Question posted in 
I am trying to update a conda environment:
conda update --all
but get the following
Fetching package metadata .............
InvalidSpecError: Invalid spec: =20190808
output of conda list is as follows:
alabaster 0.7.10 py36h174008c_0
anaconda custom py36ha4fed55_0
anaconda-client 1.6.14 py36_0
anaconda-navigator 1.6.4 py36_0
anaconda-project 0.8.2 py36h9ee5d53_0
apipkg 1.5 <pip>
appnope 0.1.0 py36hf537a9a_0
appnope 0.1.0 <pip>
appscript 1.0.1 py36h9e71e49_1
arrow-cpp 0.8.0 py36_4 conda-forge
asn1crypto 0.24.0 py36_0
astroid 1.6.3 py36_0
astropy 3.0.2 py36h917ab60_1
attrs 18.1.0 py36_0
babel 2.5.3 py36_0
backcall 0.1.0 <pip>
backcall 0.1.0 py36_0
backports 1.0 py36ha3c1827_1
backports.shutil_get_terminal_size 1.0.0 py36hd7a2ee4_2
bash_kernel 0.7.1 <pip>
bctpy 0.5.0 <pip>
beautifulsoup4 4.6.0 py36h72d3c9f_1
billiard 3.5.0.4 <pip>
biopython 1.72 py36h6440ff4_0 anaconda
bitarray 0.8.1 py36h1de35cc_1
bkcharts 0.2 py36h073222e_0
blas 1.0 mkl
blaze 0.11.3 py36h02e7a37_0
bleach 2.1.3 py36_0
bleach 2.1.3 <pip>
blosc 1.14.3 hd9629dc_0
bokeh 0.12.16 py36_0
boto 2.48.0 py36hdbc59ac_1
bottleneck 1.2.1 py36hbd380ad_0
brainnetworks 0.3.2 <pip>
bz2file 0.98 py_0 conda-forge
bzip2 1.0.6 h1de35cc_5
ca-certificates 2018.03.07 0
cairo 1.14.12 he60d9cb_2
certifi 2018.4.16 py36_0
cffi 1.11.5 py36h342bebf_0
cffi 1.13.2 <pip>
chardet 3.0.4 py36h96c241c_1
click 6.7 py36hec950be_0
click-plugins 1.0.3 <pip>
cligj 0.4.0 <pip>
cloog 0.18.0 0
cloudpickle 0.5.3 py36_0
clyent 1.2.2 py36hae3ad88_0
colorama 0.3.9 py36hd29a30c_0
configparser 3.5.0 <pip>
connectome-builder 1.21 <pip>
contextlib2 0.5.5 py36hd66e5e7_0
cryptography 2.2.2 py36h1de35cc_0
curl 7.60.0 ha441bb4_0
cvxopt 1.2.0 py36hb579ef3_0
cycler 0.10.0 py36hfc81398_0
cython 0.28.2 py36h1de35cc_0
cytoolz 0.9.0.1 py36h1de35cc_0
dask 0.17.5 py36_0
dask-core 0.17.5 py36_0
datashape 0.5.4 py36hfb22df8_0
dbus 1.13.2 h760590f_1
decorator 4.3.0 <pip>
decorator 4.3.0 py36_0
descartes 1.1.0 <pip>
dipy 0.15.0 py36h7eb728f_0 conda-forge
distributed 1.21.8 py36_0
docutils 0.14 py36hbfde631_0
entropy-estimators 1.0 <pip>
entrypoints 0.2.3 py36hd81d71f_2
entrypoints 0.2.3 <pip>
et_xmlfile 1.0.1 py36h1315bdc_0
execnet 1.5.0 <pip>
expat 2.2.5 hb8e80ba_0
fastcache 1.0.2 py36h1de35cc_2
fasteners 0.14.1 <pip>
feather-format 0.4.0 py36_2 conda-forge
feather-format 0.4.0 <pip>
ffmpeg 4.0 hc84425e_0
filelock 3.0.4 py36_0
Fiona 1.7.13 <pip>
flake8 3.5.0 py36_1
