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Warning related to JULIA_PKGDIR seen during update #67

Closed
mjsteinbaugh opened this issue Jan 4, 2019 · 4 comments · Fixed by #157
Closed

Warning related to JULIA_PKGDIR seen during update #67

mjsteinbaugh opened this issue Jan 4, 2019 · 4 comments · Fixed by #157

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@mjsteinbaugh
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Issue: julia returned a warning during my most recent conda update.

Here's the warning returned to my console:

Preparing transaction: done
Verifying transaction: done
Executing transaction: | ERROR: KeyError: key "JULIA_PKGDIR"                                                           $
Stacktrace:
 [1] (::getfield(Base, Symbol("##418#419")))(::String) at ./                                                           $
 [2] access_env at ./env.jl:45 [inlined]
 [3] getindex(::Base.EnvDict, ::String) at ./env.jl:76
 [4] top-level scope at none:0

WARNING conda.core.link:run_script(818): pre-unlink script f                                                           $
consider notifying the package maintainer                |   Updating registry at `~/.julia/registries/Gene            $
  Updating git-repo `https://github.com/JuliaRegistries/General.git`
    Fetching: [>                                        ]  0.0 %
    Resolving Deltas: [==============================>          ]  72.5 %
 Resolving package versions...
                                                                                                         do            $

Environment (conda list):

