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bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
MIT License
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Conda install - UnsatisfiableError for python version #32088

Closed neoformit closed 2 years ago

neoformit commented 2 years ago

I am trying to update a Bioconda package (see pull request) to include a dependency required for the package to run correctly on headless Linux distros (xorg-libxrender). Despite setting python version to >=3.6 in both the host and run requirements in meta.yaml, conda installing the build artifact still fails with this error on a remote VM (Ubuntu 20.04 LTS, new conda env, python=3.9). Weirdly, the install succeeds on my local machine in the base Conda environment (which also has python=3.9).

Expected behaviour

The Conda package should be installable for environments with Python version above 3.6.

Actual behaviour

Conda sets a requirement of python>=3.10 and the install fails.

$ conda install -c https://179611-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages smudgeplot

UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

  - smudgeplot -> python[version='>=3.10,<3.11.0a0']

Your python: python=3.9

If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.

The following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.31=0
  - python=3.9 -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.31
endrebak commented 2 years ago

Were you able to solve it? It seems like the PR is closed. Was the fix to just set the Python version in the host and run requirements?

neoformit commented 2 years ago

Hey @endrebak no never fixed, the PR got merged regardless so I wondered if it might be some issue with the build artefact. I haven't been able to test as the build didn't seem to have updated last time I checked (10 hrs after merge). Maybe close and I'll reopen if it's still a problem? Thanks.

bgruening commented 2 years ago

@neoformit please do not use conda install use conda create this will setup you up a python environment with the needd Python version.

Merry Xmas!

neoformit commented 2 years ago

Hey @bgruening the issue is not that Conda isn't installing the specified Python version, it's that it specifies python==3.10 which is mentioned nowhere in the meta.yml. Conda's default Python should be fine for running this package. I haven't been able to confirm whether this is actually still an issue because the build hasn't updated since the PR was merged (12 days ago) - it still installs build #1. I'll open another issue for this.

bgruening commented 2 years ago

There is no general conda-default-python version. But you have in your base environment a python version that is dependent in you miniconda version. If you have in your base environment python 3.10, conda will try to install your additional packages against your base python version. This you prevent by using conda create.

If you look at https://anaconda.org/bioconda/smudgeplot/files you see that the _2 builds are only available for python 3.10. So if you install your package with python 3.9 you will get _1 as this is the only available version for that python version.

neoformit commented 2 years ago

Thanks for your help @bgruening that has clarified things a bit - I didn't think to look at build files on anaconda.org.

I still don't understand why Conda has decided that python>=3.10 is a requirement for this build? The only specification in meta.yml is for python >=3.6. The only change I made since the last build was to add the host dependency xorg-libxrender which definitely does not require 3.10.

As for installing the new "Python 3.10" build...

Specifications:

Your python: python=3.10

If python is on the left-most side of the chain, that's the version you've asked for. When python appears to the right, that indicates that the thing on the left is somehow not available for the python version you are constrained to. Note that conda will not change your python version to a different minor version unless you explicitly specify that.

The following specifications were found to be incompatible with your system:

Your installed version is: 2.31



It looks like conda can't see a `python=3.10` version available on bioconda.
bgruening commented 2 years ago

This is because conda is searching for python version compatible with your python version in your current base environment.

This one works for me conda create -n smudgeplot -c bioconda python=3.10 smudgeplot --dry.

bgruening commented 2 years ago

Can you please try the new release we just merged?

neoformit commented 2 years ago

Thanks for spending time on this @bgruening - it's still confusing but I'm certainly learning more about conda.

Can you please try the new release we just merged?

I just tried conda create -n smudgeplot -c bioconda smudgeplot on the same two VMs. They both install build r36h516909a_0 which is apparently from two years ago and not even on the latest version of smudgeplot! Base is on python=3.9.7.

However, it seems to get the right build when I install on my dev machine (desktop Ubuntu 20.04). So I'm guessing this is something to do with the machines, or their conda installations (conda=4.11.0)?

