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conda bug prevents installing anything that depends on petsc #147

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tlunet opened this issue Jul 4, 2022 · 3 comments
Closed
1 task done

conda bug prevents installing anything that depends on petsc #147

tlunet opened this issue Jul 4, 2022 · 3 comments
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@tlunet
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tlunet commented Jul 4, 2022 •
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Solution to issue cannot be found in the documentation.

  • I checked the documentation.

Issue

Hi,

a weird issue occurs on my side when updating conda environment today :

Collecting package metadata (current_repodata.json): failed

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/prog/anaconda/lib/python3.8/site-packages/conda/exceptions.py", line 1114, in __call__
        return func(*args, **kwargs)
      File "/prog/anaconda/lib/python3.8/site-packages/conda/cli/main.py", line 86, in main_subshell
        exit_code = do_call(args, p)
      File "/prog/anaconda/lib/python3.8/site-packages/conda/cli/conda_argparse.py", line 90, in do_call
        return getattr(module, func_name)(args, parser)
      File "/prog/anaconda/lib/python3.8/site-packages/conda/cli/main_update.py", line 20, in execute
        install(args, parser, 'update')
      File "/prog/anaconda/lib/python3.8/site-packages/conda/cli/install.py", line 259, in install
        unlink_link_transaction = solver.solve_for_transaction(
      File "/prog/anaconda/lib/python3.8/site-packages/conda/core/solve.py", line 152, in solve_for_transaction
        unlink_precs, link_precs = self.solve_for_diff(update_modifier, deps_modifier,
      File "/prog/anaconda/lib/python3.8/site-packages/conda/core/solve.py", line 195, in solve_for_diff
        final_precs = self.solve_final_state(update_modifier, deps_modifier, prune, ignore_pinned,
      File "/prog/anaconda/lib/python3.8/site-packages/conda/core/solve.py", line 300, in solve_final_state
        ssc = self._collect_all_metadata(ssc)
      File "/prog/anaconda/lib/python3.8/site-packages/conda/common/io.py", line 86, in decorated
        return f(*args, **kwds)
      File "/prog/anaconda/lib/python3.8/site-packages/conda/core/solve.py", line 463, in _collect_all_metadata
        index, r = self._prepare(prepared_specs)
      File "/prog/anaconda/lib/python3.8/site-packages/conda/core/solve.py", line 1058, in _prepare
        reduced_index = get_reduced_index(self.prefix, self.channels,
      File "/prog/anaconda/lib/python3.8/site-packages/conda/core/index.py", line 290, in get_reduced_index
        push_record(record)
      File "/prog/anaconda/lib/python3.8/site-packages/conda/core/index.py", line 264, in push_record
        combined_depends = record.combined_depends
      File "/prog/anaconda/lib/python3.8/site-packages/conda/models/records.py", line 340, in combined_depends
        result = {ms.name: ms for ms in MatchSpec.merge(self.depends)}
      File "/prog/anaconda/lib/python3.8/site-packages/conda/models/match_spec.py", line 476, in merge
        reduce(lambda x, y: x._merge(y, union), group) if len(group) > 1 else group[0]
      File "/prog/anaconda/lib/python3.8/site-packages/conda/models/match_spec.py", line 476, in <lambda>
        reduce(lambda x, y: x._merge(y, union), group) if len(group) > 1 else group[0]
      File "/prog/anaconda/lib/python3.8/site-packages/conda/models/match_spec.py", line 506, in _merge
        final = this_component.merge(that_component)
      File "/prog/anaconda/lib/python3.8/site-packages/conda/models/match_spec.py", line 757, in merge
        raise ValueError("Incompatible component merge:\n  - %r\n  - %r"
    ValueError: Incompatible component merge:
      - '*complex*'
      - 'complex_*'

After searching a bit, it appears to arise when anaconda is comparing version specifications, and find incompatibility between two build of petsc, namely :

petsc=[build=*complex*]
petsc[version='>=3.17.3,<3.18.0a0',build=complex_*]

And because *complex* is not equal to complex_*, conda crashes 😅

After looking a bit at the recent changes, I noticed the change at line 27 in 7c2b211 that may have something to do with it (but I'm not so sure at all, it's just a first hypothesis).

