gnestor
commented
7 years ago @minrk Any ideas?
Open ellisonbg opened 7 years ago
gnestor
commented
7 years ago @minrk Any ideas?
minrk
commented
7 years ago Can you include conda list and/or pip list? What version of nbformat do you have? Can you include more log output, including the last successful safe and the first failed one? Is this a local filesystem or NFS? Do you have more than one notebook server running?
ellisonbg
commented
7 years ago Here are the packages:
_license 1.1 py34_0
abstract-rendering 0.5.1 np19py34_0
alabaster 0.7.3 py34_0
alabaster 0.7.10 <pip>
alembic 0.8.8 <pip>
anaconda custom py35_0
ansible 1.9.4 <pip>
appdirs 1.4.3 <pip>
appnope 0.1.0 py35_0
appscript 1.0.1 py34_0
argcomplete 0.8.9 py34_0
argparse 1.4.0 <pip>
args 0.1.0 <pip>
arrow 0.8.0 <pip>
asn1crypto 0.22.0 <pip>
asn1crypto 0.22.0 py35_0
astroid 1.5.3 <pip>
astropy 1.0.3 np19py34_0
Babel 2.4.0 <pip>
babel 1.3 py34_0
backports 1.0 py35_0
backports.shutil_get_terminal_size 1.0.0 py35_0 conda-forge
bash_kernel 0.4.1 <pip>
bcolz 0.9.0 np19py34_0
beautiful-soup 4.3.2 py34_0
beautifulsoup4 4.5.1 <pip>
binaryornot 0.4.0 <pip>
binstar 0.11.0 py34_0
bitarray 0.8.1 py34_0
blaze-core 0.8.0 np19py34_0
bleach 2.0.0 <pip>
blz 0.6.2 np19py34_1
bokeh 0.10.0 py35_0
bokeh-0.12.3dev4-88 g50b3d45 <pip>
boto 2.38.0 py34_0
bottleneck 1.0.0 np19py34_0
Bottleneck 1.2.0 <pip>
bqplot 0.6.1 <pip>
bs4 0.0.1 <pip>
certifi 2016.9.26 py35_0 conda-forge
cffi 1.10.0 py35_0
cffi 1.10.0 <pip>
chainer 1.4.1 <pip>
chardet 2.3.0 <pip>
click 6.6 <pip>
clint 0.5.1 <pip>
cloudpickle 0.2.1 <pip>
cloudpickle 0.2.2 py35_0
clyent 0.3.4 py34_0
colorama 0.3.3 py34_0
colorama 0.3.7 <pip>
CommonMark 0.5.4 <pip>
configobj 5.0.6 py34_0
cookiecutter 1.4.0 <pip>
cookies 2.2.1 <pip>
cryptography 1.8.1 py35_0
cryptography 1.8.1 <pip>
curl 7.43.0 0
cycler 0.10.0 <pip>
cycler 0.9.0 py34_0 conda-forge
cython 0.22.1 py34_0
cytoolz 0.7.3 py34_0
dask 0.15.0 py35_0
dask 0.11.0 <pip>
datashape 0.4.5 np19py34_0
decorator 4.0.10 <pip>
decorator 4.0.11 <pip>
decorator 4.0.10 py35_0 conda-forge
dill 0.2.6 <pip>
docutils 0.12 py34_0
docutils 0.13.1 <pip>
dynd-python 0.6.5 np19py34_0
ecdsa 0.13 <pip>
empyrical 0.2.2 <pip>
entrypoints 0.2.2 <pip>
entrypoints 0.2.2 py35_0 conda-forge
fastcache 1.0.2 py34_0
filelock 2.0.5 <pip>
flask 0.10.1 py35_1
