conda update breaks conda #6787
Description
I'm submitting a...
- [ ✓] bug report
- feature request
Current Behavior
Updating conda breaks conda.
(base) [user@comet-ln40 ~]$ conda install -c atztogo phonopy
Solving environment: failed
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/home/protik/anaconda3/lib/python3.6/site-packages/conda/common/io.py", line 399, in backdown_thread_pool
yield ThreadPoolExecutor(max_workers)
File "/home/protik/anaconda3/lib/python3.6/site-packages/conda/core/index.py", line 214, in get_reduced_index
new_records = query_all(spec)
File "/home/protik/anaconda3/lib/python3.6/site-packages/conda/core/index.py", line 187, in query_all
return tuple(concat(future.result() for future in as_completed(futures)))
File "/home/protik/anaconda3/lib/python3.6/site-packages/conda/core/index.py", line 187, in <genexpr>
return tuple(concat(future.result() for future in as_completed(futures)))
File "/home/protik/anaconda3/lib/python3.6/concurrent/futures/_base.py", line 217, in as_completed
fs = set(fs)
File "/home/protik/anaconda3/lib/python3.6/site-packages/conda/core/index.py", line 186, in <genexpr>
futures = (executor.submit(sd.query, spec) for sd in subdir_datas)
File "/home/protik/anaconda3/lib/python3.6/concurrent/futures/thread.py", line 123, in submit
self._adjust_thread_count()
File "/home/protik/anaconda3/lib/python3.6/concurrent/futures/thread.py", line 142, in _adjust_thread_count
t.start()
File "/home/protik/anaconda3/lib/python3.6/threading.py", line 846, in start
_start_new_thread(self._bootstrap, ())
RuntimeError: can't start new thread
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/protik/anaconda3/lib/python3.6/site-packages/conda/exceptions.py", line 743, in __call__
return func(*args, **kwargs)
File "/home/protik/anaconda3/lib/python3.6/site-packages/conda/cli/main.py", line 78, in _main
exit_code = do_call(args, p)
File "/home/protik/anaconda3/lib/python3.6/site-packages/conda/cli/conda_argparse.py", line 76, in do_call
exit_code = getattr(module, func_name)(args, parser)
File "/home/protik/anaconda3/lib/python3.6/site-packages/conda/cli/main_remove.py", line 84, in execute
txn = solver.solve_for_transaction(force_remove=args.force)
File "/home/protik/anaconda3/lib/python3.6/site-packages/conda/core/solve.py", line 504, in solve_for_transaction
force_remove, force_reinstall)
File "/home/protik/anaconda3/lib/python3.6/site-packages/conda/core/solve.py", line 437, in solve_for_diff
final_precs = self.solve_final_state(deps_modifier, prune, ignore_pinned, force_remove)
File "/home/protik/anaconda3/lib/python3.6/site-packages/conda/core/solve.py", line 178, in solve_final_state
index, r = self._prepare(prepared_specs)
File "/home/protik/anaconda3/lib/python3.6/site-packages/conda/core/solve.py", line 560, in _prepare
self.subdirs, prepared_specs)
File "/home/protik/anaconda3/lib/python3.6/site-packages/conda/core/index.py", line 249, in get_reduced_index
return reduced_index
File "/home/protik/anaconda3/lib/python3.6/contextlib.py", line 126, in __exit__
raise RuntimeError("generator didn't stop after throw()")
RuntimeError: generator didn't stop after throw()Steps to Reproduce
conda update conda
conda install <something>
Expected Behavior
Conda should gracefully update instead breaking everything.
