Failed process: error while adding python cis library

General Usage
, ,
1

I want to add cis library which has api in python.
using CondaPkg; CondaPkg.add("cis")

image
image816Γ—969 161 KB

@abraemer

2

I haven’t used CondaPkg.jl so I don’t know what this error means.

However I moved the topic from Tooling to General Usage which I feel is more appropriate so you are more likely to get help from someone with more experience in Python things.

3

Can you show more of the output at the bottom?

2 Likes
4
See more of output at the bottom 
    CondaPkg Found dependencies: /tmp/jl_RMuNbM/CondaPkg.toml
    CondaPkg Found dependencies: /home/raman/.julia/packages/PythonCall/S5MOg/CondaPkg.toml
    CondaPkg Resolving changes
             + cis
             + libstdcxx-ng
             + python
    CondaPkg Creating environment
             β”‚ /home/raman/.julia/artifacts/7973f2c7725e2d0eef7a95159454c4145f0945a2/bin/micromamba
             β”‚ -r /home/raman/.julia/scratchspaces/0b3b1443-0f03-428d-bdfb-f27f9c1191ea/root
             β”‚ create
             β”‚ -y
             β”‚ -p /tmp/jl_RMuNbM/.CondaPkg/env
             β”‚ --override-channels
             β”‚ --no-channel-priority
             β”‚ cis[version='*']
             β”‚ libstdcxx-ng[version='>=3.4,<13.0']
             β”‚ python[version='>=3.8,<4',channel='conda-forge',build='*cpython*']
             β”” -c conda-forge

Transaction

  Prefix: /tmp/jl_RMuNbM/.CondaPkg/env

  Updating specs:

   - cis=*
   - libstdcxx-ng[version='>=3.4,<13.0']
   - conda-forge::python[version='>=3.8,<4',build=*cpython*]


  Package                           Version  Build                    Channel           Size
──────────────────────────────────────────────────────────────────────────────────────────────
  Install:
──────────────────────────────────────────────────────────────────────────────────────────────