$ conda list

# Name                    Version                   Build  Channel
alabaster                 0.7.12                     py_0    conda-forge
anaconda                  custom           py36hbbc8b67_0
anaconda-client           1.7.1                      py_0    conda-forge
anaconda-project          0.8.2                      py_1    conda-forge
appdirs                   1.4.3                      py_1    conda-forge
arpack                    3.6.3           blas_openblash77d739c_2  [blas_openblas]  conda-forge
asn1crypto                0.24.0                py36_1003    conda-forge
astroid                   2.1.0                 py36_1000    conda-forge
astropy                   3.1.1            py36h470a237_0    conda-forge
atk                       2.25.90              h05f3006_1    conda-forge
atomicwrites              1.2.1                      py_0    conda-forge
attrs                     18.2.0                     py_0    conda-forge
automat                   0.7.0                      py_1    conda-forge
babel                     2.6.0                      py_1    conda-forge
backcall                  0.1.0                      py_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.os              0.1.1                 py36_1000    conda-forge
backports.shutil_get_terminal_size 1.0.0                      py_3    conda-forge
bcftools                  1.9                  h4da6232_0    bioconda
beautifulsoup4            4.7.0                 py36_1000    conda-forge
bedtools                  2.27.1               he941832_2    bioconda
bitarray                  0.8.3            py36h470a237_0    conda-forge
bkcharts                  0.2                      py36_0    conda-forge
blas                      1.1                    openblas    conda-forge
blaze                     0.11.3                   py36_0    conda-forge
bleach                    3.0.2                      py_1    conda-forge
blinker                   1.4                        py_1    conda-forge
blosc                     1.15.1               hfc679d8_0    conda-forge
bokeh                     1.0.3                 py36_1000    conda-forge
boto                      2.49.0                     py_0    conda-forge
boto3                     1.9.72                     py_0    conda-forge
botocore                  1.12.73                    py_0    conda-forge
bottleneck                1.2.1            py36h7eb728f_1    conda-forge
bz2file                   0.98                       py_0    conda-forge
bzip2                     1.0.6                h470a237_2    conda-forge
ca-certificates           2018.11.29           ha4d7672_0    conda-forge
cairo                     1.14.12              h276e583_5    conda-forge
certifi                   2018.11.29            py36_1000    conda-forge
cffi                      1.11.5           py36h5e8e0c9_1    conda-forge
chardet                   3.0.4                 py36_1003    conda-forge
click                     7.0                        py_0    conda-forge
cloudpickle               0.6.1                      py_0    conda-forge
clyent                    1.2.2                      py_1    conda-forge
colorama                  0.4.1                      py_0    conda-forge
constantly                15.1.0                     py_0    conda-forge
contextlib2               0.5.5                      py_2    conda-forge
cryptography              2.2.1            py36hdffb7b8_1    conda-forge
cryptography-vectors      2.4.2                   py_1000    conda-forge
curl                      7.63.0               h74213dd_0    conda-forge
cycler                    0.10.0                     py_1    conda-forge
cython                    0.29.2           py36hfc679d8_0    conda-forge
cytoolz                   0.9.0.1          py36h470a237_1    conda-forge
dask                      1.0.0                      py_0    conda-forge
dask-core                 1.0.0                      py_0    conda-forge
datashape                 0.5.4                    py36_0    conda-forge
dbus                      1.13.0               h3a4f0e9_0    conda-forge
decorator                 4.3.0                      py_0    conda-forge
deeptools                 3.1.3            py36h470a237_0    bioconda
defusedxml                0.5.0                      py_1    conda-forge
distributed               1.25.1                py36_1000    conda-forge
docutils                  0.14                  py36_1001    conda-forge
emacs                     26.1                 h5d2cb88_0    conda-forge
entrypoints               0.2.3                 py36_1002    conda-forge
et_xmlfile                1.0.1                    py36_0    conda-forge
expat                     2.2.5                hfc679d8_2    conda-forge
fastcache                 1.0.2            py36h470a237_1    conda-forge
fftw                      3.3.8                h470a237_1    conda-forge
filelock                  3.0.10                     py_0    conda-forge
flask                     1.0.2                      py_2    conda-forge
flask-cors                3.0.7                      py_0    conda-forge
fontconfig                2.13.1               h65d0f4c_0    conda-forge
freetype                  2.9.1                h6debe1e_4    conda-forge
fribidi                   1.0.5                h470a237_0    conda-forge
gdk-pixbuf                2.36.12              h4ab6910_1    conda-forge
gensim                    3.5.0                    py36_0    conda-forge
get_terminal_size         1.0.0                haa9412d_0
gettext                   0.19.8.1             h5e8e0c9_1    conda-forge
gevent                    1.3.7            py36h470a237_0    conda-forge
giflib                    5.1.4                h470a237_1    conda-forge
glib                      2.56.2               h464dc38_1    conda-forge
glob2                     0.6                        py_0    conda-forge
gmp                       6.1.2                hfc679d8_0    conda-forge
gmpy2                     2.0.8            py36hb705a9b_2    conda-forge
gnutls                    3.6.5                ha0399c4_1    conda-forge
gobject-introspection     1.56.1           py36haaf12d0_1    conda-forge
graphite2                 1.3.13               hfc679d8_0    conda-forge
greenlet                  0.4.13                   py36_0    conda-forge