Environment Information
`conda info`
active environment : base
active env location : /home/protik/anaconda3
shell level : 1
user config file : /home/protik/.condarc
populated config files : /home/protik/.condarc
conda version : 4.4.7
conda-build version : 3.0.27
python version : 3.6.3.final.0
base environment : /home/protik/anaconda3 (writable)
channel URLs : https://repo.continuum.io/pkgs/main/linux-64
https://repo.continuum.io/pkgs/main/noarch
https://repo.continuum.io/pkgs/free/linux-64
https://repo.continuum.io/pkgs/free/noarch
https://repo.continuum.io/pkgs/r/linux-64
https://repo.continuum.io/pkgs/r/noarch
https://repo.continuum.io/pkgs/pro/linux-64
https://repo.continuum.io/pkgs/pro/noarch
package cache : /home/protik/anaconda3/pkgs
/home/protik/.conda/pkgs
envs directories : /home/protik/anaconda3/envs
/home/protik/.conda/envs
platform : linux-64
user-agent : conda/4.4.7 requests/2.18.4 CPython/3.6.3 Linux/2.6.32-696.18.7.el6.x86_64 centos/6.7 glibc/2.12
UID:GID : 511506:8288
netrc file : None
offline mode : False
`conda config --show-sources`
==> /home/protik/anaconda3/.condarc <==
pinned_packages:
- conda-canary::conda
==> /home/protik/.condarc <==
report_errors: True
`conda list --show-channel-urls`
# packages in environment at /home/user/anaconda3:
#
_ipyw_jlab_nb_ext_conf 0.1.0 py36he11e457_0 defaults
alabaster 0.7.10 py36h306e16b_0 defaults
anaconda custom py36hbbc8b67_0 defaults
anaconda-client 1.6.5 py36h19c0dcd_0 defaults
anaconda-navigator 1.6.9 py36h11ddaaa_0 defaults
anaconda-project 0.8.0 py36h29abdf5_0 defaults
ase 3.15.0 <pip>
ase 3.15.0 py36_3 conda-forge
asn1crypto 0.22.0 py36h265ca7c_1 defaults
astroid 1.5.3 py36hbdb9df2_0 defaults
astropy 2.0.2 py36ha51211e_4 defaults
babel 2.5.0 py36h7d14adf_0 defaults
backports 1.0 py36hfa02d7e_1 defaults
backports.shutil_get_terminal_size 1.0.0 py36hfea85ff_2 defaults
beautifulsoup4 4.6.0 py36h49b8c8c_1 defaults
bitarray 0.8.1 py36h5834eb8_0 defaults
bkcharts 0.2 py36h735825a_0 defaults
blaze 0.11.3 py36h4e06776_0 defaults
bleach 2.0.0 py36h688b259_0 defaults
bokeh 0.12.10 py36hbb0e44a_0 defaults
boto 2.48.0 py36h6e4cd66_1 defaults
bottleneck 1.2.1 py36haac1ea0_0 defaults
bzip2 1.0.6 h0376d23_1 defaults
ca-certificates 2017.08.26 h1d4fec5_0 defaults
cairo 1.14.10 haa5651f_5 defaults
certifi 2017.7.27.1 py36h8b7b77e_0 defaults
cffi 1.10.0 py36had8d393_1 defaults
chardet 3.0.4 py36h0f667ec_1 defaults
click 6.7 py36h5253387_0 defaults
cloudpickle 0.4.0 py36h30f8c20_0 defaults
clyent 1.2.2 py36h7e57e65_1 defaults
colorama 0.3.9 py36h489cec4_0 defaults
conda 4.4.7 py36_0 defaults
conda-build 3.0.27 py36h940a66d_0 defaults
conda-env 2.6.0 h36134e3_1 defaults