Finally, I could avoid the crash (and perform an update) by forcing conda to merge the two specifications when identifying petsc (hard coded in conda code), but I'm not sure this is a valid and safe way to solve it ...

PS : depending on the conda update (if only one package, ...), the exception can also be :

ValueError: Incompatible component merge:
      - '*real*'
      - 'real_*'

Installed packages

# packages in environment at /prog/anaconda:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
absl-py                   0.13.0                   pypi_0    pypi
alabaster                 0.7.12                     py_0    conda-forge
alsa-lib                  1.2.6.1              h7f98852_0    conda-forge
anyio                     3.6.1            py38h578d9bd_0    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0           py38h0a891b7_2    conda-forge
arrow                     1.2.2              pyhd8ed1ab_0    conda-forge
asgiref                   3.5.2              pyhd8ed1ab_0    conda-forge
astroid                   2.6.6                    pypi_0    pypi
atomicwrites              1.4.0              pyh9f0ad1d_0    conda-forge
attr                      2.5.1                h166bdaf_0    conda-forge
attrs                     21.4.0             pyhd8ed1ab_0    conda-forge
autopep8                  1.6.0              pyhd8ed1ab_1    conda-forge
babel                     2.10.3             pyhd8ed1ab_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.11.1             pyha770c72_0    conda-forge
binaryornot               0.4.4                      py_1    conda-forge
black                     22.6.0             pyhd8ed1ab_0    conda-forge
bleach                    5.0.1              pyhd8ed1ab_0    conda-forge
brotli                    1.0.9                h166bdaf_7    conda-forge
brotli-bin                1.0.9                h166bdaf_7    conda-forge
brotli-python             1.0.9            py38hfa26641_7    conda-forge
brotlipy                  0.7.0           py38h0a891b7_1004    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.18.1               h7f98852_0    conda-forge
ca-certificates           2022.6.15            ha878542_0    conda-forge
certifi                   2022.6.15        py38h578d9bd_0    conda-forge
cffi                      1.15.1           py38h4a40e3a_0    conda-forge
chardet                   5.0.0            py38h578d9bd_0    conda-forge
charset-normalizer        2.1.0              pyhd8ed1ab_0    conda-forge
click                     8.1.3            py38h578d9bd_0    conda-forge
cloudpickle               2.1.0              pyhd8ed1ab_0    conda-forge
cma                       3.1.0                    pypi_0    pypi
colorama                  0.4.5              pyhd8ed1ab_0    conda-forge
coloredlogs               15.0.1                   pypi_0    pypi
conda                     4.13.0           py38h578d9bd_1    conda-forge
conda-build               3.21.9           py38h578d9bd_1    conda-forge
conda-env                 2.6.0                         1    conda-forge
conda-package-handling    1.8.1            py38h0a891b7_1    conda-forge
conda-verify              3.1.1           py38h578d9bd_1004    conda-forge
cookiecutter              2.1.1              pyh6c4a22f_0    conda-forge
coverage                  6.4.1            py38h0a891b7_0    conda-forge
cryptography              37.0.2           py38h2b5fc30_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
dash                      2.5.1              pyhd8ed1ab_0    conda-forge
dataclasses               0.8                pyhc8e2a94_3    conda-forge
dbus                      1.13.6               h5008d03_3    conda-forge
debugpy                   1.6.0            py38hfa26641_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
diff-match-patch          20200713           pyh9f0ad1d_0    conda-forge
dill                      0.3.5.1            pyhd8ed1ab_0    conda-forge
docutils                  0.18.1           py38h578d9bd_1    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
expat                     2.4.8                h27087fc_0    conda-forge
fastapi                   0.78.0             pyhd8ed1ab_0    conda-forge
fftw                      3.3.10          mpi_openmpi_h36312d9_2    conda-forge
filelock                  3.7.1              pyhd8ed1ab_0    conda-forge
flake8                    4.0.1              pyhd8ed1ab_2    conda-forge
flake8-bugbear            22.7.1             pyhd8ed1ab_0    conda-forge
flake8-comprehensions     3.10.0             pyhd8ed1ab_0    conda-forge
flask                     2.1.2              pyhd8ed1ab_1    conda-forge
flask-compress            1.12               pyhd8ed1ab_0    conda-forge
flit-core                 3.7.1              pyhd8ed1ab_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.0               h8e229c2_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.33.3           py38h0a891b7_0    conda-forge
freetype                  2.10.4               h0708190_1    conda-forge