flask 1.0.2 py36_1
flask-cors 3.0.4 py36_0
fontconfig 2.12.6 h9850fc5_0
freetype 2.8 h12048fb_1
funcsigs 1.0.2 <pip>
future 0.16.0 <pip>
future 0.17.1 py36_0
futures 3.1.1 <pip>
gast 0.2.2 <pip>
gcc 4.8.5 8
geopandas 0.4.0 <pip>
get_terminal_size 1.0.0 h7520d66_0
gettext 0.19.8.1 h15daf44_3
gevent 1.3.0 py36h1de35cc_0
glib 2.56.1 h35bc53a_0
glob2 0.6 py36h94c9186_0
glpk 4.65 h0a95893_1001 conda-forge
gmp 6.1.2 hb37e062_1
gmpy2 2.0.8 py36hf9c35bd_2
gnutls 3.5.17 0 conda-forge
greenlet 0.4.13 py36h1de35cc_0
gsl 2.4 h1de35cc_4
h5py 2.8.0 py36h967a92a_0
hdf5 1.8.18 h017327d_1
heapdict 1.0.0 py36_2
hide-code 0.5.2 <pip>
html5lib 1.0.1 <pip>
html5lib 1.0.1 py36h2f9c1c0_0
icu 58.2 h4b95b61_1
idna 2.6 py36h8628d0a_1
igraph 0.7.1 h0a67f88_1005 conda-forge
imageio 2.3.0 py36_0
imagesize 1.0.0 py36_0
infomap 1.0.0b8 <pip>
intel-openmp 2018.0.0 8
ipykernel 4.8.2 py36_0
ipykernel 4.8.2 <pip>
ipython 6.5.0 <pip>
ipython 6.4.0 py36_0
ipython-genutils 0.2.0 <pip>
ipython_genutils 0.2.0 py36h241746c_0
ipywidgets 7.2.1 <pip>
ipywidgets 7.2.1 py36_0
isl 0.12.2 1
isodate 0.6.0 <pip>
isort 4.3.4 py36_0
itsdangerous 0.24 py36h49fbb8d_1
jbig 2.1 h4d881f8_0
jdcal 1.4 py36_0
jedi 0.12.0 <pip>
jedi 0.12.0 py36_1
jinja2 2.10 py36hd36f9c5_0
Jinja2 2.10 <pip>
jpeg 9b he5867d9_2
jsoncpp 1.8.4 h04f5b5a_0
jsonschema 2.6.0 <pip>
jsonschema 2.6.0 py36hb385e00_0
jupyter 1.0.0 py36_4
jupyter 1.0.0 <pip>
jupyter-client 5.2.3 <pip>
jupyter-console 5.2.0 <pip>
jupyter-core 4.4.0 <pip>
jupyter_client 5.2.3 py36_0
jupyter_console 5.2.0 py36hccf5b1c_1
jupyter_core 4.4.0 py36h79cf704_0
jupyterlab 0.32.1 py36_0
jupyterlab_launcher 0.10.5 py36_0
Keras 2.3.1 <pip>
Keras-Applications 1.0.8 <pip>
Keras-Preprocessing 1.1.0 <pip>
kiwisolver 1.0.1 py36h792292d_0
lazy-object-proxy 1.3.1 py36h2fbbe47_0
libcurl 7.60.0 hf30b1f0_0
libcxx 4.0.1 h579ed51_0
libcxxabi 4.0.1 hebd6815_0
libedit 3.1.20170329 hb402a30_2
libffi 3.2.1 h475c297_4
libgfortran 3.0.1 h93005f0_2
libiconv 1.15 hdd342a3_7
libidn11 1.33 0 conda-forge
libopus 1.2.1 h169cedb_0
libpng 1.6.34 he12f830_0
libsodium 1.0.16 h3efe00b_0
libssh2 1.8.0 h322a93b_4
libtiff 4.0.9 hcb84e12_1
libvpx 1.7.0 h378b8a2_0
libxml2 2.9.8 hab757c2_1
libxslt 1.1.32 hb819dd2_0
line-profiler 2.1.2 <pip>
llvmlite 0.23.1 py36hc454e04_0
locket 0.2.0 py36hca03003_1
lxml 4.2.1 py36h7166777_0
lzo 2.10 h362108e_2
Markdown 2.6.11 <pip>
MarkupSafe 1.0 <pip>
markupsafe 1.0 py36h3a1e703_1
matplotlib 2.2.3 <pip>