conda-verify 2.0.0 py36h98955d8_0 defaults
contextlib2 0.5.5 py36h6c84a62_0 defaults
cryptography 2.0.3 py36ha225213_1 defaults
curl 7.55.1 hcb0b314_2 defaults
cycler 0.10.0 py36h93f1223_0 defaults
cython 0.26.1 py36h21c49d0_0 defaults
cytoolz 0.8.2 py36h708bfd4_0 defaults
dask 0.15.3 py36hdc2c8aa_0 defaults
dask-core 0.15.3 py36h10e6167_0 defaults
datashape 0.5.4 py36h3ad6b5c_0 defaults
dbus 1.10.22 h3b5a359_0 defaults
decorator 4.1.2 py36hd076ac8_0 defaults
distributed 1.19.1 py36h25f3894_0 defaults
docutils 0.14 py36hb0f60f5_0 defaults
entrypoints 0.2.3 py36h1aec115_2 defaults
et_xmlfile 1.0.1 py36hd6bccc3_0 defaults
expat 2.2.4 hc00ebd1_1 defaults
fastcache 1.0.2 py36h5b0c431_0 defaults
filelock 2.0.12 py36hacfa1f5_0 defaults
flask 0.12.2 py36hb24657c_0 defaults
flask-cors 3.0.3 py36h2d857d3_0 defaults
fontconfig 2.12.4 h88586e7_1 defaults
freetype 2.8 h52ed37b_0 defaults
get_terminal_size 1.0.0 haa9412d_0 defaults
gevent 1.2.2 py36h2fe25dc_0 defaults
glib 2.53.6 hc861d11_1 defaults
glob2 0.5 py36h2c1b292_1 defaults
gmp 6.1.2 hb3b607b_0 defaults
gmpy2 2.0.8 py36h55090d7_1 defaults
graphite2 1.3.10 hc526e54_0 defaults
greenlet 0.4.12 py36h2d503a6_0 defaults
gst-plugins-base 1.12.2 he3457e5_0 defaults
gstreamer 1.12.2 h4f93127_0 defaults
h5py 2.7.0 py36he81ebca_1 defaults
harfbuzz 1.5.0 h2545bd6_0 defaults
hdf5 1.10.1 hb0523eb_0 defaults
heapdict 1.0.0 py36h79797d7_0 defaults
html5lib 0.999999999 py36h2cfc398_0 defaults
icu 58.2 h211956c_0 defaults
idna 2.6 py36h82fb2a8_1 defaults
imageio 2.2.0 py36he555465_0 defaults
imagesize 0.7.1 py36h52d8127_0 defaults
intel-openmp 2018.0.0 h15fc484_7 defaults
ipykernel 4.6.1 py36hbf841aa_0 defaults
ipython 6.1.0 py36hc72a948_1 defaults
ipython_genutils 0.2.0 py36hb52b0d5_0 defaults
ipywidgets 7.0.0 py36h7b55c3a_0 defaults
isort 4.2.15 py36had401c0_0 defaults
itsdangerous 0.24 py36h93cc618_1 defaults
jbig 2.1 hdba287a_0 defaults
jdcal 1.3 py36h4c697fb_0 defaults
jedi 0.10.2 py36h552def0_0 defaults
jinja2 2.9.6 py36h489bce4_1 defaults
jpeg 9b habf39ab_1 defaults
jsonschema 2.6.0 py36h006f8b5_0 defaults
jupyter 1.0.0 py36h9896ce5_0 defaults
jupyter_client 5.1.0 py36h614e9ea_0 defaults
jupyter_console 5.2.0 py36he59e554_1 defaults
jupyter_core 4.3.0 py36h357a921_0 defaults
jupyterlab 0.27.0 py36h86377d0_2 defaults
jupyterlab_launcher 0.4.0 py36h4d8058d_0 defaults
lazy-object-proxy 1.3.1 py36h10fcdad_0 defaults
libedit 3.1 heed3624_0 defaults
libffi 3.2.1 h4deb6c0_3 defaults
libgcc-ng 7.2.0 h7cc24e2_2 defaults
libgfortran-ng 7.2.0 h9f7466a_2 defaults
libpng 1.6.32 hda9c8bc_2 defaults
libsodium 1.0.13 h31c71d8_2 defaults
libssh2 1.8.0 h8c220ad_2 defaults