future                    0.18.2           py38h578d9bd_5    conda-forge
gettext                   0.19.8.1          h73d1719_1008    conda-forge
giflib                    5.2.1                h36c2ea0_2    conda-forge
glib                      2.70.2               h780b84a_4    conda-forge
glib-tools                2.70.2               h780b84a_4    conda-forge
glob2                     0.7                        py_0    conda-forge
gmp                       6.2.1                h58526e2_0    conda-forge
gmpy2                     2.1.2            py38h8384b0a_0    conda-forge
gst-plugins-base          1.20.3               hf6a322e_0    conda-forge
gstreamer                 1.20.3               hd4edc92_0    conda-forge
h11                       0.13.0             pyhd8ed1ab_1    conda-forge
hdf5                      1.12.1          mpi_openmpi_hb3f3608_4    conda-forge
humanfriendly             10.0                     pypi_0    pypi
hypre                     2.25.0          mpi_openmpi_ha709252_0    conda-forge
icu                       70.1                 h27087fc_0    conda-forge
idna                      3.3                pyhd8ed1ab_0    conda-forge
imagesize                 1.4.1              pyhd8ed1ab_0    conda-forge
importlib-metadata        4.11.4           py38h578d9bd_0    conda-forge
importlib_metadata        4.11.4               hd8ed1ab_0    conda-forge
importlib_resources       5.8.0              pyhd8ed1ab_0    conda-forge
inflection                0.5.1              pyh9f0ad1d_0    conda-forge
iniconfig                 1.1.1              pyh9f0ad1d_0    conda-forge
intervaltree              3.0.2                      py_0    conda-forge
ipykernel                 6.15.0             pyh210e3f2_0    conda-forge
ipython                   7.33.0           py38h578d9bd_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
isort                     5.10.1             pyhd8ed1ab_0    conda-forge
itsdangerous              2.1.2              pyhd8ed1ab_0    conda-forge
jack                      1.9.18            h8c3723f_1002    conda-forge
jedi                      0.18.1           py38h578d9bd_1    conda-forge
jeepney                   0.8.0              pyhd8ed1ab_0    conda-forge
jellyfish                 0.9.0            py38h0a891b7_1    conda-forge
jinja2                    3.0.3              pyhd8ed1ab_0    conda-forge
jinja2-time               0.2.0              pyhd8ed1ab_3    conda-forge
jpeg                      9e                   h166bdaf_2    conda-forge
jsonschema                4.6.1              pyhd8ed1ab_0    conda-forge
jupyter_client            7.3.4              pyhd8ed1ab_0    conda-forge
jupyter_core              4.10.0           py38h578d9bd_0    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
keyring                   23.6.0           py38h578d9bd_0    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.3            py38h43d8883_0    conda-forge
krb5                      1.19.3               h3790be6_0    conda-forge
lazy-object-proxy         1.7.1            py38h0a891b7_1    conda-forge
lcms2                     2.12                 hddcbb42_0    conda-forge
ld_impl_linux-64          2.36.1               hea4e1c9_2    conda-forge
lerc                      3.0                  h9c3ff4c_0    conda-forge
libarchive                3.5.2                hb890918_3    conda-forge
libblas                   3.9.0           15_linux64_openblas    conda-forge
libbrotlicommon           1.0.9                h166bdaf_7    conda-forge
libbrotlidec              1.0.9                h166bdaf_7    conda-forge
libbrotlienc              1.0.9                h166bdaf_7    conda-forge
libcap                    2.64                 ha37c62d_0    conda-forge
libcblas                  3.9.0           15_linux64_openblas    conda-forge
libclang                  14.0.6          default_h2e3cab8_0    conda-forge
libclang13                14.0.6          default_h3a83d3e_0    conda-forge
libcups                   2.3.3                hf5a7f15_1    conda-forge
libcurl                   7.83.1               h7bff187_0    conda-forge
libdb                     6.2.32               h9c3ff4c_0    conda-forge
libdeflate                1.12                 h166bdaf_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libevent                  2.1.10               h9b69904_4    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libflac                   1.3.4                h27087fc_0    conda-forge
libgcc-ng                 12.1.0              h8d9b700_16    conda-forge
libgfortran-ng            12.1.0              h69a702a_16    conda-forge
libgfortran5              12.1.0              hdcd56e2_16    conda-forge
libglib                   2.70.2               h174f98d_4    conda-forge
libgomp                   12.1.0              h8d9b700_16    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
liblapack                 3.9.0           15_linux64_openblas    conda-forge