matplotlib 2.2.2 py36ha7267d0_0
mccabe 0.6.1 py36hdaeb55d_0
metakernel 0.20.14 py_0 conda-forge
metis 5.1.0 h0a44026_1003 conda-forge
mistune 0.8.3 py36h1de35cc_1
mistune 0.8.3 <pip>
mizani 0.4.6 <pip>
mkl 2018.0.3 1
mkl-service 1.1.2 py36h7ea6df4_4
mkl_fft 1.0.1 py36h917ab60_0
mkl_random 1.0.1 py36h78cc56f_0
mock 2.0.0 <pip>
monotonic 1.5 <pip>
more-itertools 4.1.0 py36_0
mpc 1.0.3 h7a72875_5
mpfr 3.1.5 h711e7fd_2
mpmath 1.0.0 py36hf1b8295_2
msgpack 1.0.0 <pip>
msgpack-python 0.5.6 py36h04f5b5a_0
multipledispatch 0.5.0 py36_0
munch 2.3.2 <pip>
navigator-updater 0.1.0 py36_0
nbconvert 5.3.1 py36h810822e_0
nbconvert 5.3.1 <pip>
nbformat 4.4.0 <pip>
nbformat 4.4.0 py36h827af21_0
ncurses 6.1 h0a44026_0
nettle 3.3 0 conda-forge
networkx 2.1 py36_0
neurdflib 5.0.0.post1 <pip>
nibabel 2.3.3 py_0 conda-forge
nibabel 2.3.0 <pip>
nilearn 0.4.1 <pip>
nilearn 0.5.0 pyh24bf2e0_0 conda-forge
nipy 0.4.2 <pip>
nipy 0.4.1 py36h917ab60_1001 conda-forge
nipype 1.1.9.dev0 <pip>
nltk 3.3.0 py36_0
nose 1.3.7 py36h73fae2b_2
notebook 5.5.0 py36_0
notebook 5.6.0 <pip>
numba 0.38.0 py36h1702cab_0
numexpr 2.6.5 py36h057f876_0
numpy 1.14.3 py36h9bb19eb_1
numpy 1.16.2 <pip>
numpy-base 1.14.3 py36h479e554_1
numpydoc 0.8.0 py36_0
oct2py 4.0.6 py_1 conda-forge
octave_kernel 0.28.4 py_1 conda-forge
odo 0.5.1 py36hc1af34a_0
olefile 0.45.1 py36_0
openpyxl 2.5.3 py36_0
openssl 1.0.2o h26aff7b_0
packaging 17.1 py36_0
palettable 3.1.1 <pip>
pandas 0.23.0 py36h1702cab_0
pandas 0.23.4 <pip>
pandoc 1.19.2.1 ha5e8f32_1
pandocfilters 1.4.2 <pip>
pandocfilters 1.4.2 py36h3b0b094_1
parquet-cpp 1.4.0.pre 2 conda-forge
parso 0.2.0 py36_0
parso 0.2.0 <pip>
partd 0.3.8 py36hf5c4cb8_0
path.py 11.0.1 py36_0
pathlib2 2.3.2 py36_0
patsy 0.5.0 py36_0
pbr 4.2.0 <pip>
pcre 8.42 h378b8a2_0
pdfkit 0.6.1 <pip>
pep8 1.7.1 py36_0
pexpect 4.5.0 <pip>
pexpect 4.5.0 py36_0
pfile-tools 0.3.2 <pip>
pickleshare 0.7.4 py36hf512f8e_0
pickleshare 0.7.4 <pip>
pillow 5.1.0 py36hfcce615_0
pip 18.0 <pip>
pip 10.0.1 py36_0
pixman 0.34.0 h1de35cc_1003 conda-forge
pkginfo 1.4.2 py36_1
plotnine 0.4.0 <pip>
pluggy 0.6.0 py36hb1d0581_0
ply 3.11 py36_0
prometheus-client 0.3.1 <pip>
prompt-toolkit 1.0.15 <pip>
prompt_toolkit 1.0.15 py36haeda067_0
prov 1.5.3 <pip>
psutil 5.4.5 py36h1de35cc_0
ptitprince 0.1.5 <pip>
ptyprocess 0.5.2 <pip>
ptyprocess 0.5.2 py36he6521c3_0
py 1.5.3 py36_0
pyarrow 0.9.0.post1 <pip>
pyarrow 0.8.0 py36_0 conda-forge
pycairo 1.18.0 py36ha54c0a8_1000 conda-forge