libstdcxx-ng 7.2.0 h7a57d05_2 defaults
libtiff 4.0.8 h90200ff_9 defaults
libtool 2.4.6 hd50d1a6_0 defaults
libxcb 1.12 h84ff03f_3 defaults
libxml2 2.9.4 h6b072ca_5 defaults
libxslt 1.1.29 hcf9102b_5 defaults
llvmlite 0.20.0 py36_0 defaults
locket 0.2.0 py36h787c0ad_1 defaults
lxml 4.1.0 py36h5b66e50_0 defaults
lzo 2.10 h1bfc0ba_1 defaults
markupsafe 1.0 py36hd9260cd_1 defaults
matplotlib 2.1.0 py36hba5de38_0 defaults
mccabe 0.6.1 py36h5ad9710_1 defaults
mistune 0.7.4 py36hbab8784_0 defaults
mkl 2018.0.0 hb491cac_4 defaults
mkl-service 1.1.2 py36h17a0993_4 defaults
monty 1.0.2 <pip>
mpc 1.0.3 hf803216_4 defaults
mpfr 3.1.5 h12ff648_1 defaults
mpmath 0.19 py36h8cc018b_2 defaults
msgpack-python 0.4.8 py36hec4c5d1_0 defaults
multipledispatch 0.4.9 py36h41da3fb_0 defaults
navigator-updater 0.1.0 py36h14770f7_0 defaults
nbconvert 5.3.1 py36hb41ffb7_0 defaults
nbformat 4.4.0 py36h31c9010_0 defaults
ncurses 6.0 h06874d7_1 defaults
networkx 2.0 py36h7e96fb8_0 defaults
nltk 3.2.4 py36h1a0979f_0 defaults
nose 1.3.7 py36hcdf7029_2 defaults
notebook 5.0.0 py36h0b20546_2 defaults
numba 0.35.0 np113py36_10 defaults
numexpr 2.6.2 py36hdd3393f_1 defaults
numpy 1.13.3 py36ha12f23b_0 defaults
numpydoc 0.7.0 py36h18f165f_0 defaults
odo 0.5.1 py36h90ed295_0 defaults
olefile 0.44 py36h79f9f78_0 defaults
openpyxl 2.4.8 py36h41dd2a8_1 defaults
openssl 1.0.2l h077ae2c_5 defaults
packaging 16.8 py36ha668100_1 defaults
palettable 3.1.0 <pip>
pandas 0.20.3 py36h842e28d_2 defaults
pandoc 1.19.2.1 hea2e7c5_1 defaults
pandocfilters 1.4.2 py36ha6701b7_1 defaults
pango 1.40.11 h8191d47_0 defaults
partd 0.3.8 py36h36fd896_0 defaults
patchelf 0.9 hf79760b_2 defaults
path.py 10.3.1 py36he0c6f6d_0 defaults
pathlib2 2.3.0 py36h49efa8e_0 defaults
patsy 0.4.1 py36ha3be15e_0 defaults
pcre 8.41 hc71a17e_0 defaults
pep8 1.7.0 py36h26ade29_0 defaults
pexpect 4.2.1 py36h3b9d41b_0 defaults
phonopy 1.12.4+11 py36_0 atztogo
pickleshare 0.7.4 py36h63277f8_0 defaults
pillow 4.2.1 py36h9119f52_0 defaults
pip 9.0.1 py36h8ec8b28_3 defaults
pixman 0.34.0 h83dc358_2 defaults
pkginfo 1.4.1 py36h215d178_1 defaults
ply 3.10 py36hed35086_0 defaults
prompt_toolkit 1.0.15 py36h17d85b1_0 defaults
psutil 5.4.0 py36h84c53db_0 defaults
ptyprocess 0.5.2 py36h69acd42_0 defaults
py 1.4.34 py36h0712aa3_1 defaults
pycodestyle 2.3.1 py36hf609f19_0 defaults
pycosat 0.6.3 py36h0a5515d_0 defaults
pycparser 2.18 py36hf9f622e_1 defaults
pycrypto 2.6.1 py36h6998063_1 defaults
pycurl 7.43.0 py36h5e72054_3 defaults
PyDispatcher 2.0.5 <pip>
pyflakes 1.6.0 py36h7bd6a15_0 defaults
pygments 2.2.0 py36h0d3125c_0 defaults
pylint 1.7.4 py36hb9d4533_0 defaults
pymatgen 2017.12.30 <pip>
