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Upgrading cmake required manual upgrade of libuv #171

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jorisvandenbossche opened this issue Dec 28, 2022 · 1 comment
Open
1 task done

Upgrading cmake required manual upgrade of libuv #171

jorisvandenbossche opened this issue Dec 28, 2022 · 1 comment
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@jorisvandenbossche
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jorisvandenbossche commented Dec 28, 2022 •
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Solution to issue cannot be found in the documentation.

  • I checked the documentation.

Issue

I had an old environment with cmake 3.16.4, and updated cmake in this env to 3.25.1 (as a side effect of installing ccache, conda install ccache).

This also updated several other libraries (including dependencies of cmake), but it did not update libuv (all other dependencies of cmake seemed to be updated).
Afterwards when running cmake I got an error like cmake: symbol lookup error: cmake: undefined symbol: uv_fs_get_system_error. Doing a manual conda update libuv (upgrading from 1.34.0 to 1.44.2) resolved the error.

I would expect that updating cmake would therefore also trigger an update of libuv.

Installed packages

$ conda list
# packages in environment at /home/joris/miniconda3:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
anyio                     3.6.2              pyhd8ed1ab_0    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0          py310h5764c6d_3    conda-forge
asttokens                 2.2.1              pyhd8ed1ab_0    conda-forge
attrs                     22.1.0             pyh71513ae_1    conda-forge
babel                     2.11.0             pyhd8ed1ab_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.11.1             pyha770c72_0    conda-forge
bleach                    5.0.1              pyhd8ed1ab_0    conda-forge
brotlipy                  0.7.0           py310h5764c6d_1005    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.18.1               h7f98852_0    conda-forge
ca-certificates           2022.12.7            ha878542_0    conda-forge
certifi                   2022.12.7          pyhd8ed1ab_0    conda-forge
cffi                      1.15.1          py310h255011f_2    conda-forge
charset-normalizer        2.1.1              pyhd8ed1ab_0    conda-forge
conda                     22.9.0          py310hff52083_2    conda-forge
conda-package-handling    2.0.2              pyh38be061_0    conda-forge
conda-package-streaming   0.7.0              pyhd8ed1ab_1    conda-forge
cryptography              38.0.4          py310h600f1e7_0    conda-forge
curl                      7.86.0               h2283fc2_1    conda-forge
debugpy                   1.6.4           py310hd8f1fbe_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
executing                 1.2.0              pyhd8ed1ab_0    conda-forge
expat                     2.5.0                h27087fc_0    conda-forge
flit-core                 3.8.0              pyhd8ed1ab_0    conda-forge
fmt                       9.1.0                h924138e_0    conda-forge
gettext                   0.21.1               h27087fc_0    conda-forge
git                       2.38.1          pl5321h8df7355_1    conda-forge
icu                       70.1                 h27087fc_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
importlib-metadata        4.11.3          py310hff52083_1    conda-forge
importlib_metadata        4.11.3               hd8ed1ab_1    conda-forge
importlib_resources       5.10.1             pyhd8ed1ab_0    conda-forge
ipykernel                 6.17.1             pyh210e3f2_0    conda-forge
ipython                   8.3.0           py310hff52083_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
jedi                      0.18.2             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
json5                     0.9.5              pyh9f0ad1d_0    conda-forge
jsonschema                4.17.3             pyhd8ed1ab_0    conda-forge
jupyter_client            7.4.8              pyhd8ed1ab_0    conda-forge
jupyter_core              5.1.0           py310hff52083_0    conda-forge
jupyter_server            1.17.0             pyhd8ed1ab_0    conda-forge
jupyterlab                3.4.5              pyhd8ed1ab_0    conda-forge
jupyterlab-markup         1.1.0                    pypi_0    pypi
jupyterlab-myst           0.1.6                    pypi_0    pypi
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_server         2.13.0             pyhd8ed1ab_1    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
krb5                      1.19.3               h08a2579_0    conda-forge
ld_impl_linux-64          2.39                 hcc3a1bd_1    conda-forge
libarchive                3.5.2                hada088e_3    conda-forge
libcurl                   7.86.0               h2283fc2_1    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 12.2.0              h65d4601_19    conda-forge
libgomp                   12.2.0              h65d4601_19    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
libmamba                  1.1.0                h70b1f8a_2    conda-forge
libmambapy                1.1.0           py310h69aa5bf_2    conda-forge
libnghttp2                1.47.0               hff17c54_1    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsolv                   0.7.22               h6239696_0    conda-forge
libsqlite                 3.40.0               h753d276_0    conda-forge
libssh2                   1.10.0               hf14f497_3    conda-forge
libstdcxx-ng              12.2.0              h46fd767_19    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libxml2                   2.10.3               h7463322_0    conda-forge
libzlib                   1.2.13               h166bdaf_4    conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
mamba                     1.1.0           py310h51d5547_2    conda-forge