  + libstdcxx-ng                     12.3.0  hc0a3c3a_7               conda-forge     Cached
  + _libgcc_mutex                       0.1  conda_forge              conda-forge     Cached
  + ld_impl_linux-64                   2.40  hf3520f5_3               conda-forge     Cached
  + ca-certificates                2024.6.2  hbcca054_0               conda-forge     Cached
  + python_abi                         3.11  4_cp311                  conda-forge     Cached
  + libgomp                          13.2.0  h77fa898_7               conda-forge     Cached
  + _openmp_mutex                       4.5  2_gnu                    conda-forge     Cached
  + libgcc-ng                        13.2.0  h77fa898_7               conda-forge     Cached
  + xorg-xf86vidmodeproto             2.3.1  h7f98852_1002            conda-forge     Cached
  + xorg-xproto                      7.0.31  h7f98852_1007            conda-forge     Cached
  + xorg-kbproto                      1.0.7  h7f98852_1002            conda-forge     Cached
  + xorg-renderproto                 0.11.1  h7f98852_1002            conda-forge     Cached
  + xorg-libxdmcp                     1.1.3  h7f98852_0               conda-forge     Cached
  + pthread-stubs                       0.4  h36c2ea0_1001            conda-forge     Cached
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  + graphite2                        1.3.13  h59595ed_1003            conda-forge     Cached
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  + libev                              4.33  hd590300_2               conda-forge     Cached
  + alsa-lib                         1.2.12  h4ab18f5_0               conda-forge     Cached
  + xorg-xextproto                    7.3.0  h0b41bf4_1003            conda-forge     Cached
  + libbrotlicommon                   1.1.0  hd590300_1               conda-forge     Cached
  + attr                              2.5.1  h166bdaf_1               conda-forge     Cached
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  + libgettextpo                     0.22.5  h59595ed_2               conda-forge     Cached
  + libasprintf                      0.22.5  h661eb56_2               conda-forge     Cached
  + libiconv                           1.17  hd590300_2               conda-forge     Cached
  + snappy                            1.2.0  hdb0a2a9_1               conda-forge     Cached
  + mpg123                           1.32.6  h59595ed_0               conda-forge     Cached
  + libopus                           1.3.1  h7f98852_1               conda-forge     Cached
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  + yaml                              0.2.5  h7f98852_2               conda-forge     Cached
  + libgfortran5                     13.2.0  hca663fb_7               conda-forge     Cached
  + geos                             3.12.1  h59595ed_0               conda-forge     Cached
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  + keyutils                          1.6.1  h166bdaf_0               conda-forge     Cached
  + libaec                            1.1.3  h59595ed_0               conda-forge     Cached
  + openssl                           3.3.1  h4ab18f5_0               conda-forge     Cached
  + libxcrypt                        4.4.36  hd590300_1               conda-forge     Cached
  + libzlib                           1.3.1  h4ab18f5_1               conda-forge     Cached
  + libffi                            3.4.2  h7f98852_5               conda-forge     Cached
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  + ncurses                             6.5  h59595ed_0               conda-forge     Cached
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  + libnsl                            2.0.1  hd590300_0               conda-forge     Cached
  + libexpat                          2.6.2  h59595ed_0               conda-forge     Cached
  + xz                                5.2.6  h166bdaf_0               conda-forge     Cached
  + libbrotlienc                      1.1.0  hd590300_1               conda-forge     Cached
  + libbrotlidec                      1.1.0  hd590300_1               conda-forge     Cached
  + libcap                             2.69  h0f662aa_0               conda-forge     Cached
  + libgettextpo-devel               0.22.5  h59595ed_2               conda-forge     Cached
  + libasprintf-devel                0.22.5  h661eb56_2               conda-forge     Cached
  + libvorbis                         1.3.7  h9c3ff4c_0               conda-forge     Cached
  + libxcb                             1.15  h0b41bf4_0               conda-forge     Cached
  + libgfortran-ng                   13.2.0  h69a702a_7               conda-forge     Cached
  + mysql-common                      8.3.0  hf1915f5_4               conda-forge     Cached
  + libevent                         2.1.12  hf998b51_1               conda-forge     Cached
  + libnghttp2                       1.58.0  h47da74e_1               conda-forge     Cached
  + libpng                           1.6.43  h2797004_0               conda-forge     Cached
  + hdf4                             4.2.15  h2a13503_7               conda-forge     Cached
  + libssh2                          1.11.0  h0841786_0               conda-forge     Cached
  + zstd                              1.5.6  ha6fb4c9_0               conda-forge     Cached
  + zlib                              1.3.1  h4ab18f5_1               conda-forge     Cached
  + tk                               8.6.13  noxft_h4845f30_101       conda-forge     Cached
  + libsqlite                        3.46.0  hde9e2c9_0               conda-forge     Cached