freetype 2.5.5 0
future 0.16.0 <pip>
geopy 1.11.0 <pip>
get_terminal_size 1.0.0 py35_0
gnureadline 6.3.3 <pip>
greenlet 0.4.7 py34_0
grin 1.2.1 <pip>
h5py 2.7.0 np113py35_0
hdf5 1.8.17 8 conda-forge
HeapDict 1.0.0 <pip>
html5lib 0.999999999 <pip>
icu 54.1 0
idna 2.5 <pip>
idna 2.5 py35_0
imagesize 0.7.1 <pip>
inflection 0.3.1 <pip>
invoke 0.18.1 py35_0 conda-forge
ipykernel 4.3.1 <pip>
ipykernel 4.5.1 py35_0 conda-forge
ipykernel 4.6.1 <pip>
ipyleaflet 0.2.0 <pip>
ipython 6.1.0 py35_0 conda-forge
ipython-genutils 0.2.0 <pip>
ipython-qtconsole 3.2.0 py34_0
ipython_genutils 0.1.0 py35_0
ipythonblocks 1.7.0 <pip>
ipywidgets 5.2.2 py35_2 conda-forge
isort 4.2.15 <pip>
itsdangerous 0.24 py35_0
jbig 2.1 0
jdcal 1.0 py34_0
jedi 0.10.0 py35_0 conda-forge
jedi 0.10.2 <pip>
jinja2 2.8 py35_1 conda-forge
Jinja2 2.9.6 <pip>
jinja2-time 0.2.0 <pip>
joblib 0.11 <pip>
jpeg 8d 2 r
jsonschema 2.6.0 <pip>
jsonschema 2.5.1 py35_0 conda-forge
jupyter 1.0.0 py35_3
jupyter-client 5.0.1 <pip>
jupyter-client 4.1.1 <pip>
jupyter-core 4.3.0 <pip>
jupyter-core 4.0.6 <pip>
jupyter-dashboards 0.5.0 <pip>
jupyter-lightsaber 1.0.5 <pip>
jupyter-lightsaber-yoda 1.0.5 <pip>
jupyter-tree-filter 1.4.1 <pip>
jupyter_client 4.4.0 py35_0 conda-forge
jupyter_console 5.0.0 py35_0 conda-forge
jupyter_core 4.2.0 py35_0 conda-forge
jupyterlab-launcher 0.4.0 <pip>
Keras 1.2.2 <pip>
keras 2.0.6 py35_0 conda-forge
launcher 1.0.0 3
lazy-object-proxy 1.3.1 <pip>
libdynd 0.6.5 0
libgcc 4.8.5 1 r
libgfortran 3.0.0 0 conda-forge
libpng 1.6.17 0
libsodium 1.0.10 0 conda-forge
libtiff 4.0.6 1
libxml2 2.9.2 1 r
libxslt 1.1.28 2
lightning-python 1.2.1 <pip>
llvmlite 0.5.0 py34_0
locket 0.2.0 <pip>
locket 0.2.0 py35_1
lxml 3.4.4 py34_0
Mako 1.0.6 <pip>
markdown2 2.3.4 <pip>
markupsafe 0.23 py35_2
MarkupSafe 1.0 <pip>
matplotlib 2.0.0 <pip>
mccabe 0.6.1 <pip>
medium 0.3.0 <pip>
mistune 0.7.3 py35_1
mistune 0.7.4 <pip>
mkl 2017.0.3 0
mock 2.0.0 py35_0 conda-forge
more-itertools 3.0.0 <pip>
msgpack-python 0.4.8 <pip>
multipledispatch 0.4.8 <pip>
multipledispatch 0.4.7 py34_0
mypy 0.470 <pip>
nbconvert 5.1.1 <pip>
nbconvert 4.2.0 py35_0 conda-forge
nbdime 0.2.0.dev0 <pip>
nbformat 4.3.0 <pip>
nbformat 4.1.0 py35_0 conda-forge
nbsphinx 0.2.13 <pip>
ncurses 5.9 1 r
ndg-httpsclient 0.4.2 <pip>
networkx 1.10 py35_0
