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micromamba 2.0 fails to install from tmp #3469

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3 tasks done
msmitherdc opened this issue Sep 26, 2024 · 7 comments
Open
3 tasks done

micromamba 2.0 fails to install from tmp #3469

msmitherdc opened this issue Sep 26, 2024 · 7 comments
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@jjerphan

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@msmitherdc
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Troubleshooting docs

  • My problem is not solved in the Troubleshooting docs

Anaconda default channels

  • I do NOT use the Anaconda default channels (pkgs/* etc.)

How did you install Mamba?

Micromamba

Search tried in issue tracker

searched

Latest version of Mamba

  • My problem is not solved with the latest version

Tried in Conda?

Not applicable

Describe your issue

caused by 2.0 release, works fine when pinned to 1.5.10

#0 28.95 Transaction
#0 28.95
#0 28.95   Prefix: /opt/conda/envs/grid
#0 28.95
#0 28.95   Updating specs:
#0 28.95
#0 28.95    - file:///tmp/linux-64/gdalplugins-3.9.2-h3fd9d12_0.tar.bz2
#0 28.95    - file:///tmp/linux-64/nginx-1.25.3-h6578b86_2.tar.bz2
#0 28.95    - file:///tmp/linux-64/instantclient-19.8.0.0.0-3.tar.bz2
#0 28.95    - file:///tmp/linux-64/mrsid-9.5.5.5244-0.tar.bz2
#0 28.95
#0 28.95
#0 28.95   Package             Version  Build       Channel     Size
#0 28.95 ─────────────────────────────────────────────────────────────
#0 28.95   Install:
#0 28.95 ─────────────────────────────────────────────────────────────
#0 28.95
#0 28.95   + gdalplugins         3.9.2  h3fd9d12_0  /tmp
#0 28.95   + instantclient  19.8.0.0.0  3           /tmp
#0 28.95   + mrsid          9.5.5.5244  0           /tmp
#0 28.95   + nginx              1.25.3  h6578b86_2  /tmp
#0 28.95
#0 28.95   Summary:
#0 28.95
#0 28.95   Install: 4 packages
#0 28.95
#0 28.95   Total download: 0 B
#0 28.95
#0 28.95 ─────────────────────────────────────────────────────────────
#0 28.95
#0 28.95
#0 28.95
#0 28.95 Transaction starting
#0 28.95 Linking gdalplugins-3.9.2-h3fd9d12_0
#0 28.95 error    libmamba Download didn't finish!
#0 28.95 error    libmamba Cannot find a valid extracted directory cache for 'gdalplugins-3.9.2-h3fd9d12_0.tar.bz2'
#0 28.95 critical libmamba Package cache error.

always fails when installing local packages from file:///tmp/. Falling back to 1.5.10-0 and it works fine

mamba info / micromamba info

#0 0.388        libmamba version : 2.0.0
#0 0.388      micromamba version : 2.0.0
#0 0.388            curl version : libcurl/8.9.1 OpenSSL/3.3.2 zlib/1.3.1 zstd/1.5.6 libssh2/1.11.0 nghttp2/1.58.0
#0 0.388      libarchive version : libarchive 3.7.4 zlib/1.2.13 bz2lib/1.0.8 libzstd/1.5.6
#0 0.388        envs directories : /opt/conda/envs
#0 0.388           package cache : /opt/conda/pkgs
#0 0.388                           /home/gridusr/.mamba/pkgs
#0 0.388             environment : base (active)
#0 0.388            env location : /opt/conda
#0 0.388       user config files : /home/gridusr/.mambarc
#0 0.388  populated config files :
#0 0.388        virtual packages : __unix=0=0
#0 0.388                           __linux=4.14.352=0
#0 0.388                           __glibc=2.34=0
#0 0.388                           __archspec=1=x86_64_v4
#0 0.388                channels : https://conda.anaconda.org/conda-forge/linux-64
#0 0.388                           https://conda.anaconda.org/conda-forge/noarch
#0 0.388        base environment : /opt/conda
#0 0.388                platform : linux-64
#0 12.88 conda-forge/linux-64                                        Using cache
#0 12.88 conda-forge/noarch                                          Using cache