  + libzip                           1.10.1  h2629f0a_3               conda-forge     Cached
  + pcre2                             10.43  hcad00b1_0               conda-forge     Cached
  + libedit                    3.1.20191231  he28a2e2_2               conda-forge     Cached
  + readline                            8.2  h8228510_1               conda-forge     Cached
  + xorg-libsm                        1.2.4  h7391055_0               conda-forge     Cached
  + libudunits2                      2.2.28  h40f5838_3               conda-forge     Cached
  + expat                             2.6.2  h59595ed_0               conda-forge     Cached
  + libxml2                          2.12.7  hc051c1a_1               conda-forge     Cached
  + brotli-bin                        1.1.0  hd590300_1               conda-forge     Cached
  + gettext                          0.22.5  h59595ed_2               conda-forge     Cached
  + xcb-util-wm                       0.4.1  h8ee46fc_1               conda-forge     Cached
  + xcb-util-keysyms                  0.4.0  h8ee46fc_1               conda-forge     Cached
  + xcb-util                          0.4.0  hd590300_1               conda-forge     Cached
  + xorg-libx11                       1.8.9  h8ee46fc_0               conda-forge     Cached
  + xcb-util-renderutil               0.3.9  hd590300_1               conda-forge     Cached
  + libopenblas                      0.3.27  pthreads_h413a1c8_0      conda-forge     Cached
  + freetype                         2.12.1  h267a509_2               conda-forge     Cached
  + mysql-libs                        8.3.0  hca2cd23_4               conda-forge     Cached
  + blosc                            1.21.5  hc2324a3_1               conda-forge     Cached
  + libtiff                           4.6.0  h1dd3fc0_3               conda-forge     Cached
  + nss                               3.100  hca3bf56_0               conda-forge     Cached
  + libglib                          2.80.2  hf974151_0               conda-forge     Cached
  + krb5                             1.21.2  h659d440_0               conda-forge     Cached
  + sqlite                           3.46.0  h6d4b2fc_0               conda-forge     Cached
  + udunits2                         2.2.28  h40f5838_3               conda-forge     Cached
  + libllvm15                        15.0.7  hb3ce162_4               conda-forge     Cached
  + libllvm18                        18.1.7  hb77312f_0               conda-forge     Cached
  + brotli                            1.1.0  hd590300_1               conda-forge     Cached
  + libgpg-error                       1.49  h4f305b6_0               conda-forge     Cached
  + libflac                           1.4.3  h59595ed_0               conda-forge     Cached
  + xcb-util-image                    0.4.0  h8ee46fc_1               conda-forge     Cached
  + xorg-libxrender                  0.9.11  hd590300_0               conda-forge     Cached
  + xorg-libxext                      1.3.4  h0b41bf4_2               conda-forge     Cached
  + xkeyboard-config                   2.42  h4ab18f5_0               conda-forge     Cached
  + libblas                           3.9.0  22_linux64_openblas      conda-forge     Cached
  + fontconfig                       2.14.2  h14ed4e7_0               conda-forge     Cached
  + openjpeg                          2.5.2  h488ebb8_0               conda-forge     Cached
  + lcms2                              2.16  hb7c19ff_0               conda-forge     Cached
  + glib-tools                       2.80.2  hb6ce0ca_0               conda-forge     Cached
  + dbus                             1.13.6  h5008d03_3               conda-forge     Cached
  + libpq                              16.3  ha72fbe1_0               conda-forge     Cached
  + libcups                           2.3.3  h4637d8d_4               conda-forge     Cached
  + libcurl                           8.8.0  hca28451_0               conda-forge     Cached
  + libclang-cpp15                   15.0.7  default_h127d8a8_5       conda-forge     Cached
  + libclang13                       18.1.7  default_h087397f_0       conda-forge     Cached
  + libgcrypt                        1.10.3  hd590300_0               conda-forge     Cached
  + libsndfile                        1.2.2  hc60ed4a_1               conda-forge     Cached
  + libxkbcommon                      1.7.0  h662e7e4_0               conda-forge     Cached
  + libcblas                          3.9.0  22_linux64_openblas      conda-forge     Cached
  + liblapack                         3.9.0  22_linux64_openblas      conda-forge     Cached
  + hdf5                             1.14.3  nompi_hdf9ad27_105       conda-forge     Cached
  + proj                              9.4.0  hb784bbd_2               conda-forge     Cached
  + libsystemd0                         255  h3516f8a_1               conda-forge     Cached
  + libnetcdf                         4.9.2  nompi_h135f659_114       conda-forge     Cached
  + pulseaudio-client                  17.0  hb77b528_0               conda-forge     Cached
  + tzdata                            2024a  h0c530f3_0               conda-forge     Cached
  + font-ttf-dejavu-sans-mono          2.37  hab24e00_0               conda-forge     Cached
  + font-ttf-inconsolata              3.000  h77eed37_0               conda-forge     Cached
  + font-ttf-source-code-pro          2.038  h77eed37_0               conda-forge     Cached
  + font-ttf-ubuntu                    0.83  h77eed37_2               conda-forge     Cached
  + fonts-conda-forge                     1  0                        conda-forge     Cached
  + fonts-conda-ecosystem                 1  0                        conda-forge     Cached