liblief                   0.11.5               h9c3ff4c_1    conda-forge
libllvm11                 11.1.0               hf817b99_3    conda-forge
libllvm14                 14.0.6               he0ac6c6_0    conda-forge
libnghttp2                1.47.0               h727a467_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libogg                    1.3.4                h7f98852_1    conda-forge
libopenblas               0.3.20          pthreads_h78a6416_0    conda-forge
libopus                   1.3.1                h7f98852_1    conda-forge
libpng                    1.6.37               h21135ba_2    conda-forge
libpq                     14.4                 hd77ab85_0    conda-forge
libsndfile                1.0.31               h9c3ff4c_1    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libspatialindex           1.9.3                h9c3ff4c_4    conda-forge
libssh2                   1.10.0               ha56f1ee_2    conda-forge
libstdcxx-ng              12.1.0              ha89aaad_16    conda-forge
libtiff                   4.4.0                hc85c160_1    conda-forge
libtool                   2.4.6             h9c3ff4c_1008    conda-forge
libudev1                  249                  h166bdaf_4    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libvorbis                 1.3.7                h9c3ff4c_0    conda-forge
libwebp                   1.2.2                h3452ae3_0    conda-forge
libwebp-base              1.2.2                h7f98852_1    conda-forge
libxcb                    1.13              h7f98852_1004    conda-forge
libxkbcommon              1.0.3                he3ba5ed_0    conda-forge
libxml2                   2.9.14               h22db469_2    conda-forge
libzlib                   1.2.12               h166bdaf_1    conda-forge
llvmlite                  0.38.1           py38h38d86a4_0    conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
markdown                  3.3.7              pyhd8ed1ab_0    conda-forge
markupsafe                2.1.1            py38h0a891b7_1    conda-forge
matplotlib                3.5.2            py38h578d9bd_0    conda-forge
matplotlib-base           3.5.2            py38h826bfd8_0    conda-forge
matplotlib-inline         0.1.3              pyhd8ed1ab_0    conda-forge
mccabe                    0.6.1                      py_1    conda-forge
metis                     5.1.0             h58526e2_1006    conda-forge
mistune                   0.8.4           py38h497a2fe_1005    conda-forge
mpc                       1.2.1                h9f54685_0    conda-forge
mpfr                      4.1.0                h9202a9a_1    conda-forge
mpi                       1.0                     openmpi    conda-forge
mpi4py                    3.1.1                    pypi_0    pypi
mpi4py-fft                2.0.4            py38h6d9dd19_2    conda-forge
mpmath                    1.2.1              pyhd8ed1ab_0    conda-forge
multidict                 6.0.2                    pypi_0    pypi
mumps-include             5.2.1               ha770c72_11    conda-forge
mumps-mpi                 5.2.1               hfb3545b_11    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
mypy_extensions           0.4.3            py38h578d9bd_5    conda-forge
mysql-common              8.0.29               haf5c9bc_1    conda-forge
mysql-libs                8.0.29               h28c427c_1    conda-forge
nbclient                  0.6.6              pyhd8ed1ab_0    conda-forge
nbconvert                 6.5.0              pyhd8ed1ab_0    conda-forge
nbconvert-core            6.5.0              pyhd8ed1ab_0    conda-forge
nbconvert-pandoc          6.5.0              pyhd8ed1ab_0    conda-forge
nbformat                  5.4.0              pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  h27087fc_1    conda-forge
nest-asyncio              1.5.5              pyhd8ed1ab_0    conda-forge
networkx                  2.8.4              pyhd8ed1ab_0    conda-forge
notebook                  6.4.12             pyha770c72_0    conda-forge
nspr                      4.32                 h9c3ff4c_1    conda-forge
nss                       3.78                 h2350873_0    conda-forge
numba                     0.55.2           py38hdc3674a_0    conda-forge
numpy                     1.22.4           py38h99721a1_0    conda-forge
numpydoc                  1.4.0              pyhd8ed1ab_0    conda-forge
openjpeg                  2.4.0                hb52868f_1    conda-forge
openmpi                   4.1.4              ha1ae619_100    conda-forge
openssl                   1.1.1p               h166bdaf_0    conda-forge
ortools                   9.0.9048                 pypi_0    pypi
packaging                 21.3               pyhd8ed1ab_0    conda-forge
pandas                    1.4.3            py38h47df419_0    conda-forge
pandoc                    2.18                 ha770c72_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
parmetis                  4.0.3             he9a3056_1005    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