Update: also tried a fresh Miniconda install on a blank EC2 server also on Ubuntu 20.04 (conda=4.10.3 python=3.9.7). Same result as above (installed build r36h516909a_0) .

neoformit commented 2 years ago

@bgruening Just tried this again on a VM - this command now completes without error: conda create -n smudgeplot -c bioconda python=3.10 smudgeplot

But it still installs smudgeplot version 0.2.3 build r36h516909a_0 (over two years old).

bgruening commented 2 years ago

Please try this here:

bag@bag:~$ conda create -n smudgeplot --override-channels  -c conda-forge -c bioconda python=3.10 smudgeplot --dry
Collecting package metadata (current_repodata.json): done
Solving environment: \ WARNING conda.resolve:_get_sat_solver_cls(57): Could not run SAT solver through interface 'pycryptosat'.
failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/bag/miniconda3/envs/smudgeplot

  added / updated specs:
    - python=3.10
    - smudgeplot

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    _r-mutex-1.0.1             |      anacondar_1           3 KB  conda-forge
    binutils_linux-64-2.36     |       hf3e587d_4          24 KB  conda-forge
    bwidget-1.9.14             |       ha770c72_1         120 KB  conda-forge
    curl-7.81.0                |       h494985f_0          90 KB  conda-forge
    fontconfig-2.13.96         |       ha180cfb_0         372 KB  conda-forge
    gcc_linux-64-9.4.0         |       h391b98a_4          24 KB  conda-forge
    gfortran_impl_linux-64-9.4.0|      h0003116_12        14.6 MB  conda-forge
    gfortran_linux-64-9.4.0    |       hf0ab688_4          24 KB  conda-forge
    gsl-2.7                    |       he838d99_0         3.2 MB  conda-forge
    gxx_linux-64-9.4.0         |       h0316aca_4          24 KB  conda-forge
    harfbuzz-3.4.0             |       hb4a5f5f_0         2.2 MB  conda-forge
    krb5-1.19.2                |       h48eae69_3         1.4 MB  conda-forge
    libcurl-7.81.0             |       h494985f_0         340 KB  conda-forge
    libdeflate-1.10            |       h7f98852_0          77 KB  conda-forge
    libglib-2.70.2             |       h174f98d_4         3.1 MB  conda-forge
    libnghttp2-1.46.0          |       ha19adfc_0         801 KB  conda-forge
    libssh2-1.10.0             |       ha35d2d1_2         233 KB  conda-forge
    libtiff-4.3.0              |       h542a066_3         638 KB  conda-forge
    numpy-1.22.2               |  py310h454958d_0         6.9 MB  conda-forge
    pango-1.48.10              |       h54213e6_2         403 KB  conda-forge
    python-3.10.2              |hc74c709_3_cpython        30.1 MB  conda-forge
    python_abi-3.10            |          2_cp310           4 KB  conda-forge
    r-argparse-2.1.3           |    r41hc72bb7e_0         162 KB  conda-forge
    r-assertthat-0.2.1         |    r41hc72bb7e_2          70 KB  conda-forge
    r-backports-1.4.1          |    r41hcfec24a_0         110 KB  conda-forge
    r-base-4.1.2               |       hde4fec0_0        24.6 MB  conda-forge
    r-brio-1.1.3               |    r41hcfec24a_0          40 KB  conda-forge
    r-callr-3.7.0              |    r41hc72bb7e_0         439 KB  conda-forge
    r-cli-3.2.0                |    r41h03ef668_0         1.1 MB  conda-forge
    r-colorspace-2.0_2         |    r41hcfec24a_0         2.6 MB  conda-forge
    r-crayon-1.5.0             |    r41hc72bb7e_0         164 KB  conda-forge
    r-desc-1.4.0               |    r41hc72bb7e_0         557 KB  conda-forge
    r-diffobj-0.3.5            |    r41hcfec24a_0         1.0 MB  conda-forge
    r-digest-0.6.29            |    r41h03ef668_0         208 KB  conda-forge
    r-ellipsis-0.3.2           |    r41hcfec24a_0          42 KB  conda-forge