  + python                           3.11.9  hb806964_0_cpython       conda-forge     Cached
  + cairo                            1.18.0  h3faef2a_0               conda-forge     Cached
  + harfbuzz                          8.5.0  hfac3d4d_0               conda-forge     Cached
  + wheel                            0.43.0  pyhd8ed1ab_1             conda-forge     Cached
  + setuptools                       70.0.0  pyhd8ed1ab_0             conda-forge     Cached
  + pip                                24.0  pyhd8ed1ab_0             conda-forge     Cached
  + tomli                             2.0.1  pyhd8ed1ab_0             conda-forge     Cached
  + ply                                3.11  pyhd8ed1ab_2             conda-forge     Cached
  + zipp                             3.19.2  pyhd8ed1ab_0             conda-forge     Cached
  + locket                            1.0.0  pyhd8ed1ab_0             conda-forge     Cached
  + six                              1.16.0  pyh6c4a22f_0             conda-forge     Cached
  + pyshp                             2.3.1  pyhd8ed1ab_0             conda-forge     Cached
  + munkres                           1.1.4  pyh9f0ad1d_0             conda-forge     Cached
  + toml                             0.10.2  pyhd8ed1ab_0             conda-forge     Cached
  + pyparsing                         3.1.2  pyhd8ed1ab_0             conda-forge     Cached
  + cycler                           0.12.1  pyhd8ed1ab_0             conda-forge     Cached
  + pytz                             2024.1  pyhd8ed1ab_0             conda-forge     Cached
  + python-tzdata                    2024.1  pyhd8ed1ab_0             conda-forge     Cached
  + certifi                        2024.6.2  pyhd8ed1ab_0             conda-forge     Cached
  + toolz                            0.12.1  pyhd8ed1ab_0             conda-forge     Cached
  + packaging                          24.1  pyhd8ed1ab_0             conda-forge     Cached
  + fsspec                         2024.6.0  pyhff2d567_0             conda-forge     Cached
  + cloudpickle                       3.0.0  pyhd8ed1ab_0             conda-forge     Cached
  + click                             8.1.7  unix_pyh707e725_0        conda-forge     Cached
  + antlr-python-runtime             4.11.1  pyhd8ed1ab_0             conda-forge     Cached
  + importlib-metadata                7.1.0  pyha770c72_0             conda-forge     Cached
  + python-dateutil                   2.9.0  pyhd8ed1ab_0             conda-forge     Cached
  + partd                             1.4.2  pyhd8ed1ab_0             conda-forge     Cached
  + importlib_metadata                7.1.0  hd8ed1ab_0               conda-forge     Cached
  + glib                             2.80.2  hf974151_0               conda-forge     Cached
  + markupsafe                        2.1.5  py311h459d7ec_0          conda-forge     Cached
  + tornado                           6.4.1  py311h331c9d8_0          conda-forge     Cached
  + pillow                           10.3.0  py311h18e6fac_0          conda-forge     Cached
  + kiwisolver                        1.4.5  py311h9547e67_1          conda-forge     Cached
  + pyyaml                            6.0.1  py311h459d7ec_1          conda-forge     Cached
  + python-xxhash                     3.4.1  py311h459d7ec_0          conda-forge     Cached
  + numpy                            1.26.4  py311h64a7726_0          conda-forge     Cached
  + psutil                            5.9.8  py311h459d7ec_0          conda-forge     Cached
  + fonttools                        4.53.0  py311h331c9d8_0          conda-forge     Cached
  + pyproj                            3.6.1  py311hc21b84f_7          conda-forge     Cached
  + sip                              6.7.12  py311hb755f60_0          conda-forge     Cached
  + gstreamer                        1.24.4  haf2f30d_0               conda-forge     Cached
  + contourpy                         1.2.1  py311h9547e67_0          conda-forge     Cached
  + shapely                           2.0.4  py311h0bed3d6_1          conda-forge     Cached
  + cftime                            1.6.4  py311h18e1886_0          conda-forge     Cached
  + scipy                            1.13.1  py311h517d4fd_0          conda-forge     Cached
  + pyhdf                            0.11.4  py311h389aa87_1          conda-forge     Cached
  + pandas                            2.2.2  py311h14de704_1          conda-forge     Cached
  + pyqt5-sip                       12.12.2  py311hb755f60_5          conda-forge     Cached
  + gst-plugins-base                 1.24.4  h9ad1361_0               conda-forge     Cached
  + matplotlib-base                   3.8.4  py311ha4ca890_2          conda-forge     Cached
  + netcdf4                           1.6.5  nompi_py311h74118c1_102  conda-forge     Cached
  + qt-main                          5.15.8  hc9dc06e_21              conda-forge     Cached
  + cartopy                          0.23.0  py311h14de704_1          conda-forge     Cached
  + pyqt                             5.15.9  py311hf0fb5b6_5          conda-forge     Cached
  + matplotlib                        3.8.4  py311h38be061_2          conda-forge     Cached
  + jinja2                            3.1.4  pyhd8ed1ab_0             conda-forge     Cached
  + dask-core                      2024.5.2  pyhd8ed1ab_0             conda-forge     Cached
  + cf-units                          3.2.0  py311h18e1886_5          conda-forge     Cached
  + iris                              3.9.0  pyha770c72_0             conda-forge     Cached
  + cis                               1.7.9  py311h38be061_0          conda-forge     Cached