gst-plugins-base          1.12.5               hde13a9d_0    conda-forge
gstreamer                 1.12.5               h5856ed1_0    conda-forge
gtk2                      2.24.31              hde048ef_0    conda-forge
h5py                      2.9.0            py36he5c79e1_0    conda-forge
harfbuzz                  1.9.0                h04dbb29_1    conda-forge
hdf5                      1.10.4          nompi_h5598ddc_1105    conda-forge
heapdict                  1.0.0                 py36_1000    conda-forge
homer                     4.9.1           pl526h2d50403_6    bioconda
html5lib                  1.0.1                      py_0    conda-forge
htslib                    1.9                  hc238db4_4    bioconda
hyperlink                 17.3.1                     py_0    conda-forge
icu                       58.2                 hfc679d8_0    conda-forge
idna                      2.8                   py36_1000    conda-forge
imageio                   2.4.1                 py36_1000    conda-forge
imagesize                 1.1.0                      py_0    conda-forge
importlib_metadata        0.6                      py36_0    conda-forge
incremental               17.5.0                     py_0    conda-forge
intel-openmp              2019.1                      144
ipykernel                 5.1.0           py36h24bf2e0_1001    conda-forge
ipython                   7.2.0           py36h24bf2e0_1000    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.4.2                      py_0    conda-forge
isort                     4.3.4                 py36_1000    conda-forge
itsdangerous              1.1.0                      py_0    conda-forge
jbig                      2.1               h470a237_1001    conda-forge
jdcal                     1.4                        py_1    conda-forge
jedi                      0.13.2                py36_1000    conda-forge
jeepney                   0.4                        py_0    conda-forge
jinja2                    2.10                       py_1    conda-forge
jmespath                  0.9.3                      py_1    conda-forge
jpeg                      9c                   h470a237_1    conda-forge
jsonschema                3.0.0a3               py36_1000    conda-forge
julia                     1.0.3           blas_openblash977ebb0_0  [blas_openblas]  conda-forge
jupyter                   1.0.0                      py_1    conda-forge
jupyter_client            5.2.4                      py_0    conda-forge
jupyter_console           6.0.0                      py_0    conda-forge
jupyter_core              4.4.0                      py_0    conda-forge
jupyterlab                0.35.4                   py36_0    conda-forge
jupyterlab_launcher       0.13.1                     py_2    conda-forge
jupyterlab_server         0.2.0                      py_0    conda-forge
keyring                   17.1.1                py36_1000    conda-forge
kiwisolver                1.0.1            py36h2d50403_2    conda-forge
krb5                      1.16.2               hbb41f41_0    conda-forge
lazy-object-proxy         1.3.1            py36h470a237_0    conda-forge
libcurl                   7.63.0               hbdb9355_0    conda-forge
libdeflate                1.0                  h470a237_0    bioconda
libedit                   3.1.20170329         haf1bffa_1    conda-forge
libevent                  2.0.22               hdffb7b8_2    conda-forge
libffi                    3.2.1                hfc679d8_5    conda-forge
libgcc                    7.2.0                h69d50b8_2    conda-forge
libgcc-ng                 7.2.0                hdf63c60_3    conda-forge
libgfortran               3.0.0                         1    conda-forge
libgfortran-ng            7.2.0                hdf63c60_3    conda-forge
libgit2                   0.27.7               h5ee2e84_0    conda-forge
libiconv                  1.15                 h470a237_3    conda-forge
libopenblas               0.2.20               h9ac9557_7
libpng                    1.6.36               ha92aebf_0    conda-forge
libsodium                 1.0.16               h470a237_1    conda-forge
libssh2                   1.8.0                h5b517e9_3    conda-forge
libstdcxx-ng              7.2.0                hdf63c60_3    conda-forge
libtiff                   4.0.10               he6b73bb_1    conda-forge
libtool                   2.4.6                h470a237_2    conda-forge
libuuid                   2.32.1               h470a237_2    conda-forge
libxcb                    1.13                 h470a237_2    conda-forge
libxml2                   2.9.8                h422b904_5    conda-forge
libxslt                   1.1.32               h88dbc4e_2    conda-forge
llvmlite                  0.26.0           py36hd28b015_0    conda-forge
locket                    0.2.0                      py_2    conda-forge
lxml                      4.2.5            py36hc9114bc_0    conda-forge
lzo                       2.10                 h470a237_0    conda-forge
markupsafe                1.1.0            py36h470a237_0    conda-forge
matplotlib                3.0.2            py36h8a2030e_1    conda-forge
matplotlib-base           3.0.2            py36h20b835b_1    conda-forge
mccabe                    0.6.1                      py_1    conda-forge
metis                     5.1.0                hfc679d8_3    conda-forge
mistune                   0.8.4            py36h470a237_0    conda-forge
mkl                       2019.1                      144
mkl-service               1.1.2            py36h651fb7a_4
mkl_fft                   1.0.10                   py36_0    conda-forge
mkl_random                1.0.2                    py36_0    conda-forge
more-itertools            4.3.0                 py36_1000    conda-forge
mpc                       1.1.0                hb705a9b_6    conda-forge
mpfr                      4.0.1                h16a7912_0    conda-forge
mpmath                    1.1.0                      py_0    conda-forge
msgpack-python            0.6.0            py36h2d50403_0    conda-forge
multipledispatch          0.6.0                      py_0    conda-forge
nbconvert                 5.3.1                      py_1    conda-forge
nbformat                  4.4.0                      py_1    conda-forge
ncurses                   6.1                  hfc679d8_2    conda-forge