nlopt 2.4.2 1 r
nltk 3.0.3 np19py34_0
node-webkit 0.10.1 0
nose 1.3.7 py35_1
nose 1.3.7 <pip>
notebook 5.0.0 py35_0 conda-forge
numba 0.19.1 np19py34_0
numexpr 2.4.3 np19py34_0
numexpr 2.5.2 <pip>
numpy 1.12.0 <pip>
numpy 1.13.1 py35_0
numpy 1.11.0 <pip>
numpydoc 0.6.0 <pip>
odo 0.3.2 np19py34_0
openpyxl 1.8.5 py34_0
openssl 1.0.2j 0
packaging 16.8 py35_0
packaging 16.8 <pip>
palettable 2.1.1 <pip>
pamela 0.2.1 <pip>
pandas 0.20.2 np113py35_0
pandas-datareader 0.3.0.post0 <pip>
pandocfilters 1.4.1 <pip>
paramiko 1.16.0 <pip>
partd 0.3.8 py35_0
path.py 8.1.2 <pip>
path.py 8.2.1 py35_0
patsy 0.4.1 <pip>
patsy 0.3.0 np19py34_0
pbr 1.10.0 py35_0 conda-forge
pcre 8.31 0
pep8 1.6.2 py34_0
pexpect 4.2.0 <pip>
pexpect 4.0.1 <pip>
pexpect 4.2.1 py35_0 conda-forge
pickleshare 0.7.4 py35_0
pickleshare 0.7.2 <pip>
pillow 3.0.0 py35_0
pip 9.0.1 py35_1
pkginfo 1.4.1 <pip>
plotly 1.9.10 <pip>
ply 3.6 py34_0
poyo 0.4.0 <pip>
prompt-toolkit 1.0.14 <pip>
prompt-toolkit 1.0.3 <pip>
prompt_toolkit 1.0.9 py35_0 conda-forge
protobuf 3.2.0 <pip>
protobuf 2.6.1 <pip>
protobuf 3.0.0 py35_0 conda-forge
psutil 5.2.2 py35_0
psutil 4.3.1 <pip>
ptyprocess 0.5.1 <pip>
ptyprocess 0.5.1 py35_0 conda-forge
py 1.4.34 <pip>
py 1.4.27 py34_0
pyarrow 0.7.1 <pip>
pyasn1 0.2.3 <pip>
pyasn1 0.2.3 py35_0
pycosat 0.6.1 py34_0
pycparser 2.17 <pip>
pycparser 2.17 py35_0
pycrypto 2.6.1 <pip>
pycrypto 2.6.1 py34_0
pycurl 7.19.5.1 py34_2
pyenchant 1.6.8 <pip>
pyflakes 0.9.2 py34_0
pyflakes 1.0.0 <pip>
pyfolio 0.7.0 <pip>
PyGithub 1.29 <pip>
Pygments 2.1.3 <pip>
pygments 2.1.3 py35_1 conda-forge
Pygments 2.2.0 <pip>
pylint 1.7.2 <pip>
pymc3 3.0 <pip>
pymysql 0.6.6 py35_0
pyopenssl 17.0.0 py35_0
pyOpenSSL 17.0.0 <pip>
pyparsing 2.2.0 <pip>
pyparsing 2.0.3 py35_0
pyqt 5.6.0 py35_0
pytables 3.2.0 np19py34_0
pytest 3.2.2 <pip>
pytest 2.7.1 py34_0
python 3.5.2 3 conda-forge
python-dateutil 2.5.3 <pip>
python-dateutil 2.6.0 py35_0 conda-forge
python-editor 1.0.1 <pip>
python-oauth2 1.0.1 <pip>
python.app 1.2 py35_4
pythonwhat 2.6.0 <pip>
pythreejs 0.2.0b2 <pip>
pytz 2016.7 <pip>
pytz 2016.7 py35_0 conda-forge
pytz 2017.2 <pip>
pyyaml 3.12 py35_0
pyzmq 15.1.0 <pip>
pyzmq 16.0.2 py35_0 conda-forge
qt 5.6.0 0
qtconsole 4.2.1 py35_0 conda-forge
Quandl 3.1.0 <pip>
quilt 2.7.0 <pip>
r-assertthat 0.1 r3.2.2_2a r