patch                     2.7.6             h7f98852_1002    conda-forge
patchelf                  0.14.5               h58526e2_0    conda-forge
pathspec                  0.9.0              pyhd8ed1ab_0    conda-forge
pcre                      8.45                 h9c3ff4c_0    conda-forge
petsc                     3.17.3          real_h1c6c8d6_100    conda-forge
petsc4py                  3.17.2          real_h9dce1aa_100    conda-forge
pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    9.1.1            py38h0ee0e06_1    conda-forge
pip                       22.1.2             pyhd8ed1ab_0    conda-forge
pkginfo                   1.8.3              pyhd8ed1ab_0    conda-forge
platformdirs              2.5.1              pyhd8ed1ab_0    conda-forge
plotly                    5.9.0              pyhd8ed1ab_0    conda-forge
pluggy                    1.0.0            py38h578d9bd_3    conda-forge
portaudio                 19.6.0               h57a0ea0_5    conda-forge
prometheus_client         0.14.1             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.30             pyha770c72_0    conda-forge
protobuf                  3.17.3                   pypi_0    pypi
psutil                    5.9.1            py38h0a891b7_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptscotch                  6.0.9                h0a9c416_2    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pulseaudio                14.0                 h7f54b18_8    conda-forge
py                        1.11.0             pyh6c4a22f_0    conda-forge
py-lief                   0.11.5           py38h709712a_1    conda-forge
pybind11                  2.9.2            py38h43d8883_1    conda-forge
pybind11-global           2.9.2            py38h43d8883_1    conda-forge
pycodestyle               2.8.0              pyhd8ed1ab_0    conda-forge
pycosat                   0.6.3           py38h0a891b7_1010    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pydantic                  1.9.1            py38h0a891b7_0    conda-forge
pydocstyle                6.1.1              pyhd8ed1ab_0    conda-forge
pyflakes                  2.4.0              pyhd8ed1ab_0    conda-forge
pygments                  2.12.0             pyhd8ed1ab_0    conda-forge
pylint                    2.9.6                    pypi_0    pypi
pyls-spyder               0.4.0              pyhd8ed1ab_0    conda-forge
pyopenssl                 22.0.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyqt                      5.15.4           py38h7492b6b_1    conda-forge
pyqt5-sip                 12.9.0           py38hfa26641_1    conda-forge
pyqtwebengine             5.15.4           py38h7492b6b_1    conda-forge
pyrsistent                0.18.1           py38h0a891b7_1    conda-forge
pysocks                   1.7.1            py38h578d9bd_5    conda-forge
pytest                    7.1.2            py38h578d9bd_0    conda-forge
pytest-cov                3.0.0              pyhd8ed1ab_0    conda-forge
python                    3.8.13          h582c2e5_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.15.3             pyhd8ed1ab_0    conda-forge
python-levenshtein        0.12.2           py38h0a891b7_2    conda-forge
python-libarchive-c       4.0              py38h578d9bd_1    conda-forge
python-lsp-black          1.2.1              pyhd8ed1ab_0    conda-forge
python-lsp-jsonrpc        1.0.0              pyhd8ed1ab_0    conda-forge
python-lsp-server         1.4.1              pyhd8ed1ab_1    conda-forge
python-slugify            6.1.2              pyhd8ed1ab_0    conda-forge
python_abi                3.8                      2_cp38    conda-forge
pytoolconfig              1.2.1              pyhd8ed1ab_0    conda-forge
pytz                      2022.1             pyhd8ed1ab_0    conda-forge
pyxdg                     0.28               pyhd8ed1ab_0    conda-forge
pyyaml                    6.0              py38h0a891b7_4    conda-forge
pyzmq                     23.2.0           py38hfc09fa9_0    conda-forge
qdarkstyle                3.0.3              pyhd8ed1ab_0    conda-forge
qstylizer                 0.2.1              pyhd8ed1ab_0    conda-forge
qt-main                   5.15.4               ha5833f6_2    conda-forge
qt-webengine              5.15.4               hcbadb6c_3    conda-forge
qtawesome                 1.1.1              pyhd8ed1ab_0    conda-forge
qtconsole                 5.3.1              pyhd8ed1ab_0    conda-forge
qtconsole-base            5.3.1              pyha770c72_0    conda-forge
qtpy                      2.1.0              pyhd8ed1ab_0    conda-forge
readline                  8.1.2                h0f457ee_0    conda-forge
requests                  2.28.1             pyhd8ed1ab_0    conda-forge
ripgrep                   13.0.0               h2f28480_2    conda-forge
rope                      1.2.0              pyhd8ed1ab_0    conda-forge
rtree                     1.0.0            py38h02d302b_1    conda-forge
ruamel_yaml               0.15.80         py38h0a891b7_1007    conda-forge