pycodestyle 2.3.1 py36h83e8646_0
pycodestyle_magic 0.1 <pip>
pycosat 0.6.3 py36hee92d8f_0
pycparser 2.18 py36h724b2fc_1
pycrypto 2.6.1 py36h1de35cc_8
pycurl 7.43.0.1 py36hdbc3d79_0
pydicom 1.2.2 py_0 conda-forge
pydicom 1.1.0 <pip>
pydot 1.2.4 <pip>
pydotplus 2.0.2 <pip>
pyevtk 1.1.0 <pip>
pyflakes 1.6.0 py36hea45e83_0
pygments 2.2.0 py36h240cd3f_0
Pygments 2.2.0 <pip>
PyHamcrest 1.9.0 <pip>
pylint 1.8.4 py36_0
pyodbc 4.0.23 py36h0a44026_0
pyopenssl 18.0.0 py36_0
pyparsing 2.2.0 py36hb281f35_0
pyproj 1.9.5.1 <pip>
pyqt 5.9.2 py36h11d3b92_0
pysocks 1.6.8 py36_0
pytables 3.4.4 py36hca30cd5_0
pytest 3.5.1 py36_0
pytest-arraydiff 0.2 py36_0
pytest-astropy 0.3.0 py36_0
pytest-doctestplus 0.1.3 py36_0
pytest-forked 0.2 <pip>
pytest-openfiles 0.3.0 py36_0
pytest-remotedata 0.2.1 py36_0
pytest-xdist 1.22.5 <pip>
python 3.6.5 hc167b69_1
python-dateutil 2.7.2 <pip>
python-dateutil 2.7.3 py36_0
python-igraph 0.7.1.post6 py36h1de35cc_1005 conda-forge
python-louvain 0.13 <pip>
python.app 2 py36_8
pytz 2018.4 py36_0
pywavelets 0.5.2 py36h2710a04_0
pyyaml 3.12 py36h2ba1e63_1
pyzmq 17.0.0 <pip>
pyzmq 17.0.0 py36h1de35cc_1
qt 5.9.5 h02808f3_0
qtawesome 0.4.4 py36h468c6fb_0
qtconsole 4.3.1 py36hd96c0ff_0
qtconsole 4.3.1 <pip>
qtpy 1.4.1 py36_0
rdflib 4.2.2 <pip>
readline 7.0 hc1231fa_4
redis 2.10.6 <pip>
requests 2.18.4 py36h4516966_1
rope 0.10.7 py36h68959ac_0
rpy2 3.2.2 <pip>
rq 0.12.0 <pip>
ruamel_yaml 0.15.35 py36h1de35cc_1
sas7bdat 2.1.1 <pip>
saspy 2.2.6 <pip>
scikit-image 0.13.1 py36h1de35cc_1
scikit-learn 0.19.1 py36hffbff8c_0
scipy 1.4.1 <pip>
scipy 1.1.0 py36hcaad992_0
scipy 1.0.1 <pip>
seaborn 0.9.0 py36_0
send2trash 1.5.0 py36_0
Send2Trash 1.5.0 <pip>
setuptools 39.1.0 <pip>
setuptools 39.1.0 py36_0
Shapely 1.6.4.post2 <pip>
simplegeneric 0.8.1 py36_2
simplegeneric 0.8.1 <pip>
SimpleITK 1.2.0 <pip>
simplejson 3.16.0 <pip>
singledispatch 3.4.0.3 py36hf20db9d_0
sip 4.19.8 py36h0a44026_0
six 1.11.0 <pip>
six 1.11.0 py36h0e22d5e_1
snappy 1.1.7 he62c110_3
snowballstemmer 1.2.1 py36h6c7b616_0
sortedcollections 0.6.1 py36_0
sortedcontainers 1.5.10 py36_0
sos 0.9.16.1 <pip>
sos-bash 0.9.12.2 <pip>
sos-bioinfo 0.9.10.1 <pip>
sos-javascript 0.9.12.2 <pip>
sos-julia 0.9.12.1 <pip>
sos-matlab 0.9.12.1 <pip>
sos-notebook 0.9.16.0 <pip>
sos-pbs 0.9.16.0 <pip>
sos-python 0.9.12.1 <pip>
sos-r 0.9.12.3 <pip>
sos-rq 0.9.16.1 <pip>
sos-ruby 0.9.15.0 <pip>
sos-sas 0.9.12.3 <pip>