  Summary:

  Install: 197 packages

  Total download: 0 B

──────────────────────────────────────────────────────────────────────────────────────────────



Transaction starting
Linking libstdcxx-ng-12.3.0-hc0a3c3a_7
Linking _libgcc_mutex-0.1-conda_forge
Linking ld_impl_linux-64-2.40-hf3520f5_3
Linking ca-certificates-2024.6.2-hbcca054_0
Linking python_abi-3.11-4_cp311
Linking libgomp-13.2.0-h77fa898_7
Linking _openmp_mutex-4.5-2_gnu
Linking libgcc-ng-13.2.0-h77fa898_7
Linking xorg-xf86vidmodeproto-2.3.1-h7f98852_1002
Linking xorg-xproto-7.0.31-h7f98852_1007
Linking xorg-kbproto-1.0.7-h7f98852_1002
Linking xorg-renderproto-0.11.1-h7f98852_1002
Linking xorg-libxdmcp-1.1.3-h7f98852_0
Linking pthread-stubs-0.4-h36c2ea0_1001
Linking pixman-0.43.2-h59595ed_0
Linking graphite2-1.3.13-h59595ed_1003
Linking c-ares-1.28.1-hd590300_0
Linking libev-4.33-hd590300_2
Linking alsa-lib-1.2.12-h4ab18f5_0
Linking xorg-xextproto-7.3.0-h0b41bf4_1003
Linking libbrotlicommon-1.1.0-hd590300_1
Linking attr-2.5.1-h166bdaf_1
Linking gettext-tools-0.22.5-h59595ed_2
Linking libgettextpo-0.22.5-h59595ed_2
Linking libasprintf-0.22.5-h661eb56_2
Linking libiconv-1.17-hd590300_2
Linking snappy-1.2.0-hdb0a2a9_1
Linking mpg123-1.32.6-h59595ed_0
Linking libopus-1.3.1-h7f98852_1
Linking libogg-1.3.4-h7f98852_1
Linking lame-3.100-h166bdaf_1003
Linking lz4-c-1.9.4-hcb278e6_0
Linking libwebp-base-1.4.0-hd590300_0
Linking libjpeg-turbo-3.0.0-hd590300_1
Linking xorg-libxau-1.0.11-hd590300_0
Linking xorg-libice-1.1.1-hd590300_0
Linking nspr-4.35-h27087fc_0
Linking icu-73.2-h59595ed_0
Linking libdeflate-1.20-hd590300_0
Linking lerc-4.0.0-h27087fc_0
Linking yaml-0.2.5-h7f98852_2
Linking libgfortran5-13.2.0-hca663fb_7
Linking geos-3.12.1-h59595ed_0
Linking xxhash-0.8.2-hd590300_0
Linking keyutils-1.6.1-h166bdaf_0
Linking libaec-1.1.3-h59595ed_0
Linking openssl-3.3.1-h4ab18f5_0
Linking libxcrypt-4.4.36-hd590300_1
Linking libzlib-1.3.1-h4ab18f5_1
Linking libffi-3.4.2-h7f98852_5
Linking bzip2-1.0.8-hd590300_5
Linking ncurses-6.5-h59595ed_0
Linking libuuid-2.38.1-h0b41bf4_0
Linking libnsl-2.0.1-hd590300_0
Linking libexpat-2.6.2-h59595ed_0
Linking xz-5.2.6-h166bdaf_0
Linking libbrotlienc-1.1.0-hd590300_1
Linking libbrotlidec-1.1.0-hd590300_1
Linking libcap-2.69-h0f662aa_0
Linking libgettextpo-devel-0.22.5-h59595ed_2
Linking libasprintf-devel-0.22.5-h661eb56_2
Linking libvorbis-1.3.7-h9c3ff4c_0
Linking libxcb-1.15-h0b41bf4_0
Linking libgfortran-ng-13.2.0-h69a702a_7
Linking mysql-common-8.3.0-hf1915f5_4
Linking libevent-2.1.12-hf998b51_1
Linking libnghttp2-1.58.0-h47da74e_1
Linking libpng-1.6.43-h2797004_0
Linking hdf4-4.2.15-h2a13503_7
Linking libssh2-1.11.0-h0841786_0
Linking zstd-1.5.6-ha6fb4c9_0
Linking zlib-1.3.1-h4ab18f5_1
Linking tk-8.6.13-noxft_h4845f30_101
Linking libsqlite-3.46.0-hde9e2c9_0
Linking libzip-1.10.1-h2629f0a_3
Linking pcre2-10.43-hcad00b1_0
Linking libedit-3.1.20191231-he28a2e2_2
Linking readline-8.2-h8228510_1
Linking xorg-libsm-1.2.4-h7391055_0
Linking libudunits2-2.2.28-h40f5838_3
Linking expat-2.6.2-h59595ed_0
Linking libxml2-2.12.7-hc051c1a_1
Linking brotli-bin-1.1.0-hd590300_1
Linking gettext-0.22.5-h59595ed_2
Linking xcb-util-wm-0.4.1-h8ee46fc_1
Linking xcb-util-keysyms-0.4.0-h8ee46fc_1
Linking xcb-util-0.4.0-hd590300_1
Linking xorg-libx11-1.8.9-h8ee46fc_0
Linking xcb-util-renderutil-0.3.9-hd590300_1
Linking libopenblas-0.3.27-pthreads_h413a1c8_0
Linking freetype-2.12.1-h267a509_2
Linking mysql-libs-8.3.0-hca2cd23_4
Linking blosc-1.21.5-hc2324a3_1
Linking libtiff-4.6.0-h1dd3fc0_3
Linking nss-3.100-hca3bf56_0
Linking libglib-2.80.2-hf974151_0
Linking krb5-1.21.2-h659d440_0
Linking sqlite-3.46.0-h6d4b2fc_0
Linking udunits2-2.2.28-h40f5838_3
Linking libllvm15-15.0.7-hb3ce162_4
Linking libllvm18-18.1.7-hb77312f_0
Linking brotli-1.1.0-hd590300_1
Linking libgpg-error-1.49-h4f305b6_0
Linking libflac-1.4.3-h59595ed_0
Linking xcb-util-image-0.4.0-h8ee46fc_1
Linking xorg-libxrender-0.9.11-hd590300_0
Linking xorg-libxext-1.3.4-h0b41bf4_2
Linking xkeyboard-config-2.42-h4ab18f5_0
Linking libblas-3.9.0-22_linux64_openblas
Linking fontconfig-2.14.2-h14ed4e7_0
Linking openjpeg-2.5.2-h488ebb8_0
Linking lcms2-2.16-hb7c19ff_0
Linking glib-tools-2.80.2-hb6ce0ca_0
Linking dbus-1.13.6-h5008d03_3
Linking libpq-16.3-ha72fbe1_0
Linking libcups-2.3.3-h4637d8d_4
Linking libcurl-8.8.0-hca28451_0
Linking libclang-cpp15-15.0.7-default_h127d8a8_5
Linking libclang13-18.1.7-default_h087397f_0
Linking libgcrypt-1.10.3-hd590300_0
Linking libsndfile-1.2.2-hc60ed4a_1
Linking libxkbcommon-1.7.0-h662e7e4_0
Linking libcblas-3.9.0-22_linux64_openblas
Linking liblapack-3.9.0-22_linux64_openblas
Linking hdf5-1.14.3-nompi_hdf9ad27_105
Linking proj-9.4.0-hb784bbd_2
Linking libsystemd0-255-h3516f8a_1
Linking libnetcdf-4.9.2-nompi_h135f659_114
Linking pulseaudio-client-17.0-hb77b528_0
Linking tzdata-2024a-h0c530f3_0
Linking font-ttf-dejavu-sans-mono-2.37-hab24e00_0
Linking font-ttf-inconsolata-3.000-h77eed37_0
Linking font-ttf-source-code-pro-2.038-h77eed37_0
Linking font-ttf-ubuntu-0.83-h77eed37_2
Linking fonts-conda-forge-1-0
Linking fonts-conda-ecosystem-1-0
Linking python-3.11.9-hb806964_0_cpython
Linking cairo-1.18.0-h3faef2a_0
Linking harfbuzz-8.5.0-hfac3d4d_0
Linking wheel-0.43.0-pyhd8ed1ab_1
Linking setuptools-70.0.0-pyhd8ed1ab_0
critical libmamba filesystem error: cannot copy: Input/output error [/home/raman/.julia/scratchspaces/0b3b1443-0f03-428d-bdfb-f27f9c1191ea/root/pkgs/setuptools-70.0.0-pyhd8ed1ab_0/site-packages/setuptools/_distutils/command/sdist.py] [/tmp/jl_RMuNbM/.CondaPkg/env/lib/python3.11/site-packages/setuptools/_distutils/command/sdist.py]
5

Your problem is on this line. Drill into that.

6

How to solve that problem? I have two version of python installed on my PC.

7

I have no idea. Why is there a file system error? Is your disk full?

Does /home/raman/.julia/scratchspaces/0b3b1443-0f03-428d-bdfb-f27f9c1191ea/root/pkgs/setuptools-70.0.0-pyhd8ed1ab_0/site-packages/setuptools/_distutils/command/sdist.py exist? Can you access it?

Does /tmp/jl_RMuNbM/.CondaPkg/env/lib/python3.11/site-packages/setuptools/_distutils/command/sdist.py exist? Can you copy a file there?