scalapack                 2.2.0                h67de57e_1    conda-forge
scipy                     1.8.1            py38h1ee437e_0    conda-forge
scotch                    6.0.9                hb2e6521_2    conda-forge
secretstorage             3.3.2            py38h578d9bd_1    conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                63.1.0           py38h578d9bd_0    conda-forge
shapely                   1.7.1                    pypi_0    pypi
sip                       6.5.1            py38h709712a_2    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sniffio                   1.2.0            py38h578d9bd_3    conda-forge
snowballstemmer           2.2.0              pyhd8ed1ab_0    conda-forge
sortedcontainers          2.4.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.3.1              pyhd8ed1ab_0    conda-forge
sphinx                    5.0.2              pyh6c4a22f_0    conda-forge
sphinxcontrib-applehelp   1.0.2                      py_0    conda-forge
sphinxcontrib-devhelp     1.0.2                      py_0    conda-forge
sphinxcontrib-htmlhelp    2.0.0              pyhd8ed1ab_0    conda-forge
sphinxcontrib-jsmath      1.0.1                      py_0    conda-forge
sphinxcontrib-qthelp      1.0.3                      py_0    conda-forge
sphinxcontrib-serializinghtml 1.1.5              pyhd8ed1ab_2    conda-forge
spyder                    5.3.1            py38h578d9bd_0    conda-forge
spyder-kernels            2.3.1            py38h578d9bd_0    conda-forge
spyder-notebook           0.1.4                      py_0    spyder-ide
sqlite                    3.39.0               h4ff8645_0    conda-forge
starlette                 0.19.1             pyhd8ed1ab_0    conda-forge
suitesparse               5.10.1               h9e50725_1    conda-forge
superlu                   5.2.2                h00795ac_0    conda-forge
superlu_dist              7.2.0                h34f6f4d_0    conda-forge
sympy                     1.10.1           py38h578d9bd_0    conda-forge
tabulate                  0.8.10             pyhd8ed1ab_0    conda-forge
tbb                       2021.5.0             h924138e_1    conda-forge
tenacity                  8.0.1              pyhd8ed1ab_0    conda-forge
termcolor                 1.1.0                    pypi_0    pypi
terminado                 0.15.0           py38h578d9bd_0    conda-forge
text-unidecode            1.3                        py_0    conda-forge
textdistance              4.3.0              pyhd8ed1ab_0    conda-forge
three-merge               0.1.1              pyh9f0ad1d_0    conda-forge
tinycss2                  1.1.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
tomlkit                   0.11.0             pyha770c72_0    conda-forge
torcpy                    0.1.1                    pypi_0    pypi
tornado                   6.2              py38h0a891b7_0    conda-forge
tqdm                      4.64.0             pyhd8ed1ab_0    conda-forge
traitlets                 5.3.0              pyhd8ed1ab_0    conda-forge
typed-ast                 1.5.4            py38h0a891b7_0    conda-forge
typing                    3.10.0.0           pyhd8ed1ab_0    conda-forge
typing-extensions         4.3.0                hd8ed1ab_0    conda-forge
typing_extensions         4.3.0              pyha770c72_0    conda-forge
ujson                     5.3.0            py38hfa26641_0    conda-forge
unicodedata2              14.0.0           py38h0a891b7_1    conda-forge
unidecode                 1.3.4              pyhd8ed1ab_0    conda-forge
urllib3                   1.26.9             pyhd8ed1ab_0    conda-forge
uvicorn                   0.17.6           py38h578d9bd_1    conda-forge
watchdog                  2.1.9            py38h578d9bd_0    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
werkzeug                  2.1.2              pyhd8ed1ab_1    conda-forge
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
wrapt                     1.14.1           py38h0a891b7_0    conda-forge
wurlitzer                 3.0.2              pyhd8ed1ab_2    conda-forge
xcb-util                  0.4.0                h166bdaf_0    conda-forge
xcb-util-image            0.4.0                h166bdaf_0    conda-forge
xcb-util-keysyms          0.4.0                h166bdaf_0    conda-forge
xcb-util-renderutil       0.3.9                h166bdaf_0    conda-forge
xcb-util-wm               0.4.1                h166bdaf_0    conda-forge
xorg-libxau               1.0.9                h7f98852_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
yapf                      0.32.0             pyhd8ed1ab_0    conda-forge
yarl                      1.4.2                    pypi_0    pypi
zeromq                    4.3.4                h9c3ff4c_1    conda-forge
zipp                      3.8.0              pyhd8ed1ab_0    conda-forge
zlib                      1.2.12               h166bdaf_1    conda-forge
zstd                      1.5.2                h8a70e8d_2    conda-forge

