conda-forge
constantly                15.1.0                     py_0    conda-forge
contextlib2               0.6.0.post1                py_0    conda-forge
cryptography              2.8              py27hafa8578_0    conda-forge
curl                      7.65.3               h22ea746_0    conda-forge
cvxopt                    1.2.3           py27h43946de_203    conda-forge
cycler                    0.10.0                     py_2    conda-forge
cypari2                   2.1.1            py27h7c56200_0    conda-forge
cysignals                 1.10.2           py27hba7914e_1    conda-forge
cython                    0.29.14          py27h4a8c4bd_0    conda-forge
decorator                 4.4.1                      py_0    conda-forge
defusedxml                0.6.0                      py_0    conda-forge
docutils                  0.15.2                   py27_0    conda-forge
dsdp                      5.8               h7674d01_1203    conda-forge
ecl                       16.1.2            h0672242_1004    conda-forge
eclib                     20190226             he5f4af6_2    conda-forge
ecm                       7.0.4             h65ac59c_1002    conda-forge
entrypoints               0.3                   py27_1000    conda-forge
enum34                    1.1.6                 py27_1002    conda-forge
expat                     2.2.5             h4a8c4bd_1004    conda-forge
fastcache                 1.1.0            py27h0b31af3_0    conda-forge
fflas-ffpack              2.4.3                h75e9206_1    conda-forge
fftw                      3.3.8           nompi_h44ae4c8_1110    conda-forge
flask                     0.11.1                     py_1    conda-forge
flask-autoindex           0.6.2                      py_0    conda-forge
flask-babel               0.12.2                     py_0    conda-forge
flask-oldsessions         0.10                       py_0    conda-forge
flask-openid              1.2.5                 py27_1003    conda-forge
flask-silk                0.2                        py_0    conda-forge
flintqs                   1.0               hc269f14_1000    conda-forge
fontconfig                2.13.1            h6b1039f_1001    conda-forge
fplll                     5.2.1             hc88034f_1000    conda-forge
fpylll                    0.4.1dev        py27heb9bef1_1000    conda-forge
freetype                  2.10.0               h24853df_1    conda-forge
fribidi                   1.0.5             h01d97ff_1002    conda-forge
functools32               3.2.3.2                    py_3    conda-forge
future                    0.18.2                   py27_0    conda-forge
futures                   3.3.0                    py27_0    conda-forge
gap-core                  4.10.2               h9d095d4_4    conda-forge
gap-defaults              4.10.2                        4    conda-forge
gettext                   0.19.8.1          h46ab8bc_1002    conda-forge
gf2x                      1.2               h79ef2f9_1003    conda-forge
gfan                      0.6.2             h8d1d06b_1001    conda-forge
gfortran_impl_osx-64      7.3.0                hf4212f2_2    conda-forge
gfortran_osx-64           7.3.0                h22b1bf0_6    conda-forge
giac                      1.5.0.63             h63cb9ca_2    conda-forge
giflib                    5.1.7                h01d97ff_1    conda-forge
givaro                    4.1.1                hd0e5c4b_0    conda-forge
glib                      2.58.3          py27h577aef8_1002    conda-forge
glpk                      4.65              h65ac59c_1002    conda-forge
gmp                       6.1.2             h0a44026_1000    conda-forge
gmpy2                     2.1.0b1          py27h4160ff4_0    conda-forge
graphite2                 1.3.13            h2098e52_1000    conda-forge
gsl                       2.5                  ha2d443c_1    conda-forge
harfbuzz                  2.4.0                hd8d2a14_3    conda-forge
hyperlink                 17.3.1                     py_0    conda-forge
icu                       64.2                 h6de7cb9_1    conda-forge
idna                      2.8                   py27_1000    conda-forge
imagesize                 1.1.0                      py_0    conda-forge
iml                       1.0.5             hd3f3b21_1002    conda-forge
importlib_metadata        0.23                     py27_0    conda-forge
incremental               17.5.0                     py_0    conda-forge
ipaddress                 1.0.23                     py_0    conda-forge
ipykernel                 4.10.0                   py27_0    conda-forge
ipython                   5.8.0                    py27_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.5.1                      py_0    conda-forge
isl                       0.19                          0    conda-forge
itsdangerous              1.1.0                      py_0    conda-forge
jinja2                    2.10.3                     py_0    conda-forge
jmol                      14.29.15                      2    conda-forge
jpeg                      9c                h1de35cc_1001    conda-forge
jsonschema                3.0.0a3               py27_1000    conda-forge
jupyter_client            5.3.3                    py27_1    conda-forge
jupyter_core              4.6.1                    py27_0    conda-forge
kiwisolver                1.1.0            py27ha1b3eb9_0    conda-forge
krb5                      1.16.3            hcfa6398_1001    conda-forge
lcalc                     1.23              h3002b05_1004    conda-forge
ld64                      409.12               h3c32e8a_4    conda-forge
libblas                   3.8.0               14_openblas    conda-forge