nettle                    3.4.1                h470a237_2    conda-forge
networkx                  2.2                        py_1    conda-forge
nltk                      3.2.5                      py_0    conda-forge
nose                      1.3.7                 py36_1002    conda-forge
notebook                  5.7.4                 py36_1000    conda-forge
numba                     0.41.0           py36hf8a1672_0    conda-forge
numexpr                   2.6.9            py36hf8a1672_0    conda-forge
numpy                     1.15.4          py36_blas_openblashb06ca3d_0  [blas_openblas]  conda-forge
numpy-base                1.14.3           py36h0ea5e3f_1
numpydoc                  0.8.0                      py_1    conda-forge
oauthlib                  2.1.0                      py_0    conda-forge
odo                       0.5.1                      py_1    conda-forge
olefile                   0.46                       py_0    conda-forge
openblas                  0.3.3                ha44fe06_1    conda-forge
openlibm                  0.5.4                h470a237_0    conda-forge
openpyxl                  2.5.12                     py_0    conda-forge
openspecfun               0.5.3                h26a2512_0    conda-forge
openssl                   1.0.2p               h470a237_2    conda-forge
packaging                 18.0                       py_0    conda-forge
pandas                    0.23.4           py36hf8a1672_0    conda-forge
pandoc                    2.5                           0    conda-forge
pandocfilters             1.4.2                      py_1    conda-forge
pango                     1.40.14              he752989_2    conda-forge
parso                     0.3.1                      py_0    conda-forge
partd                     0.3.9                      py_0    conda-forge
patchelf                  0.9                  hfc679d8_2    conda-forge
path.py                   11.5.0                     py_0    conda-forge
pathlib2                  2.3.3                 py36_1000    conda-forge
patsy                     0.5.1                      py_0    conda-forge
pcre                      8.41                 hfc679d8_3    conda-forge
pcre2                     10.23                         2    conda-forge
pep8                      1.7.1                      py_0    conda-forge
perl                      5.26.2               h470a237_0    conda-forge
pexpect                   4.6.0                 py36_1000    conda-forge
pickleshare               0.7.5                 py36_1000    conda-forge
pillow                    5.4.0            py36hc736899_0    conda-forge
pip                       18.1                  py36_1000    conda-forge
pixman                    0.34.0               h470a237_3    conda-forge
pkginfo                   1.4.2                      py_1    conda-forge
plotly                    3.4.2                      py_0    conda-forge
pluggy                    0.8.0                      py_0    conda-forge
ply                       3.11                       py_1    conda-forge
prometheus_client         0.5.0                      py_0    conda-forge
prompt_toolkit            2.0.7                      py_0    conda-forge
psutil                    5.4.8            py36h470a237_0    conda-forge
pthread-stubs             0.4                  h470a237_1    conda-forge
ptyprocess                0.6.0                 py36_1000    conda-forge
py                        1.7.0                      py_0    conda-forge
py2bit                    0.3.0                    py36_1    bioconda
pyasn1                    0.4.4                      py_1    conda-forge
pyasn1-modules            0.2.3                      py_0    conda-forge
pybigwig                  0.3.12           py36hdfb72b2_2    bioconda
pycodestyle               2.4.0                      py_1    conda-forge
pycosat                   0.6.3            py36h470a237_1    conda-forge
pycparser                 2.19                       py_0    conda-forge
pycrypto                  2.6.1            py36h470a237_2    conda-forge
pycurl                    7.43.0.2         py36hb7f436b_0
pyflakes                  2.0.0                      py_0    conda-forge
pygments                  2.3.1                      py_0    conda-forge
pyhamcrest                1.9.0                      py_2    conda-forge
pyjwt                     1.7.1                      py_0    conda-forge
pylint                    2.2.2                 py36_1000    conda-forge
pyodbc                    4.0.24           py36hfc679d8_0    conda-forge
pyopenssl                 18.0.0                py36_1000    conda-forge
pyparsing                 2.3.0                      py_0    conda-forge
pyqt                      5.6.0            py36h8210e8a_8    conda-forge
pyrsistent                0.14.8           py36h470a237_0    conda-forge
pysam                     0.15.1           py36h0380709_0    bioconda
pysocks                   1.6.8                 py36_1002    conda-forge
pytables                  3.4.4            py36h72a6d90_4    conda-forge
pytest                    4.0.2                 py36_1000    conda-forge
pytest-arraydiff          0.3                        py_0    conda-forge
pytest-astropy            0.4.0                      py_0    conda-forge
pytest-doctestplus        0.1.3                      py_0    conda-forge
pytest-openfiles          0.3.1                      py_0    conda-forge
pytest-remotedata         0.3.1                      py_0    conda-forge
python                    3.6.7                h5001a0f_1    conda-forge
python-crfsuite           0.9.6            py36h2d50403_0    conda-forge
python-dateutil           2.7.5                      py_0    conda-forge
pytz                      2018.7                     py_0    conda-forge
pywavelets                1.0.1            py36h7eb728f_0    conda-forge
pyyaml                    3.13             py36h470a237_1    conda-forge
pyzmq                     17.1.2           py36hae99301_1    conda-forge
qt                        5.6.2               h679f5bc_11    conda-forge
qtawesome                 0.5.5              pyh8a2030e_0    conda-forge
qtconsole                 4.4.3                      py_0    conda-forge
qtpy                      1.5.2              pyh8a2030e_0    conda-forge
readline                  7.0                  haf1bffa_1    conda-forge