markupsafe                2.1.1           py310h5764c6d_2    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mistune                   0.8.4           py310h6acc77f_1005    conda-forge
nbclassic                 0.4.8              pyhd8ed1ab_0    conda-forge
nbclient                  0.7.2              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                  5.7.0              pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  h27087fc_1    conda-forge
nest-asyncio              1.5.6              pyhd8ed1ab_0    conda-forge
notebook                  6.4.11             pyha770c72_0    conda-forge
notebook-shim             0.2.2              pyhd8ed1ab_0    conda-forge
numpy                     1.23.1                   pypi_0    pypi
openssl                   3.0.7                h0b41bf4_1    conda-forge
packaging                 21.3               pyhd8ed1ab_0    conda-forge
pandoc                    2.19.2               h32600fe_1    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pcre2                     10.40                hc3806b6_0    conda-forge
perl                      5.32.1          2_h7f98852_perl5    conda-forge
pexpect                   4.8.0              pyh1a96a4e_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pip                       22.3.1             pyhd8ed1ab_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_0    conda-forge
platformdirs              2.5.2              pyhd8ed1ab_1    conda-forge
prometheus_client         0.15.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.33             pyha770c72_0    conda-forge
psutil                    5.9.4           py310h5764c6d_0    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pybind11-abi              4                    hd8ed1ab_3    conda-forge
pycosat                   0.6.4           py310h5764c6d_1    conda-forge
pycparser                 2.21                     pypi_0    pypi
pygments                  2.13.0             pyhd8ed1ab_0    conda-forge
pyopenssl                 22.1.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyrsistent                0.19.2          py310h5764c6d_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.10.8          h4a9ceb5_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.16.2             pyhd8ed1ab_0    conda-forge
python_abi                3.10                    3_cp310    conda-forge
pytz                      2022.6             pyhd8ed1ab_0    conda-forge
pyzmq                     24.0.1          py310h330234f_1    conda-forge
readline                  8.1.2                h0f457ee_0    conda-forge
reproc                    14.2.3               h7f98852_0    conda-forge
reproc-cpp                14.2.3               h9c3ff4c_0    conda-forge
requests                  2.28.1             pyhd8ed1ab_1    conda-forge
ruamel_yaml               0.15.80         py310h5764c6d_1008    conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                65.5.1             pyhd8ed1ab_0    conda-forge
six                       1.16.0                   pypi_0    pypi
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.3.2.post1        pyhd8ed1ab_0    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
terminado                 0.17.1             pyh41d4057_0    conda-forge
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
toolz                     0.12.0             pyhd8ed1ab_0    conda-forge
tornado                   6.2             py310h5764c6d_1    conda-forge
traitlets                 5.6.0              pyhd8ed1ab_0    conda-forge
typing_extensions         4.4.0              pyha770c72_0    conda-forge
tzdata                    2022g                h191b570_0    conda-forge
urllib3                   1.26.13            pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          1.4.2              pyhd8ed1ab_0    conda-forge
wheel                     0.38.4             pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
yaml-cpp                  0.7.0                h27087fc_2    conda-forge
youtube-dl                2021.12.17               pypi_0    pypi
zeromq                    4.3.4                h9c3ff4c_1    conda-forge
zipp                      3.11.0             pyhd8ed1ab_0    conda-forge
zstandard                 0.19.0          py310hdeb6495_1    conda-forge
zstd                      1.5.2                h6239696_4    conda-forge

Environment info

$ conda info

     active environment : base
    active env location : /home/joris/miniconda3
            shell level : 1
       user config file : /home/joris/.condarc
 populated config files : /home/joris/.condarc
          conda version : 22.9.0
    conda-build version : not installed
         python version : 3.10.8.final.0
       virtual packages : __linux=5.4.0=0
                          __glibc=2.31=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /home/joris/miniconda3  (writable)
      conda av data dir : /home/joris/miniconda3/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://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/joris/miniconda3/pkgs
                          /home/joris/.conda/pkgs
       envs directories : /home/joris/miniconda3/envs
                          /home/joris/.conda/envs
               platform : linux-64
             user-agent : conda/22.9.0 requests/2.28.1 CPython/3.10.8 Linux/5.4.0-132-generic ubuntu/20.04.5 glibc/2.31
                UID:GID : 1001:1001
             netrc file : None
           offline mode : False
@jorisvandenbossche
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Looking at https://prefix.dev/channels/conda-forge/packages/cmake, I see that libuv has no version pinnings in the list of dependencies. I suppose this is because it is not a package that is included in the global conda-forge pinning? (https://github.com/conda-forge/conda-forge-pinning-feedstock/blob/main/recipe/conda_build_config.yaml)

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