8

@mkitti My Disk is not full. Yes, these file exists. Which file should i copy to /tmp… ? :thinking: May be it is not copying due to same name file already exists in /tmp.

9

Is there any plan to have api of cis library[5. CIS as a Python library (API) β€” Community Intercomparison Suite 1.6.0 (Stable) documentation] in Julia? Please help me how i can overcome my error. :face_with_monocle:

    CondaPkg Found dependencies: /home/raman/.julia/environments/v1.10/CondaPkg.toml
    CondaPkg Found dependencies: /home/raman/.julia/packages/PythonCall/S5MOg/CondaPkg.toml
    CondaPkg Resolving changes
             + libstdcxx-ng
             + python
    CondaPkg Installing packages
             β”‚ /home/raman/.julia/artifacts/7973f2c7725e2d0eef7a95159454c4145f0945a2/bin/micromamba
             β”‚ -r /home/raman/.julia/scratchspaces/0b3b1443-0f03-428d-bdfb-f27f9c1191ea/root
             β”‚ install
             β”‚ -y
             β”‚ -p /home/raman/.julia/environments/v1.10/.CondaPkg/env
             β”‚ --override-channels
             β”‚ --no-channel-priority
             β”‚ cis[version='*']
             β”‚ libstdcxx-ng[version='>=3.4,<13.0']
             β”‚ python[version='>=3.8,<4',channel='conda-forge',build='*cpython*']
             β”” -c conda-forge
conda-forge/noarch                                  15.0MB @ 396.7kB/s 37.9s
conda-forge/linux-64                                35.3MB @ 702.2kB/s 50.5s

Transaction

  Prefix: /home/raman/.julia/environments/v1.10/.CondaPkg/env

  Updating specs:

   - cis=*
   - libstdcxx-ng[version='>=3.4,<13.0']
   - conda-forge::python[version='>=3.8,<4',build=*cpython*]


  Package         Version  Build               Channel           Size
───────────────────────────────────────────────────────────────────────
  Reinstall:
───────────────────────────────────────────────────────────────────────

  o python         3.11.9  hb806964_0_cpython  conda-forge     Cached

  Downgrade:
───────────────────────────────────────────────────────────────────────

  - libstdcxx-ng   13.2.0  hc0a3c3a_7          conda-forge     Cached
  + libstdcxx-ng   12.3.0  hc0a3c3a_7          conda-forge     Cached

  Summary:

  Reinstall: 1 packages
  Downgrade: 1 packages

  Total download: 0 B

───────────────────────────────────────────────────────────────────────



Transaction starting
Changing libstdcxx-ng-13.2.0-hc0a3c3a_7 ==> libstdcxx-ng-12.3.0-hc0a3c3a_7
Reinstalling python-3.11.9-hb806964_0_cpython

Transaction finished

To activate this environment, use:

    micromamba activate /home/raman/.julia/environments/v1.10/.CondaPkg/env

Or to execute a single command in this environment, use:

    micromamba run -p /home/raman/.julia/environments/v1.10/.CondaPkg/env mycommand
10

There is no error in what you posted. This is just the Python packager manager installing the library.

11

This is error. :point_down: See post 4.

Linking wheel-0.43.0-pyhd8ed1ab_1
Linking setuptools-70.0.0-pyhd8ed1ab_0
critical libmamba filesystem error: cannot copy: Input/output error [/home/raman/y/pkgs/setuptools-70.0.0-pyhd8ed1ab_0/site-packages/setuptools/_distutils/dist.py] [/tmp/jl_KAmyfx/.CondaPkg/env/lib/python3.11/site-packages/setuptools/_distutils/dist.py]

@ufechner7

12

I tried on Ubuntu Linux using Julia 1.10.4:

mkdir tmp
cd tmp
julia --project="."

and then in Julia:

using CondaPkg
CondaPkg.add("cis")

I get some warnings, otherwise it works fine.

