[sage-support] 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 
>::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 
>::__vdeallocate()

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

I appreciate any help you can give me.  Thanks!

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***

IPython post-mortem report

{'commit_hash': u'033ab93c7',
 'commit_source': 'installation',
 'default_encoding': 'UTF-8',
 'ipython_path': 
'/Users/myusername/.continuum/miniconda3.7/envs/sage27/lib/python2.7/site-packages/IPython',
 'ipython_version': '5.8.0',
 'os_name': 'posix',
 'platform': 'Darwin-17.7.0-x86_64-i386-64bit',
 'sys_executable': 
'/Users/myusername/.continuum/miniconda3.7/envs/sage27/bin/sage-python23',
 'sys_platform': 'darwin',
 'sys_version': '2.7.15 | packaged by conda-forge | (default, Jul  2 2019, 
00:42:22) \n[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)]'}

***



***

Crash traceback:

---
---
ImportErrorPython 2.7.15: 
/Users/myusername/.continuum/miniconda3.7/envs/sage27/bin/sage-python23
   Tue Nov 19 10:34:11 2019
A problem occurred executing Python code.  Here is the sequence of function
calls leading up to the error, with the most recent (innermost) call last.
/Users/myusername/.continuum/miniconda3.7/envs/sage27/bin/sage-ipython in 
()
  1 #!/usr/bin/env sage-python23
  2 # -*- coding: utf-8 -*-
  3 """
  4 Sage IPython startup script.
  5 """
  6 
  7 # Display startup banner. Do this before anything else to give the user
  8 # early feedback that Sage is starting.
  9 from sage.misc.banner import banner
 10 banner()
 11 
 12 from sage.repl.interpreter import SageTerminalApp
 13 
 14 app = SageTerminalApp.instance()
---> 15 app.initialize()
global app.initialize = >
 16 app.start()


 in initialize(self=, argv=None)

/Users/myusername/.continuum/miniconda3.7/envs/sage27/lib/python2.7/site-packages/traitlets/config/application.pyc
 in catch_config_error(method=, 
app=, *args=(None,), **kwargs={})
 72 TRAITLETS_APPLICATION_RAISE_CONFIG_FILE_ERROR = False
 73 else:
 74 raise ValueError("Unsupported value for environment variable: 
'TRAITLETS_APPLICATION_RAISE_CONFIG_FILE_ERROR' is set to '%s' which is none of 
 {'0', '1', 'false', 'true', ''}."% _envvar )
 75 
 76 
 77 @decorator
 78 def catch_config_error(method, app, *args, **kwargs):
 79 """Method decorator for catching invalid config 
(Trait/ArgumentErrors) during init.
 80 
 81 On a TraitError (generally caused by bad config), this will print 
the trait's
 82 message, and exit the app.
 83 
 84 For use on init methods, to prevent invoking excepthook on invalid 
input.
 85 """
 86 try:
---> 87 return method(app, *args, **kwargs)
method = 
app = 
args = (None,)
kwargs = {}
 88 except (TraitError, ArgumentError) as e:
 89 app.print_help()
 90 app.log.fatal("Bad conf

[sage-support] Re: Sage Crash Report: Missing symbols in conda build for macOS?

[Michael Boyle]

Sure.  Here it is:

> conda list
# packages in environment at 
/Users/myusername/.continuum/miniconda3.7/envs/sage27:
#
# NameVersion   Build  Channel
_r-mutex  1.0.1   anacondar_1conda-forge
alabaster 0.7.12 py_0conda-forge
appdirs   1.4.3  py_1conda-forge
appnope   0.1.0 py27_1000conda-forge
arb   2.16.0h3aece09_1000conda-forge
attrs 19.3.0 py_0conda-forge
automat   0.8.0  py_0conda-forge
babel 2.7.0  py_0conda-forge
backports 1.0py_2conda-forge
backports.functools_lru_cache 1.6.1  py_0conda-forge
backports.os  0.1.1 py27_1001conda-forge
backports.shutil_get_terminal_size 1.0.0  py_3
conda-forge
backports_abc 0.5py_1conda-forge
bdw-gc8.0.4ha1b3eb9_0conda-forge
bleach3.1.0  py_0conda-forge
brial 1.2.5  py_1conda-forge
bwidget   1.9.130conda-forge
bzip2 1.0.8h01d97ff_1conda-forge
ca-certificates   2019.9.11hecc5488_0conda-forge
cairo 1.16.0he1c11cd_1002conda-forge
cctools   921  h5ba7a2e_4conda-forge
cddlib1!0.94j   h65ac59c_1001conda-forge
certifi   2019.9.11py27_0conda-forge
cffi  1.13.2   py27h33e799b_0conda-forge
chardet   3.0.4 py27_1003conda-forge
clang 9.0.0   default_hf57f61e_4conda-forge
clang_osx-64  9.0.0h22b1bf0_3conda-forge
clangxx   9.0.0   default_hf57f61e_4conda-forge
clangxx_osx-649.0.0h22b1bf0_3conda-forge
click 7.0py_0conda-forge
cliquer   1.21  h1de35cc_1000conda-forge
compiler-rt   9.0.0h2b4a0d1_1conda-forge
configparser  3.7.3py27_1conda-forge
constantly15.1.0 py_0conda-forge
contextlib2   0.6.0.post1py_0conda-forge
cryptography  2.8  py27hafa8578_0conda-forge
curl  7.65.3   h22ea746_0conda-forge
cvxopt1.2.3   py27h43946de_203conda-forge
cycler0.10.0 py_2conda-forge
cypari2   2.1.1py27h7c56200_0conda-forge
cysignals 1.10.2   py27hba7914e_1conda-forge
cython0.29.14  py27h4a8c4bd_0conda-forge
decorator 4.4.1  py_0conda-forge
defusedxml0.6.0  py_0conda-forge
docutils  0.15.2   py27_0conda-forge
dsdp  5.8   h7674d01_1203conda-forge
ecl   16.1.2h0672242_1004conda-forge
eclib 20190226 he5f4af6_2conda-forge
ecm   7.0.4 h65ac59c_1002conda-forge
entrypoints   0.3   py27_1000conda-forge
enum341.1.6 py27_1002conda-forge
expat 2.2.5 h4a8c4bd_1004conda-forge
fastcache 1.1.0py27h0b31af3_0conda-forge
fflas-ffpack  2.4.3h75e9206_1conda-forge
fftw  3.3.8   nompi_h44ae4c8_1110conda-forge
flask 0.11.1 py_1conda-forge
flask-autoindex   0.6.2  py_0conda-forge
flask-babel   0.12.2 py_0conda-forge
flask-oldsessions 0.10   py_0conda-forge
flask-openid  1.2.5 py27_1003conda-forge
flask-silk0.2py_0conda-forge
flintqs   1.0   hc269f14_1000conda-forge
fontconfig2.13.1h6b1039f_1001conda-forge
fplll 5.2.1 hc88034f_1000conda-forge
fpylll0.4.1devpy27heb9bef1_1000conda-forge
freetype  2.10.0

Re: [sage-support] Re: Sage Crash Report: Missing symbols in conda build for macOS?

[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!

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