r-base 3.2.2 0 r
r-base64enc 0.1_3 r3.2.2_0a r
r-bh 1.58.0_1 r3.2.2_0a r
r-bitops 1.0_6 r3.2.2_2a r
r-boot 1.3_17 r3.2.2_0a r
r-bradleyterry2 1.0_6 r3.2.2_2 r
r-brglm 0.5_9 r3.2.2_2 r
r-car 2.1_0 r3.2.2_0a r
r-caret 6.0_62 r3.2.2_0a r
r-catools 1.17.1 r3.2.2_2a r
r-chron 2.3_47 r3.2.2_0a r
r-class 7.3_14 r3.2.2_0a r
r-cluster 2.0.3 r3.2.2_0a r
r-codetools 0.2_14 r3.2.2_0a r
r-colorspace 1.2_6 r3.2.2_0a r
r-data.table 1.9.6 r3.2.2_0a r
r-dbi 0.3.1 r3.2.2_3a r
r-dichromat 2.0_0 r3.2.2_3a r
r-digest 0.6.8 r3.2.2_3a r
r-dplyr 0.4.3 r3.2.2_0a r
r-essentials 1.1 r3.2.2_1a r
r-evaluate 0.8 r3.2.2_0a r
r-foreach 1.4.3 r3.2.2_0a r
r-foreign 0.8_66 r3.2.2_0a r
r-formatr 1.2.1 r3.2.2_0a r
r-ggplot2 1.0.1 r3.2.2_0a r
r-glmnet 2.0_2 r3.2.2_0a r
r-gtable 0.1.2 r3.2.2_3a r
r-gtools 3.5.0 r3.2.2_0 r
r-hexbin 1.27.1 r3.2.2_0a r
r-highr 0.5.1 r3.2.2_0a r
r-htmltools 0.2.6 r3.2.2_2a r
r-htmlwidgets 0.5 r3.2.2_0a r
r-httpuv 1.3.3 r3.2.2_0a r
r-irdisplay 0.3 r3.2.2_0a r
r-irkernel 0.5 r3.2.2_2 r
r-iterators 1.0.8 r3.2.2_0a r
r-jsonlite 0.9.17 r3.2.2_0a r
r-kernsmooth 2.23_15 r3.2.2_0a r
r-knitr 1.11 r3.2.2_0a r
r-labeling 0.3 r3.2.2_2a r
r-lattice 0.20_33 r3.2.2_0a r
r-lazyeval 0.1.10 r3.2.2_3a r
r-lme4 1.1_10 r3.2.2_0a r
r-magrittr 1.5 r3.2.2_2a r
r-maps 3.0.0_2 r3.2.2_0a r
r-markdown 0.7.7 r3.2.2_1a r
r-mass 7.3_45 r3.2.2_0a r
r-matrix 1.2_2 r3.2.2_0a r
r-matrixmodels 0.4_1 r3.2.2_0a r
r-mgcv 1.8_9 r3.2.2_0a r
r-mime 0.4 r3.2.2_0a r
r-minqa 1.2.4 r3.2.2_1a r
r-munsell 0.4.2 r3.2.2_2a r
r-nlme 3.1_122 r3.2.2_0a r
r-nloptr 1.0.4 r3.2.2_2a r
r-nnet 7.3_11 r3.2.2_0a r
r-pbkrtest 0.4_2 r3.2.2_2a r
r-plyr 1.8.3 r3.2.2_0a r
r-profilemodel 0.5_9 r3.2.2_2 r
r-proto 0.3_10 r3.2.2_2a r
r-quantmod 0.4_5 r3.2.2_0a r
r-quantreg 5.19 r3.2.2_0a r
r-r6 2.1.1 r3.2.2_0a r
r-randomforest 4.6_12 r3.2.2_0a r
r-rbokeh 0.2.2 r3.2.2_0a r
r-rcolorbrewer 1.1_2 r3.2.2_3a r
r-rcpp 0.12.2 r3.2.2_0a r
r-rcppeigen 0.3.2.5.1 r3.2.2_0a r
r-recommended 3.2.2 r3.2.2_0 r
r-repr 0.3 r3.2.2_0a r
r-reshape2 1.4.1 r3.2.2_2a r
r-rjsonio 1.3_0 r3.2.2_1a r
r-rmarkdown 0.8.1 r3.2.2_0a r
r-rpart 4.1_10 r3.2.2_0a r
r-rzmq 0.7.7 r3.2.2_2a r
r-scales 0.3.0 r3.2.2_0a r
r-shiny 0.12.2 r3.2.2_0a r
r-sparsem 1.7 r3.2.2_0a r
r-spatial 7.3_11 r3.2.2_0a r
r-stringi 1.0_1 r3.2.2_0a r
r-stringr 1.0.0 r3.2.2_0a r