    r-evaluate-0.14            |    r41hc72bb7e_2          81 KB  conda-forge
    r-fansi-1.0.2              |    r41hcfec24a_0         322 KB  conda-forge
    r-farver-2.1.0             |    r41h03ef668_0         1.5 MB  conda-forge
    r-findpython-1.0.7         |    r41hc72bb7e_0          27 KB  conda-forge
    r-ggplot2-3.3.5            |    r41hc72bb7e_0         4.0 MB  conda-forge
    r-glue-1.6.1               |    r41hcfec24a_0         154 KB  conda-forge
    r-gridextra-2.3            | r41hc72bb7e_1003         1.1 MB  conda-forge
    r-gtable-0.3.0             |    r41hc72bb7e_3         423 KB  conda-forge
    r-isoband-0.2.5            |    r41h03ef668_0         1.9 MB  conda-forge
    r-jsonlite-1.7.3           |    r41hcfec24a_0         1.0 MB  conda-forge
    r-labeling-0.4.2           |    r41hc72bb7e_1          67 KB  conda-forge
    r-lattice-0.20_45          |    r41hcfec24a_0         1.1 MB  conda-forge
    r-lifecycle-1.0.1          |    r41hc72bb7e_0         109 KB  conda-forge
    r-magrittr-2.0.2           |    r41hcfec24a_0         215 KB  conda-forge
    r-mass-7.3_55              |    r41hcfec24a_0         1.1 MB  conda-forge
    r-matrix-1.4_0             |    r41he454529_0         4.8 MB  conda-forge
    r-mgcv-1.8_38              |    r41he454529_0         3.0 MB  conda-forge
    r-munsell-0.5.0            | r41hc72bb7e_1004         247 KB  conda-forge
    r-nlme-3.1_155             |    r41h859d828_0         2.3 MB  conda-forge
    r-pillar-1.7.0             |    r41hc72bb7e_0         706 KB  conda-forge
    r-pkgconfig-2.0.3          |    r41hc72bb7e_1          25 KB  conda-forge
    r-pkgload-1.2.4            |    r41h03ef668_0         172 KB  conda-forge
    r-praise-1.0.0             | r41hc72bb7e_1005          24 KB  conda-forge
    r-processx-3.5.2           |    r41hcfec24a_0         314 KB  conda-forge
    r-ps-1.6.0                 |    r41hcfec24a_0         299 KB  conda-forge
    r-r6-2.5.1                 |    r41hc72bb7e_0          89 KB  conda-forge
    r-rcolorbrewer-1.1_2       | r41h785f33e_1003          64 KB  conda-forge
    r-rcpp-1.0.8               |    r41h03ef668_0         2.1 MB  conda-forge
    r-rematch2-2.1.2           |    r41hc72bb7e_1          52 KB  conda-forge
    r-rlang-0.4.12             |    r41hcfec24a_0         1.1 MB  conda-forge
    r-rprojroot-2.0.2          |    r41hc72bb7e_0         110 KB  conda-forge
    r-rstudioapi-0.13          |    r41hc72bb7e_0         281 KB  conda-forge
    r-scales-1.1.1             |    r41hc72bb7e_0         557 KB  conda-forge
    r-testthat-3.1.2           |    r41h03ef668_0         1.6 MB  conda-forge
    r-tibble-3.1.6             |    r41hcfec24a_0         774 KB  conda-forge
    r-utf8-1.2.2               |    r41hcfec24a_0         162 KB  conda-forge
    r-vctrs-0.3.8              |    r41hcfec24a_1         1.1 MB  conda-forge
    r-viridis-0.6.2            |    r41hc72bb7e_0         2.9 MB  conda-forge
    r-viridislite-0.4.0        |    r41hc72bb7e_0         1.3 MB  conda-forge
    r-waldo-0.3.1              |    r41hc72bb7e_0         103 KB  conda-forge
    r-withr-2.4.3              |    r41hc72bb7e_0         225 KB  conda-forge
    scipy-1.8.0                |  py310hea5193d_1        25.7 MB  conda-forge
    setuptools-60.9.1          |  py310hff52083_0         1.2 MB  conda-forge
    smudgeplot-0.2.4           |py310r41h779adbc_2          93 KB  bioconda
    xorg-libxt-1.2.1           |       h7f98852_2         375 KB  conda-forge
    ------------------------------------------------------------
                                           Total:       160.1 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
  _r-mutex           conda-forge/noarch::_r-mutex-1.0.1-anacondar_1