requests                  2.21.0                py36_1000    conda-forge
requests-oauthlib         1.0.0                      py_1    conda-forge
retrying                  1.3.3                      py_2    conda-forge
rope                      0.10.7                     py_1    conda-forge
ruamel_yaml               0.15.71          py36h470a237_0    conda-forge
s3transfer                0.1.13                py36_1001    conda-forge
samtools                  1.9                  h8ee4bcc_1    bioconda
scikit-image              0.14.1           py36hfc679d8_3    conda-forge
scikit-learn              0.20.2          py36_blas_openblash00c3548_400  [blas_openblas]  conda-for             ge
scipy                     1.2.0           py36_blas_openblashb06ca3d_200  [blas_openblas]  conda-for             ge
seaborn                   0.9.0                      py_0    conda-forge
secretstorage             3.1.0                 py36_1001    conda-forge
send2trash                1.5.0                      py_0    conda-forge
service_identity          17.0.0                     py_0    conda-forge
setuptools                40.6.3                   py36_0    conda-forge
simplegeneric             0.8.1                      py_1    conda-forge
singledispatch            3.4.0.3               py36_1000    conda-forge
sip                       4.18.1           py36hfc679d8_0    conda-forge
six                       1.12.0                py36_1000    conda-forge
smart_open                1.7.1                      py_0    conda-forge
snappy                    1.1.7                hfc679d8_2    conda-forge
snowballstemmer           1.2.1                      py_1    conda-forge
sortedcollections         1.0.1                      py_1    conda-forge
sortedcontainers          2.1.0                      py_0    conda-forge
sphinx                    1.8.3                 py36_1000    conda-forge
sphinxcontrib             1.0                      py36_1
sphinxcontrib-websupport  1.1.0                      py_1    conda-forge
spyder                    3.3.2                 py36_1001    conda-forge
spyder-kernels            0.3.0                 py36_1001    conda-forge
sqlalchemy                1.2.15           py36h470a237_0    conda-forge
sqlite                    3.26.0               hb1c47c0_0    conda-forge
statsmodels               0.9.0            py36h7eb728f_0    conda-forge
suitesparse               4.5.6           blas_openblash697e320_201  [blas_openblas]  conda-forge
sympy                     1.3                   py36_1000    conda-forge
tbb                       2019.3               h2d50403_0    conda-forge
tblib                     1.3.2                      py_1    conda-forge
terminado                 0.8.1                 py36_1001    conda-forge
testpath                  0.4.2                 py36_1000    conda-forge
tk                        8.6.9                ha92aebf_0    conda-forge
tmux                      2.7                  hc78d2af_3    conda-forge
toolz                     0.9.0                      py_1    conda-forge
tornado                   5.1.1            py36h470a237_0    conda-forge
tqdm                      4.28.1                     py_0    conda-forge
traitlets                 4.3.2                 py36_1000    conda-forge
twisted                   18.9.0           py36h470a237_0    conda-forge
twython                   3.7.0                      py_0    conda-forge
typed-ast                 1.1.1            py36h470a237_0    conda-forge
umap-learn                0.3.7                 py36_1000    conda-forge
unicodecsv                0.14.1                     py_1    conda-forge
unixodbc                  2.3.7                h09ba92c_0    conda-forge
urllib3                   1.24.1                py36_1000    conda-forge
wcwidth                   0.1.7                      py_1    conda-forge
webencodings              0.5.1                      py_1    conda-forge
werkzeug                  0.14.1                     py_0    conda-forge
wheel                     0.32.3                   py36_0    conda-forge
widgetsnbextension        3.4.2                 py36_1000    conda-forge
wrapt                     1.10.11          py36h470a237_1    conda-forge
wurlitzer                 1.0.2                 py36_1000    conda-forge
xlrd                      1.2.0                      py_0    conda-forge
xlsxwriter                1.1.2                      py_0    conda-forge
xlwt                      1.3.0                      py_1    conda-forge
xorg-fixesproto           5.0                  h470a237_2    conda-forge
xorg-kbproto              1.0.7                h470a237_2    conda-forge
xorg-libice               1.0.9                h470a237_4    conda-forge
xorg-libsm                1.2.3                h8c8a85c_0    conda-forge
xorg-libx11               1.6.6                h470a237_0    conda-forge
xorg-libxau               1.0.8                h470a237_6    conda-forge
xorg-libxaw               1.0.13               h470a237_2    conda-forge
xorg-libxdmcp             1.1.2                h470a237_7    conda-forge
xorg-libxext              1.3.3                h470a237_4    conda-forge
xorg-libxfixes            5.0.3                h470a237_4    conda-forge
xorg-libxft               2.3.2                h7c24a56_3    conda-forge
xorg-libxmu               1.1.2                h470a237_2    conda-forge
xorg-libxpm               3.5.12               h470a237_2    conda-forge
xorg-libxrender           0.9.10               h470a237_2    conda-forge
xorg-libxt                1.1.5                h470a237_2    conda-forge
xorg-renderproto          0.11.1               h470a237_2    conda-forge
xorg-xextproto            7.3.0                h470a237_2    conda-forge
xorg-xproto               7.0.31               h470a237_7    conda-forge
xz                        5.2.4                h470a237_1    conda-forge
yaml                      0.1.7                h470a237_1    conda-forge
zeromq                    4.2.5                hfc679d8_6    conda-forge
zict                      0.1.3                      py_0    conda-forge
zlib                      1.2.11               h470a237_3    conda-forge
zope                      1.0                      py36_1
zope.interface            4.6.0            py36h470a237_0    conda-forge