r-survival 2.38_3 r3.2.2_0a r
r-tidyr 0.3.1 r3.2.2_0a r
r-ttr 0.23_0 r3.2.2_0a r
r-uuid 0.1_2 r3.2.2_0a r
r-xtable 1.8_0 r3.2.2_0a r
r-xts 0.9_7 r3.2.2_0a r
r-yaml 2.1.13 r3.2.2_1a r
r-zoo 1.7_12 r3.2.2_1a r
readline 6.2 2
recommonmark 0.4.0 <pip>
redis 2.6.9 0
redis-py 2.10.3 py34_0
requests 2.13.0 <pip>
requests 2.8.1 py35_0
requests-file 1.4.2 <pip>
requests-ftp 0.3.1 <pip>
requests-toolbelt 0.7.1 <pip>
responses 0.6.0 <pip>
rope 0.9.4 py34_1
runipy 0.1.3 py34_0
scikit-image 0.11.3 np19py35_0
scikit-learn 0.18.2 np113py35_0
scipy 0.19.0 <pip>
scipy 0.19.1 np113py35_0
seaborn 0.6.0 np19py35_0
seaborn 0.7.1 <pip>
setuptools 24.0.2 <pip>
setuptools 36.5.0 <pip>
setuptools 32.3.0 py35_0 conda-forge
simplegeneric 0.8.1 py35_1
sip 4.18 py35_0 conda-forge
six 1.10.0 py35_1 conda-forge
snowballstemmer 1.2.1 <pip>
snowballstemmer 1.2.0 py34_0
sockjs-tornado 1.0.1 py34_0
Sphinx 1.5.5 <pip>
sphinx 1.3.1 py34_0
sphinx-rtd-theme 0.1.9 <pip>
sphinx_rtd_theme 0.1.7 py34_0
spyder 2.3.5.2 py34_0
spyder-app 2.3.5.2 py34_0
SQLAlchemy 1.0.11 <pip>
sqlalchemy 1.0.5 py34_0
sqlite 3.13.0 1 conda-forge
statsmodels 0.6.1 np19py34_0
statsmodels 0.8.0 <pip>
sympy 0.7.6 py34_0
sympy 0.7.6.1 <pip>
tables 3.4.2 <pip>
tblib 1.3.0 <pip>
tensorflow 1.0.0 <pip>
tensorflow 0.12.1 py35_0 conda-forge
terminado 0.6 py35_0 conda-forge
testpath 0.3 <pip>
theano 0.8.2 py35_0 conda-forge
tk 8.5.19 1 conda-forge
toolz 0.8.0 <pip>
toolz 0.8.2 py35_0
tornado 4.3 <pip>
tornado 4.5.1 <pip>
tornado 4.4.2 py35_0 conda-forge
tqdm 4.11.2 <pip>
traitlets 4.3.1 py35_0 conda-forge
traitlets 4.2.1 <pip>
traitlets 4.2.2 <pip>
traitlets 4.3.2 <pip>
twine 1.8.1 <pip>
typed-ast 0.6.3 <pip>
ujson 1.33 py34_0
vega 0.4.4 py35_1 conda-forge
wcwidth 0.1.7 py35_0 conda-forge
wcwidth 0.1.7 <pip>
webencodings 0.5.1 <pip>
werkzeug 0.10.4 py35_0
wheel 0.29.0 py35_0
whichcraft 0.4.0 <pip>
widgetsnbextension 1.2.6 py35_3 conda-forge
wrapt 1.10.11 <pip>
xlrd 1.1.0 <pip>
xlrd 0.9.3 py34_0
xlsxwriter 0.7.3 py34_0
xlwings 0.3.5 py34_0
xlwt 1.0.0 py34_0
xz 5.2.2 1
yaml 0.1.6 0
zeromq 4.1.5 0 conda-forge
zict 0.0.3 <pip>
zlib 1.2.8 3
I am opening, running, saving and closing a bunch of notebooks (dozens). After doing this for about 20-30 of them, I get an sqlite error making it impossible to save a notebook (have to restart the server).