Logs

No response

environment.yml

No response

~/.condarc

No response
@msmitherdc
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at 1.5.10-0

#27 57.03 Transaction
#27 57.03
#27 57.03   Prefix: /opt/conda/envs/grid
#27 57.03
#27 57.03   Updating specs:
#27 57.03
#27 57.03    - file:///tmp/linux-64::gdalplugins==3.9.2=h3fd9d12_0
#27 57.03    - file:///tmp/linux-64::nginx==1.25.3=h6578b86_2
#27 57.03    - file:///tmp/linux-64::instantclient==19.8.0.0.0=3
#27 57.03    - file:///tmp/linux-64::mrsid==9.5.5.5244=0
#27 57.03
#27 57.03
#27 57.03   Package                         Version  Build          Channel          Size
#27 57.03 ─────────────────────────────────────────────────────────────────────────────────
#27 57.03   Install:
#27 57.03 ─────────────────────────────────────────────────────────────────────────────────
#27 57.03
#27 57.03   + libxslt                        1.1.39  h76b75d6_0     conda-forge     254kB
#27 57.03   + expat                           2.6.3  h5888daf_0     conda-forge     138kB
#27 57.03   + cfitsio                         4.4.1  hf8ad068_0     conda-forge     924kB
#27 57.03   + libgdal-grib                    3.9.2  hc3b29a1_4     conda-forge     725kB
#27 57.03   + fmt                            11.0.2  h434a139_0     conda-forge     199kB
#27 57.03   + freetype                       2.12.1  h267a509_2     conda-forge     635kB
#27 57.03   + libpq                            16.4  h2d7952a_1     conda-forge       3MB
#27 57.03   + lcms2                            2.16  hb7c19ff_0     conda-forge     245kB
#27 57.03   + nspr                             4.35  h27087fc_0     conda-forge     227kB
#27 57.03   + pixman                         0.43.2  h59595ed_0     conda-forge     387kB
#27 57.03   + xorg-libice                     1.1.1  hd590300_0     conda-forge      58kB
#27 57.03   + kealib                          1.5.3  hf8d3e68_2     conda-forge     180kB
#27 57.03   + libglib                        2.80.5  h2ff4ddf_0     conda-forge       4MB
#27 57.03   + xorg-renderproto               0.11.1  hb9d3cd8_1003  conda-forge      12kB
#27 57.03   + xorg-xextproto                  7.3.0  hb9d3cd8_1004  conda-forge      31kB
#27 57.03   + xorg-kbproto                    1.0.7  hb9d3cd8_1003  conda-forge      30kB
#27 57.03   + xorg-xproto                    7.0.31  hb9d3cd8_1008  conda-forge      73kB
#27 57.03   + tzcode                          2024b  hb9d3cd8_0     conda-forge      69kB
#27 57.03   + pthread-stubs                     0.4  hb9d3cd8_1002  conda-forge       8kB
#27 57.03   + xorg-libxdmcp                   1.1.3  hb9d3cd8_1     conda-forge      20kB
#27 57.03   + xorg-libxau                    1.0.11  hb9d3cd8_1     conda-forge      15kB
#27 57.03   + libgdal-fits                    3.9.2  h2db6552_4     conda-forge     478kB
#27 57.03   + spdlog                         1.14.1  hed91bc2_1     conda-forge     196kB
#27 57.03   + fontconfig                     2.14.2  h14ed4e7_0     conda-forge     272kB
#27 57.03   + nss                             3.104  hd34e28f_0     conda-forge       2MB
#27 57.03   + xorg-libsm                      1.2.4  h7391055_0     conda-forge      27kB
#27 57.03   + libgdal-kea                     3.9.2  h1df15e4_4     conda-forge     481kB
#27 57.03   + postgresql                       16.4  hb2eb5c0_1     conda-forge       5MB
#27 57.03   + libxcb                         1.17.0  h8a09558_0     conda-forge     396kB
#27 57.03   + tiledb                         2.26.1  h4c922dd_1     conda-forge       5MB
#27 57.03   + libgdal-postgisraster           3.9.2  h151b34b_4     conda-forge     480kB
#27 57.03   + libgdal-pg                      3.9.2  h151b34b_4     conda-forge     527kB
#27 57.03   + xorg-libx11                     1.8.9  hb711507_1     conda-forge     832kB
#27 57.03   + libgdal-tiledb                  3.9.2  h4a3bace_4     conda-forge     682kB
#27 57.03   + xorg-libxext                    1.3.4  h0b41bf4_2     conda-forge      50kB
#27 57.03   + xorg-libxrender                0.9.11  hd590300_0     conda-forge      38kB
#27 57.03   + instantclient              19.8.0.0.0  3              /tmp             29MB
#27 57.03   + mrsid                      9.5.5.5244  0              /tmp            170MB
#27 57.03   + font-ttf-dejavu-sans-mono        2.37  hab24e00_0     conda-forge     397kB
#27 57.03   + font-ttf-inconsolata            3.000  h77eed37_0     conda-forge      97kB
#27 57.03   + font-ttf-source-code-pro        2.038  h77eed37_0     conda-forge     701kB
#27 57.03   + font-ttf-ubuntu                  0.83  h77eed37_2     conda-forge       2MB
#27 57.03   + poppler-data                   0.4.12  hd8ed1ab_0     conda-forge       2MB
#27 57.03   + fonts-conda-forge                   1  0              conda-forge       4kB
#27 57.03   + fonts-conda-ecosystem               1  0              conda-forge       4kB
#27 57.03   + cairo                          1.18.0  hebfffa5_3     conda-forge     984kB
#27 57.03   + libgd                           2.3.3  hd3e95f3_10    conda-forge     225kB
#27 57.03   + poppler                       24.08.0  h47131b8_1     conda-forge       2MB
#27 57.03   + libgdal-pdf                     3.9.2  h600f43f_4     conda-forge     668kB
#27 57.03   + libgdal                         3.9.2  ha770c72_4     conda-forge     423kB
#27 57.03   + nginx                          1.25.3  h6578b86_2     /tmp            617kB
#27 57.03   + gdalplugins                     3.9.2  h3fd9d12_0     /tmp            100kB
#27 57.03
#27 57.03   Summary:
#27 57.03
#27 57.03   Install: 52 packages
#27 57.03
#27 57.03   Total download: 236MB
#27 57.03
#27 57.03 ─────────────────────────────────────────────────────────────────────────────────
#27 57.03
#27 57.03
#27 57.03
#27 57.03 Transaction starting
#27 72.99
#27 72.99 Transaction finished