julia> using CondaPkg
 β”‚ Package CondaPkg not found, but a package named CondaPkg is available from a
 β”‚ registry. 
 β”‚ Install package?
 β”‚   (tmp) pkg> add CondaPkg 
 β”” (y/n/o) [y]: 
    Updating registry at `~/.julia/registries/General.toml`
   Resolving package versions...
   Installed MicroMamba ───── v0.1.14
   Installed micromamba_jll ─ v1.5.8+0
   Installed CondaPkg ─────── v0.2.22
   Installed Pidfile ──────── v1.3.0
   Installed JSON3 ────────── v1.14.0
    Updating `~/repos/tmp/Project.toml`
  [992eb4ea] + CondaPkg v0.2.22
    Updating `~/repos/tmp/Manifest.toml`
  [992eb4ea] + CondaPkg v0.2.22
  [692b3bcd] + JLLWrappers v1.5.0
  [0f8b85d8] + JSON3 v1.14.0
  [0b3b1443] + MicroMamba v0.1.14
  [69de0a69] + Parsers v2.8.1
  [fa939f87] + Pidfile v1.3.0
  [aea7be01] + PrecompileTools v1.2.1
  [21216c6a] + Preferences v1.4.3
  [6c6a2e73] + Scratch v1.2.1
  [856f2bd8] + StructTypes v1.10.0
  [f8abcde7] + micromamba_jll v1.5.8+0
  [0dad84c5] + ArgTools v1.1.1
  [56f22d72] + Artifacts
  [2a0f44e3] + Base64
  [ade2ca70] + Dates
  [f43a241f] + Downloads v1.6.0
  [7b1f6079] + FileWatching
  [b77e0a4c] + InteractiveUtils
  [4af54fe1] + LazyArtifacts
  [b27032c2] + LibCURL v0.6.4
  [76f85450] + LibGit2
  [8f399da3] + Libdl
  [56ddb016] + Logging
  [d6f4376e] + Markdown
  [a63ad114] + Mmap
  [ca575930] + NetworkOptions v1.2.0
  [44cfe95a] + Pkg v1.10.0
  [de0858da] + Printf
  [3fa0cd96] + REPL
  [9a3f8284] + Random
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization
  [6462fe0b] + Sockets
  [fa267f1f] + TOML v1.0.3
  [a4e569a6] + Tar v1.10.0
  [8dfed614] + Test
  [cf7118a7] + UUIDs
  [4ec0a83e] + Unicode
  [deac9b47] + LibCURL_jll v8.4.0+0
  [e37daf67] + LibGit2_jll v1.6.4+0
  [29816b5a] + LibSSH2_jll v1.11.0+1
  [c8ffd9c3] + MbedTLS_jll v2.28.2+1
  [14a3606d] + MozillaCACerts_jll v2023.1.10
  [83775a58] + Zlib_jll v1.2.13+1
  [8e850ede] + nghttp2_jll v1.52.0+1
  [3f19e933] + p7zip_jll v17.4.0+2
Precompiling project...
  5 dependencies successfully precompiled in 35 seconds. 9 already precompiled.
  1 dependency had output during precompilation:
β”Œ micromamba_jll
β”‚   Downloading artifact: micromamba
β”‚  
β”‚  [pid 6296] waiting for IO to finish:
β”‚   Handle type        uv_handle_t->data
β”‚   timer              0x1d33860->0x7f1837ba9d20
β”‚  This means that a package has started a background task or event source that has not finished running. For precompilation to complete successfully, the event source needs to be closed explicitly. See the developer documentation on fixing precompilation hangs for more help.
β”‚  
β”‚  [pid 6296] waiting for IO to finish:
β”‚   Handle type        uv_handle_t->data
β”‚   timer              0x1d33860->0x7f1837ba9d20
β”‚  This means that a package has started a background task or event source that has not finished running. For precompilation to complete successfully, the event source needs to be closed explicitly. See the developer documentation on fixing precompilation hangs for more help.
β””

I think these warnings can be ignored.

What is your output of:

versioninfo()

?

13 
julia> versioninfo()
Julia Version 1.10.4
Commit 48d4fd48430 (2024-06-04 10:41 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 4 Γ— Intel(R) Core(TM) i3-4005U CPU @ 1.70GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, haswell)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)
14

Can you install it if you use micromamba directly?

15 
 ~ ξ‚° "${SHELL}" <(curl -L micro.mamba.pm/install.sh)      ξ‚² βœ” ξ‚² 3m 36s ο‰’ 
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
100  3070  100  3070    0     0   1619      0  0:00:01  0:00:01 --:--:--  187k
Micromamba binary folder? [~/.local/bin] 
Init shell (zsh)? [Y/n] 
Configure conda-forge? [Y/n] 
Prefix location? [~/micromamba] 
Modifying RC file "/home/raman/.zshrc"
Generating config for root prefix "/home/raman/micromamba"
Setting mamba executable to: "/home/raman/.local/bin/micromamba"
Adding (or replacing) the following in your "/home/raman/.zshrc" file

# >>> mamba initialize >>>
# !! Contents within this block are managed by 'mamba init' !!
export MAMBA_EXE='/home/raman/.local/bin/micromamba';
export MAMBA_ROOT_PREFIX='/home/raman/micromamba';
__mamba_setup="$("$MAMBA_EXE" shell hook --shell zsh --root-prefix "$MAMBA_ROOT_PREFIX" 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__mamba_setup"
else
    alias micromamba="$MAMBA_EXE"  # Fallback on help from mamba activate
fi
unset __mamba_setup
# <<< mamba initialize <<<

Please restart your shell to activate micromamba or run the following:

  source ~/.bashrc (or ~/.zshrc, ~/.xonshrc, ~/.config/fish/config.fish, ...)
 οŒ’ ξ‚°  ~ ξ‚°                                                       ξ‚² βœ” ξ‚² 2m 5s ο‰’

See also :face_with_monocle:

 οŒ’ ξ‚°  ~ ξ‚° micromamba install CondaPkg                                     ξ‚² βœ” 
info     libmamba ****************** Backtrace Start ******************
debug    libmamba Loading configuration
trace    libmamba Compute configurable 'create_base'
trace    libmamba Compute configurable 'no_env'
trace    libmamba Compute configurable 'no_rc'
trace    libmamba Compute configurable 'rc_files'
trace    libmamba Compute configurable 'root_prefix'
trace    libmamba Get RC files configuration from locations up to HomeDir
trace    libmamba Configuration not found at '/home/raman/.mambarc'
trace    libmamba Configuration not found at '/home/raman/.mamba/mambarc.d'
trace    libmamba Configuration not found at '/home/raman/.mamba/mambarc'
trace    libmamba Configuration not found at '/home/raman/.mamba/.mambarc'
trace    libmamba Configuration not found at '/home/raman/.config/mamba/mambarc.d'
trace    libmamba Configuration not found at '/home/raman/.config/mamba/mambarc'
trace    libmamba Configuration not found at '/home/raman/.config/mamba/.mambarc'
trace    libmamba Configuration found at '/home/raman/.condarc'
trace    libmamba Configuration not found at '/home/raman/.conda/condarc.d'
trace    libmamba Configuration not found at '/home/raman/.conda/condarc'
trace    libmamba Configuration not found at '/home/raman/.conda/.condarc'
trace    libmamba Configuration not found at '/home/raman/.config/mamba/../conda/condarc.d'
trace    libmamba Configuration not found at '/home/raman/.config/mamba/../conda/condarc'
trace    libmamba Configuration not found at '/home/raman/.config/mamba/../conda/.condarc'
trace    libmamba Configuration not found at '/home/raman/y/.mambarc'
trace    libmamba Configuration not found at '/home/raman/y/condarc.d'
trace    libmamba Configuration not found at '/home/raman/y/condarc'
trace    libmamba Configuration not found at '/home/raman/y/.condarc'
trace    libmamba Configuration not found at '/var/lib/conda/.mambarc'
trace    libmamba Configuration not found at '/var/lib/conda/condarc.d/'
trace    libmamba Configuration not found at '/var/lib/conda/condarc'
trace    libmamba Configuration not found at '/var/lib/conda/.condarc'
trace    libmamba Configuration not found at '/etc/conda/.mambarc'
trace    libmamba Configuration not found at '/etc/conda/condarc.d/'
trace    libmamba Configuration not found at '/etc/conda/condarc'
trace    libmamba Configuration not found at '/etc/conda/.condarc'
trace    libmamba Update configurable 'no_env'
trace    libmamba Compute configurable 'envs_dirs'
trace    libmamba Compute configurable 'file_specs'
trace    libmamba Compute configurable 'spec_file_env_name'
trace    libmamba Compute configurable 'env_name'
trace    libmamba Compute configurable 'use_target_prefix_fallback'
trace    libmamba Compute configurable 'target_prefix'
trace    libmamba Get RC files configuration from locations up to TargetPrefix
trace    libmamba Configuration not found at '/home/raman/.mambarc'
trace    libmamba Configuration not found at '/home/raman/.mamba/mambarc.d'
trace    libmamba Configuration not found at '/home/raman/.mamba/mambarc'
trace    libmamba Configuration not found at '/home/raman/.mamba/.mambarc'
trace    libmamba Configuration not found at '/home/raman/.config/mamba/mambarc.d'
trace    libmamba Configuration not found at '/home/raman/.config/mamba/mambarc'
trace    libmamba Configuration not found at '/home/raman/.config/mamba/.mambarc'
trace    libmamba Configuration found at '/home/raman/.condarc'
trace    libmamba Configuration not found at '/home/raman/.conda/condarc.d'
trace    libmamba Configuration not found at '/home/raman/.conda/condarc'
trace    libmamba Configuration not found at '/home/raman/.conda/.condarc'
trace    libmamba Configuration not found at '/home/raman/.config/mamba/../conda/condarc.d'
trace    libmamba Configuration not found at '/home/raman/.config/mamba/../conda/condarc'
trace    libmamba Configuration not found at '/home/raman/.config/mamba/../conda/.condarc'
trace    libmamba Configuration not found at '/home/raman/y/.mambarc'
trace    libmamba Configuration not found at '/home/raman/y/condarc.d'
trace    libmamba Configuration not found at '/home/raman/y/condarc'
trace    libmamba Configuration not found at '/home/raman/y/.condarc'
trace    libmamba Configuration not found at '/var/lib/conda/.mambarc'
trace    libmamba Configuration not found at '/var/lib/conda/condarc.d/'
trace    libmamba Configuration not found at '/var/lib/conda/condarc'
trace    libmamba Configuration not found at '/var/lib/conda/.condarc'
trace    libmamba Configuration not found at '/etc/conda/.mambarc'
trace    libmamba Configuration not found at '/etc/conda/condarc.d/'
trace    libmamba Configuration not found at '/etc/conda/condarc'
trace    libmamba Configuration not found at '/etc/conda/.condarc'
trace    libmamba Update configurable 'no_env'
trace    libmamba Compute configurable 'relocate_prefix'
trace    libmamba Compute configurable 'target_prefix_checks'
error    libmamba No target prefix specified
critical libmamba Aborting.
info     libmamba ****************** Backtrace End ********************
16

What I do sometimes to is to delete the .julia folder and start again. But think twice before doing that, better rename it. But it helps to have a clean starting point.

@mkitti The next question I have is: Does CondaPkg use PyCall or PythonCall? These two are normally not compatible (unless you apply advanced steps).

1 Like
17

You mean i should delete Julia and reinstall it. Ok, I have no problem in doing that but tell me how to do that. I have installed it using Juliaup.

18 
cd ~
mv .julia .julia.bak
19

Should i install now using Juliaup or something else? :fearful: I think Juliaup would be better as i will be able to upgrade the in future.
So what should i do Juliaup or Julia? Will not Juliaup fine in my case?

20

If I do that on my machine and then run

julia

in the terminal Julia gets re-installed automatically. Because juliaup lives in a different directory:

ufechner@framework:~$ which julia
/home/ufechner/.juliaup/bin/julia