sphinx 1.7.4 py36_0
sphinxcontrib 1.0 py36h9364dc8_1
sphinxcontrib-websupport 1.0.1 py36h92f4a7a_1
spyder 3.2.8 py36_0
sqlalchemy 1.2.7 py36hb402a30_0
sqlite 3.23.1 hf1716c9_0
statsmodels 0.9.0 py36h1d22016_0
suitesparse 5.2.0 he235d88_0
sympy 1.1.1 py36h7f3cf04_0
tableone 0.5.13 <pip>
tabulate 0.8.2 <pip>
tbb 2018_20171205 0 conda-forge
tblib 1.3.2 py36hda67792_0
tensorflow-estimator 2.1.0 <pip>
termcolor 1.1.0 <pip>
terminado 0.8.1 <pip>
terminado 0.8.1 py36_1
testpath 0.3.1 <pip>
testpath 0.3.1 py36h625a49b_0
tk 8.6.7 h35a86e2_3
toolz 0.9.0 py36_0
tornado 5.0.2 py36_0
tornado 5.0.2 <pip>
tqdm 4.24.0 <pip>
traitlets 4.3.2 py36h65bd3ce_0
traitlets 4.3.2 <pip>
traits 4.6.0 <pip>
typing 3.6.4 py36_0
tzlocal 2.0.0 <pip>
unicodecsv 0.14.1 py36he531d66_0
unixodbc 2.3.6 h3efe00b_0
urllib3 1.22 py36h68b9469_0
vtk 8.1.0 py36h04d9db9_201
Wand 0.4.4 <pip>
wcwidth 0.1.7 py36h8c6ec74_0
wcwidth 0.1.7 <pip>
webencodings 0.5.1 py36h3b9701d_1
webencodings 0.5.1 <pip>
werkzeug 0.14.1 py36_0
wheel 0.31.1 py36_0
widgetsnbextension 3.2.1 py36_0
widgetsnbextension 3.2.1 <pip>
wrapt 1.10.11 py36hc29e774_0
x264 20131217 3 conda-forge
xlrd 1.2.0 py_0 conda-forge
xlsxwriter 1.0.4 py36_0
xlwings 0.11.8 py36_0
xlwt 1.2.0 py36h5ad1178_0
xxhash 1.2.0 <pip>
xz 5.2.4 h1de35cc_4
yaml 0.1.7 hc338f04_2
zeromq 4.2.5 h378b8a2_0
zict 0.1.3 py36h71da714_0
zlib 1.2.11 hf3cbc9b_2
2
Answers
While not a solution, we came up with a workaround, so I figured I’d post it here.
Installing a newer version of conda in an alternative location, and using this specific activate binary to activate the environment allows installs to be functional once again.
While not a solution, this may lead someone else to a fix. I ran into the same error and was able to get
conda update --allto work again by removing pyarrow and a number of its C++ dependencies:There is a version of pyarrow on both the conda-forge and default channels, and something isn’t resolving on older conda builds.
Once pyarrow is removed, you will get the same invalid specification error (above) if you attempt to reinstall the latest version of it and if you install an older version you will get the same error if you try
conda update --allafterward.Unfortunately, many packages are dependent on pyarrow, so removing it may not be a good option. I pip installed pyarrow so I can use feather format with pandas, but I can no longer conda install any package that has a dependency on pyarrow.