libbraiding               1.0                  h4a8c4bd_0    conda-forge
libbrial                  1.2.5                h4c4dbc1_1    conda-forge
libcblas                  3.8.0               14_openblas    conda-forge
libcurl                   7.65.3               h16faf7d_0    conda-forge
libcxx                    9.0.0                h89e68fa_1    conda-forge
libedit                   3.1.20170329      hcfe32e1_1001    conda-forge
libffi                    3.2.1             h6de7cb9_1006    conda-forge
libflint                  2.5.2             h6b09787_1003    conda-forge
libgd                     2.2.5             h5f83dcc_1006    conda-forge
libgfortran               4.0.0                         2    conda-forge
libhomfly                 1.02r6               h0b31af3_0    conda-forge
libiconv                  1.15              h01d97ff_1005    conda-forge
liblapack                 3.8.0               14_openblas    conda-forge
liblapacke                3.8.0               14_openblas    conda-forge
libllvm9                  9.0.0                h770b8ee_3    conda-forge
libopenblas               0.3.7                h4bb4525_3    conda-forge
libpng                    1.6.37               h2573ce8_0    conda-forge
libsodium                 1.0.17               h01d97ff_0    conda-forge
libssh2                   1.8.2                hcdc9a53_2    conda-forge
libtiff                   4.1.0                ha78913b_1    conda-forge
libwebp                   1.0.2                h20df551_3    conda-forge
libxml2                   2.9.10               h53d96d6_0    conda-forge
linbox                    1.6.3                h81b89f1_2    conda-forge
llvm-openmp               9.0.0                h40edb58_0    conda-forge
lrcalc                    1.2               h4a8c4bd_1000    conda-forge
lz4-c                     1.8.3             h6de7cb9_1001    conda-forge
m4ri                      20140914          h8da9a1a_1004    conda-forge
m4rie                     20150908          h8da9a1a_1001    conda-forge
make                      4.2.1             h1de35cc_2004    conda-forge
markupsafe                1.1.1            py27h0b31af3_0    conda-forge
matplotlib-base           2.2.4            py27h11da6c2_2    conda-forge
maxima                    5.42.2               h11d4597_2    conda-forge
metis                     5.1.0             h4a8c4bd_1005    conda-forge
mistune                   0.8.4           py27h0b31af3_1000    conda-forge
more-itertools            5.0.0                      py_0    conda-forge
mpc                       1.1.0             h4160ff4_1006    conda-forge
mpfi                      1.5.4             h4160ff4_1001    conda-forge
mpfr                      4.0.2                h44b798e_0    conda-forge
mpmath                    1.1.0                      py_0    conda-forge
nauty                     2.6.11               h0b31af3_0    conda-forge
nbconvert                 5.6.1                    py27_0    conda-forge
nbformat                  4.4.0                      py_1    conda-forge
ncurses                   6.1               h0a44026_1002    conda-forge
networkx                  2.2                        py_1    conda-forge
notebook                  5.7.8                    py27_1    conda-forge
ntl                       11.3.2            hc68a196_1000    conda-forge
numpy                     1.16.5           py27hde6bac1_0    conda-forge
olefile                   0.46                       py_0    conda-forge
openjdk                   11.0.1            h01d97ff_1017    conda-forge
openssl                   1.1.1d               h0b31af3_0    conda-forge
packaging                 19.2                       py_0    conda-forge
palp                      2.1               h0b31af3_1000    conda-forge
pandoc                    2.7.3                         0    conda-forge
pandocfilters             1.4.2                      py_1    conda-forge
pango                     1.42.4               h6691c8e_1    conda-forge
pari                      2.11.1          pl526h5f483b1_2    conda-forge
pari-galdata              0.0.20180411                  0    conda-forge
pari-seadata-small        0.0.20090618                  0    conda-forge
path.py                   11.5.2                     py_0    conda-forge
pathlib2                  2.3.5                    py27_0    conda-forge
pcre                      8.43                 h4a8c4bd_0    conda-forge
perl                      5.26.2            haec8ef5_1006    conda-forge
pexpect                   4.7.0                    py27_0    conda-forge
pickleshare               0.7.5                 py27_1000    conda-forge
pillow                    5.4.1           py27hbddbef0_1000    conda-forge
pip                       19.3.1                   py27_0    conda-forge
pixman                    0.38.0            h01d97ff_1003    conda-forge
pkg-config                0.29.2            h112b980_1005    conda-forge
pkgconfig                 1.3.1                 py27_1001    conda-forge
planarity                 3.0.0.5           h0b31af3_1002    conda-forge
ppl                       1.2               h454970b_1003    conda-forge
pplpy                     0.8.4            py27h06f2a49_0    conda-forge
prometheus_client         0.7.1                      py_0    conda-forge
prompt_toolkit            1.0.15                     py_1    conda-forge
psutil                    5.6.5            py27h0b31af3_0    conda-forge
ptyprocess                0.6.0                   py_1001    conda-forge
pyasn1                    0.4.8                      py_0    conda-forge
pyasn1-modules            0.2.7                      py_0    conda-forge
pycparser                 2.19                     py27_1    conda-forge