Details about conda and system ( conda info ):

$ conda info

     active environment : bioinfo
    active env location : /home/bioinfo/.conda/envs/bioinfo
            shell level : 2
       user config file : /home/bioinfo/.condarc
 populated config files : /home/bioinfo/.condarc
          conda version : 4.5.12
    conda-build version : not installed
         python version : 3.6.8.final.0
       base environment : /usr/local/bin/miniconda3  (read only)
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/pro/linux-64
                          https://repo.anaconda.com/pkgs/pro/noarch
          package cache : /usr/local/bin/miniconda3/pkgs
                          /home/bioinfo/.conda/pkgs
       envs directories : /home/bioinfo/.conda/envs
                          /usr/local/bin/miniconda3/envs
               platform : linux-64
             user-agent : conda/4.5.12 requests/2.21.0 CPython/3.6.8 Linux/3.10.0-957.1.3.el7.x86_64 rhel/7.6 glibc/2.17
                UID:GID : 1001:1001
             netrc file : None
           offline mode : False
@dfornika
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dfornika commented Jan 5, 2019

I haven't looked at the new Pkg system too closely, but based on some brief googling it looks like maybe JULIA_PKGDIR has been replaced by JULIA_DEPOT_PATH?

https://stackoverflow.com/a/36400065/780188
https://docs.julialang.org/en/v1.0/stdlib/Pkg/#Glossary-1