@Hind-M
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Hind-M commented Sep 30, 2024

Can you please specify the exact command that you're using and link files if used (environment yaml file, .condarc etc)?
Thanks!

@msmitherdc
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This is in a dockerfile, so no yaml or condarc file.

micromamba install --yes --name grid -c conda-forge file:///tmp/linux-64/${ORACLE_PLUGIN} file:///tmp/linux-64/${NGINX} file:///tmp/linux-64/${INSTANT_CLIENT} file:///tmp/linux-64/${MRSID_PLUGIN}

the variables contain the specific versions for the dockerfile. They are COPYied to the dockerfile before the install.

@jjerphan
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jjerphan commented Oct 1, 2024

I cannot reproduce the error when installing numpy-2.1.1-py312h58c1407_0.conda (from conda-forge) when placed on /tmp using:

micromamba install --yes --name grid file:///tmp/linux-64/numpy-2.1.1-py312h58c1407_0.conda

In the example you gave, @msmitherdc, it seems that gdalplugins-3.9.2-h3fd9d12_0.tar.bz2 (at least) is a custom conda package which is not present on conda-forge. Can you confirm?

@msmitherdc
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correct, it is custom plugins with non public code. This all works if I use the last release before 2.0 (1.5). It only fails with the new release.

@msmitherdc
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does it need to be rebuilt with updated mamba builder (which is how it is build)

@jjerphan jjerphan self-assigned this Oct 1, 2024
@jjerphan
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jjerphan commented Oct 1, 2024

Can you provide a reproducer for this issue (by providing such a conda package)?

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@msmitherdc @jjerphan @Hind-M