pygments                  2.4.2                      py_0    conda-forge
pyhamcrest                1.9.0                      py_2    conda-forge
pynac                     0.7.26           py27h7100b18_1    conda-forge
pyopenssl                 19.0.0                   py27_0    conda-forge
pyparsing                 2.4.5                      py_0    conda-forge
pyrsistent                0.15.5           py27h0b31af3_0    conda-forge
pysocks                   1.7.1                    py27_0    conda-forge
python                    2.7.15            hd51d24c_1009    conda-forge
python-dateutil           2.8.1                      py_0    conda-forge
python-openid             2.2.5                 py27_1000    conda-forge
pytz                      2019.3                     py_0    conda-forge
pyzmq                     18.1.1           py27h4bf09a9_0    conda-forge
qd                        2.3.22            hd17c0aa_1003    conda-forge
r-base                    3.6.1                h8cbdff8_5    conda-forge
ratpoints                 2.1.3             h65ac59c_1002    conda-forge
readline                  8.0                  hcfe32e1_0    conda-forge
requests                  2.22.0                   py27_1    conda-forge
rpy2                      2.8.6           py27r36hfc83f80_2    conda-forge
rubiks                    20070912          h4a8c4bd_1001    conda-forge
rw                        0.7                           1    conda-forge
sage                      8.9                      py27_0    conda-forge
sagelib                   8.9              py27h376306d_0    conda-forge
sagemath-db-combinatorial-designs 20140630                      1    conda-forge
sagemath-db-conway-polynomials 0.5.0            py27hecc5488_0    conda-forge
sagemath-db-elliptic-curves 0.8.1                hecc5488_0    conda-forge
sagemath-db-graphs        20161026                      1    conda-forge
sagemath-db-polytopes     20170220                      1    conda-forge
sagenb                    1.1.2                      py_2    conda-forge
sagetex                   3.3                        py_0    conda-forge
scandir                   1.10.0           py27h0b31af3_0    conda-forge
scipy                     1.2.1            py27h7e0e109_2    conda-forge
send2trash                1.5.0                      py_0    conda-forge
service_identity          18.1.0                     py_0    conda-forge
setuptools                41.6.0                   py27_1    conda-forge
simplegeneric             0.8.1                      py_1    conda-forge
singledispatch            3.4.0.3               py27_1000    conda-forge
singular                  4.1.1.p2             he86d511_1    conda-forge
six                       1.13.0                   py27_0    conda-forge
snowballstemmer           2.0.0                      py_0    conda-forge
sphinx                    1.8.5                    py27_0    conda-forge
sphinxcontrib-websupport  1.1.2                      py_0    conda-forge
sqlite                    3.30.1               h93121df_0    conda-forge
ssl_match_hostname        3.7.0.1                 py_1000    conda-forge
subprocess32              3.5.4            py27h0b31af3_0    conda-forge
suitesparse               4.5.6             h873bc41_1204    conda-forge
symmetrica                2.0               h6de7cb9_1007    conda-forge
sympow                    2.023.3           hf867438_1003    conda-forge
sympy                     1.4                      py27_0    conda-forge
tachyon                   0.99b6            h6e808b8_1001    conda-forge
tapi                      1000.10.8            h770b8ee_3    conda-forge
tbb                       2019.9               ha1b3eb9_0    conda-forge
terminado                 0.8.3                    py27_0    conda-forge
testpath                  0.4.4                      py_0    conda-forge
three.js                  105                           0    conda-forge
tk                        8.6.9             h2573ce8_1003    conda-forge
tktable                   2.10                 h008db23_3    conda-forge
tornado                   4.5.3           py27h1de35cc_1001    conda-forge
traitlets                 4.3.3                    py27_0    conda-forge
twisted                   18.9.0          py27h1de35cc_1000    conda-forge
typing                    3.7.4.1                  py27_0    conda-forge
urllib3                   1.25.7                   py27_0    conda-forge
wcwidth                   0.1.7                      py_1    conda-forge
webencodings              0.5.1                      py_1    conda-forge
werkzeug                  0.16.0                     py_0    conda-forge
wheel                     0.33.6                   py27_0    conda-forge
widgetsnbextension        3.5.1                    py27_0    conda-forge
xz                        5.2.4             h1de35cc_1001    conda-forge
zeromq                    4.3.2                h6de7cb9_2    conda-forge
zipp                      0.6.0                      py_0    conda-forge
zlib                      1.2.11            h0b31af3_1006    conda-forge
zn_poly                   0.9.1                h65ac59c_0    conda-forge
zope.interface            4.7.1            py27h0b31af3_0    conda-forge
zstd                      1.4.4                he7fca8b_1    conda-forge

[Isuru Fernando]

Hi,

Can you try doing the following?

conda install -n sage27 "pynac=0.7.26=py27ha01bd41_0"

Isuru

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[Michael Boyle]

That works!  Similarly

conda install -n sage "pynac=0.7.26=py36ha01bd41_0"

works for my python 3.6 attempt.  I see that you've already opened an issue on pynac-feedstock, so I'll leave you to it.

Thanks very much for you help!