Environment info

active environment : base
    active env location : /prog/anaconda
            shell level : 1
       user config file : /home/cpf5546/.condarc
 populated config files : /home/cpf5546/.condarc
          conda version : 4.13.0
    conda-build version : 3.21.9
         python version : 3.8.13.final.0
       virtual packages : __cuda=11.6=0
                          __linux=5.3.18=0
                          __glibc=2.31=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /prog/anaconda  (writable)
      conda av data dir : /prog/anaconda/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/default/linux-64
                          https://conda.anaconda.org/default/noarch
          package cache : /prog/anaconda/pkgs
                          /home/cpf5546/.conda/pkgs
       envs directories : /prog/anaconda/envs
                          /home/cpf5546/.conda/envs
               platform : linux-64
             user-agent : conda/4.13.0 requests/2.28.1 CPython/3.8.13 Linux/5.3.18-150300.59.71-default opensuse-leap/15.3 glibc/2.31
                UID:GID : 2024:2000
             netrc file : None
           offline mode : False
@tlunet tlunet added the bug label Jul 4, 2022
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dalcinl commented Jul 7, 2022

@minrk We need your input here.

This was referenced Jul 9, 2022
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minrk commented Jul 9, 2022

Arg, this is certainly a conda solver bug that it can't merge overlapping globs (conda/conda#11442). The only solution in the meantime is to be consistent with pinning.

The above 3 PRs rely on the new run_exports to ensure consistent pinning.

This was referenced Jul 10, 2022
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@timryanb timryanb mentioned this issue Jul 11, 2022
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@minrk minrk changed the title Problem with conda update with new petsc version conda bug prevents installing anything that depends on petsc Jul 12, 2022
This was referenced Jul 12, 2022
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minrk commented Jul 13, 2022

repodata patch has been applied, so this should be resolved.

@minrk minrk closed this as completed Jul 13, 2022
@shuds13 shuds13 mentioned this issue Jul 15, 2022
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