@irbin-b
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irbin-b commented Jul 15, 2019 •
edited
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I am having a very similar issue as follows:

Preparing transaction: done
Verifying transaction: done
Executing transaction: - ERROR: KeyError: key "JULIA_PKGDIR" not found
Stacktrace:
 [1] (::getfield(Base, Symbol("##417#418")))(::String) at ./env.jl:76

WARNING conda.core.link:run_script(1034): pre-unlink script failed for package conda-forge::julia-1.0.3-blas_openblash977ebb0_1
consider notifying the package maintainer
\ WARNING conda.core.link:run_script(1034): pre-unlink script failed for package defaults::qt-5.9.5-h02808f3_0
consider notifying the package maintainer
failed
ERROR conda.core.link:_execute(543): An error occurred while uninstalling package 'defaults::qt-5.9.5-h02808f3_0'.
PermissionError(1, 'Operation not permitted')
Attempting to roll back.

Rolling back transaction: done

Have you solved this problem?

@billtubbs
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I got a very similar warning updating my conda julia environment:

conda update --all

Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /Users/<..myname..>/anaconda3/envs/julia


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    curl-7.79.1                |       h97da3c1_1         141 KB  conda-forge
    gettext-0.19.8.1           |    hd1a6beb_1008         3.3 MB  conda-forge
    git-2.33.1                 | pl5321h2185044_0        13.4 MB  conda-forge
    julia-1.6.3                |       h132cb31_1        73.8 MB  conda-forge
    krb5-1.19.2                |       h289aae4_2         1.3 MB  conda-forge
    libblas-3.9.0              |12_osx64_openblas          12 KB  conda-forge
    libcblas-3.9.0             |12_osx64_openblas          12 KB  conda-forge
    libcurl-7.79.1             |       h97da3c1_1         317 KB  conda-forge
    liblapack-3.9.0            |12_osx64_openblas          12 KB  conda-forge
    libnghttp2-1.43.0          |       hfd382f3_1         874 KB  conda-forge
    libopenblas-0.3.18         |openmp_h3351f45_0         9.0 MB  conda-forge
    libopenblas-ilp64-0.3.18   |openmp_h470725b_0         8.9 MB  conda-forge
    libssh2-1.10.0             |       hd3787cc_2         221 KB  conda-forge
    libutf8proc-2.6.1          |       h35c211d_0          93 KB  conda-forge
    openblas-ilp64-0.3.18      |openmp_ha601604_0         9.9 MB  conda-forge
    openssl-3.0.0              |       h0d85af4_1         2.5 MB  conda-forge
    perl-5.32.1                | 1_h0d85af4_perl5        13.3 MB  conda-forge
    suitesparse-5.10.1         |       h7aff33d_1         2.5 MB  conda-forge
    ------------------------------------------------------------
                                           Total:       139.4 MB

The following NEW packages will be INSTALLED:

  libutf8proc        conda-forge/osx-64::libutf8proc-2.6.1-h35c211d_0
  libzlib            conda-forge/osx-64::libzlib-1.2.11-h9173be1_1013

The following packages will be UPDATED:

  ca-certificates                      2021.5.30-h033912b_0 --> 2021.10.8-h033912b_0
  curl                                    7.78.0-hb861fe1_0 --> 7.79.1-h97da3c1_1
  gettext                            0.19.8.1-h7937167_1005 --> 0.19.8.1-hd1a6beb_1008
  git                               2.33.0-pl5321h9a53687_0 --> 2.33.1-pl5321h2185044_0
  julia                                    1.6.1-h132cb31_0 --> 1.6.3-h132cb31_1
  krb5                                    1.19.2-hcfbf3a7_0 --> 1.19.2-h289aae4_2
  libblas                           3.9.0-11_osx64_openblas --> 3.9.0-12_osx64_openblas
  libcblas                          3.9.0-11_osx64_openblas --> 3.9.0-12_osx64_openblas
  libcurl                                 7.78.0-hf45b732_0 --> 7.79.1-h97da3c1_1
  libffi                                     3.3-h046ec9c_2 --> 3.4.2-he49afe7_4
  liblapack                         3.9.0-11_osx64_openblas --> 3.9.0-12_osx64_openblas
  libnghttp2                              1.43.0-h07e645a_0 --> 1.43.0-hfd382f3_1
  libopenblas                      0.3.17-openmp_h3351f45_1 --> 0.3.18-openmp_h3351f45_0
  libopenblas-ilp64                0.3.17-openmp_h470725b_1 --> 0.3.18-openmp_h470725b_0
  libssh2                                  1.9.0-h52ee1ee_6 --> 1.10.0-hd3787cc_2
  mpfr                                     4.1.0-h0f52abe_0 --> 4.1.0-h0f52abe_1
  openblas-ilp64                   0.3.17-openmp_ha601604_1 --> 0.3.18-openmp_ha601604_0
  openssl                                 1.1.1k-h0d85af4_1 --> 3.0.0-h0d85af4_1
  perl                              5.32.1-0_h0d85af4_perl5 --> 5.32.1-1_h0d85af4_perl5
  suitesparse                             5.10.1-h68a9093_0 --> 5.10.1-h7aff33d_1
  tbb                                     2020.2-h940c156_4 --> 2021.3.0-h940c156_0
  tk                                      8.6.10-h0419947_1 --> 8.6.11-h5dbffcc_1
  zlib                                 1.2.11-h7795811_1010 --> 1.2.11-h9173be1_1013


Proceed ([y]/n)? y


Downloading and Extracting Packages
curl-7.79.1          | 141 KB    | ########################################################### | 100% 
libnghttp2-1.43.0    | 874 KB    | ########################################################### | 100% 
libutf8proc-2.6.1    | 93 KB     | ########################################################### | 100% 
libopenblas-0.3.18   | 9.0 MB    | ########################################################### | 100% 
libcblas-3.9.0       | 12 KB     | ########################################################### | 100% 
suitesparse-5.10.1   | 2.5 MB    | ########################################################### | 100% 
perl-5.32.1          | 13.3 MB   | ########################################################### | 100% 
openssl-3.0.0        | 2.5 MB    | ########################################################### | 100% 
krb5-1.19.2          | 1.3 MB    | ########################################################### | 100% 
liblapack-3.9.0      | 12 KB     | ########################################################### | 100% 
git-2.33.1           | 13.4 MB   | ########################################################### | 100% 
openblas-ilp64-0.3.1 | 9.9 MB    | ########################################################### | 100% 
libblas-3.9.0        | 12 KB     | ########################################################### | 100% 
libopenblas-ilp64-0. | 8.9 MB    | ########################################################### | 100% 
gettext-0.19.8.1     | 3.3 MB    | ########################################################### | 100% 
libcurl-7.79.1       | 317 KB    | ########################################################### | 100% 
julia-1.6.3          | 73.8 MB   | ########################################################### | 100% 
libssh2-1.10.0       | 221 KB    | ########################################################### | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: / ERROR: KeyError: key "JULIA_PKGDIR" not found
Stacktrace:
 [1] (::Base.var"#509#510")(k::String)
   @ Base ./env.jl:79
 [2] access_env
   @ ./env.jl:43 [inlined]
 [3] getindex(#unused#::Base.EnvDict, k::String)
   @ Base ./env.jl:79
 [4] top-level scope
   @ none:1

WARNING conda.core.link:run_script(1229): pre-unlink script failed for package conda-forge/osx-64::julia-1.6.1-h132cb31_0
consider notifying the package maintainer

It then completes the install ending with "196 dependencies successfully precompiled in 276 seconds"

Sorry, I don't know enough about this to help. Just posting in case it helps.

Is this something we should notify conda people about?

@mkitti
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mkitti commented Oct 23, 2021

I'm not sure what other "conda people" you would notify.

This seems be a remnant of .juliarc. I'll take a closer look.

@ngam ngam mentioned this issue Dec 29, 2021
Merged
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@ngam ngam closed this as completed in #157 Dec 29, 2021
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reorganize & cleanup ngam/julia-feedstock
5 participants
@dfornika @mjsteinbaugh @billtubbs @mkitti @irbin-b