pyodbc 4.0.17 py36h999153c_0 defaults
pyopenssl 17.2.0 py36h5cc804b_0 defaults
pyparsing 2.2.0 py36hee85983_1 defaults
pyqt 5.6.0 py36h0386399_5 defaults
pysocks 1.6.7 py36hd97a5b1_1 defaults
pytables 3.4.2 py36h3b5282a_2 defaults
pytest 3.2.1 py36h11ad3bb_1 defaults
python 3.6.3 hc9025b9_1 defaults
python-dateutil 2.6.1 py36h88d3b88_1 defaults
pytz 2017.2 py36hc2ccc2a_1 defaults
pywavelets 0.5.2 py36he602eb0_0 defaults
pyyaml 3.12 py36hafb9ca4_1 defaults
pyzmq 16.0.2 py36h3b0cf96_2 defaults
qt 5.6.2 h974d657_12 defaults
qtawesome 0.4.4 py36h609ed8c_0 defaults
qtconsole 4.3.1 py36h8f73b5b_0 defaults
qtpy 1.3.1 py36h3691cc8_0 defaults
readline 7.0 hac23ff0_3 defaults
requests 2.18.4 py36he2e5f8d_1 defaults
rope 0.10.5 py36h1f8c17e_0 defaults
ruamel.yaml 0.15.35 <pip>
ruamel_yaml 0.11.14 py36ha2fb22d_2 defaults
scikit-image 0.13.0 py36had3c07a_1 defaults
scikit-learn 0.19.1 py36h7aa7ec6_0 defaults
scipy 1.0.0 <pip>
scipy 0.19.1 py36h9976243_3 defaults
seaborn 0.8.0 py36h197244f_0 defaults
setuptools 36.5.0 py36he42e2e1_0 defaults
simplegeneric 0.8.1 py36h2cb9092_0 defaults
singledispatch 3.4.0.3 py36h7a266c3_0 defaults
sip 4.18.1 py36h51ed4ed_2 defaults
six 1.11.0 py36h372c433_1 defaults
snowballstemmer 1.2.1 py36h6febd40_0 defaults
sortedcollections 0.5.3 py36h3c761f9_0 defaults
sortedcontainers 1.5.7 py36hdf89491_0 defaults
spglib 1.10.2.4 <pip>
sphinx 1.6.3 py36he5f0bdb_0 defaults
sphinxcontrib 1.0 py36h6d0f590_1 defaults
sphinxcontrib-websupport 1.0.1 py36hb5cb234_1 defaults
spyder 3.2.4 py36hbe6152b_0 defaults
sqlalchemy 1.1.13 py36hfb5efd7_0 defaults
sqlite 3.20.1 h6d8b0f3_1 defaults
statsmodels 0.8.0 py36h8533d0b_0 defaults
sympy 1.1.1 py36hc6d1c1c_0 defaults
tabulate 0.8.2 <pip>
tblib 1.3.2 py36h34cf8b6_0 defaults
terminado 0.6 py36ha25a19f_0 defaults
testpath 0.3.1 py36h8cadb63_0 defaults
tk 8.6.7 h5979e9b_1 defaults
toolz 0.8.2 py36h81f2dff_0 defaults
tornado 4.5.2 py36h1283b2a_0 defaults
traitlets 4.3.2 py36h674d592_0 defaults
typing 3.6.2 py36h7da032a_0 defaults
unicodecsv 0.14.1 py36ha668878_0 defaults
unixodbc 2.3.4 hc36303a_1 defaults
urllib3 1.22 py36hbe7ace6_0 defaults
wcwidth 0.1.7 py36hdf4376a_0 defaults
webencodings 0.5.1 py36h800622e_1 defaults
werkzeug 0.12.2 py36hc703753_0 defaults
wheel 0.29.0 py36he7f4e38_1 defaults
widgetsnbextension 3.0.2 py36hd01bb71_1 defaults
wrapt 1.10.11 py36h28b7045_0 defaults
xlrd 1.1.0 py36h1db9f0c_1 defaults
xlsxwriter 1.0.2 py36h3de1aca_0 defaults
xlwt 1.3.0 py36h7b00a1f_0 defaults
xz 5.2.3 h2bcbf08_1 defaults
yaml 0.1.7 h96e3832_1 defaults
zeromq 4.2.2 hb0b69da_1 defaults
zict 0.1.3 py36h3a3bf81_0 defaults
zlib 1.2.11 hfbfcf68_1 defaults