  binutils_impl_lin~ conda-forge/linux-64::binutils_impl_linux-64-2.36.1-h193b22a_2
  binutils_linux-64  conda-forge/linux-64::binutils_linux-64-2.36-hf3e587d_4
  bwidget            conda-forge/linux-64::bwidget-1.9.14-ha770c72_1
  bzip2              conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
  c-ares             conda-forge/linux-64::c-ares-1.18.1-h7f98852_0
  ca-certificates    conda-forge/linux-64::ca-certificates-2021.10.8-ha878542_0
  cairo              conda-forge/linux-64::cairo-1.16.0-ha00ac49_1009
  curl               conda-forge/linux-64::curl-7.81.0-h494985f_0
  font-ttf-dejavu-s~ conda-forge/noarch::font-ttf-dejavu-sans-mono-2.37-hab24e00_0
  font-ttf-inconsol~ conda-forge/noarch::font-ttf-inconsolata-3.000-h77eed37_0
  font-ttf-source-c~ conda-forge/noarch::font-ttf-source-code-pro-2.038-h77eed37_0
  font-ttf-ubuntu    conda-forge/noarch::font-ttf-ubuntu-0.83-hab24e00_0
  fontconfig         conda-forge/linux-64::fontconfig-2.13.96-ha180cfb_0
  fonts-conda-ecosy~ conda-forge/noarch::fonts-conda-ecosystem-1-0
  fonts-conda-forge  conda-forge/noarch::fonts-conda-forge-1-0
  freetype           conda-forge/linux-64::freetype-2.10.4-h0708190_1
  fribidi            conda-forge/linux-64::fribidi-1.0.10-h36c2ea0_0
  gcc_impl_linux-64  conda-forge/linux-64::gcc_impl_linux-64-9.4.0-h03d3576_12
  gcc_linux-64       conda-forge/linux-64::gcc_linux-64-9.4.0-h391b98a_4
  gettext            conda-forge/linux-64::gettext-0.19.8.1-h73d1719_1008
  gfortran_impl_lin~ conda-forge/linux-64::gfortran_impl_linux-64-9.4.0-h0003116_12
  gfortran_linux-64  conda-forge/linux-64::gfortran_linux-64-9.4.0-hf0ab688_4
  graphite2          conda-forge/linux-64::graphite2-1.3.13-h58526e2_1001
  gsl                conda-forge/linux-64::gsl-2.7-he838d99_0
  gxx_impl_linux-64  conda-forge/linux-64::gxx_impl_linux-64-9.4.0-h03d3576_12
  gxx_linux-64       conda-forge/linux-64::gxx_linux-64-9.4.0-h0316aca_4
  harfbuzz           conda-forge/linux-64::harfbuzz-3.4.0-hb4a5f5f_0
  icu                conda-forge/linux-64::icu-69.1-h9c3ff4c_0
  jbig               conda-forge/linux-64::jbig-2.1-h7f98852_2003
  jpeg               conda-forge/linux-64::jpeg-9e-h7f98852_0
  kernel-headers_li~ conda-forge/noarch::kernel-headers_linux-64-2.6.32-he073ed8_15
  krb5               conda-forge/linux-64::krb5-1.19.2-h48eae69_3
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.36.1-hea4e1c9_2
  lerc               conda-forge/linux-64::lerc-3.0-h9c3ff4c_0
  libblas            conda-forge/linux-64::libblas-3.9.0-13_linux64_openblas
  libcblas           conda-forge/linux-64::libcblas-3.9.0-13_linux64_openblas
  libcurl            conda-forge/linux-64::libcurl-7.81.0-h494985f_0
  libdeflate         conda-forge/linux-64::libdeflate-1.10-h7f98852_0
  libedit            conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2
  libev              conda-forge/linux-64::libev-4.33-h516909a_1
  libffi             conda-forge/linux-64::libffi-3.4.2-h7f98852_5
  libgcc-devel_linu~ conda-forge/linux-64::libgcc-devel_linux-64-9.4.0-hd854feb_12
  libgcc-ng          conda-forge/linux-64::libgcc-ng-11.2.0-h1d223b6_12
  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-11.2.0-h69a702a_12
  libgfortran5       conda-forge/linux-64::libgfortran5-11.2.0-h5c6108e_12
  libglib            conda-forge/linux-64::libglib-2.70.2-h174f98d_4
  libgomp            conda-forge/linux-64::libgomp-11.2.0-h1d223b6_12
  libiconv           conda-forge/linux-64::libiconv-1.16-h516909a_0
  liblapack          conda-forge/linux-64::liblapack-3.9.0-13_linux64_openblas
  libnghttp2         conda-forge/linux-64::libnghttp2-1.46.0-ha19adfc_0
  libnsl             conda-forge/linux-64::libnsl-2.0.0-h7f98852_0
  libopenblas        conda-forge/linux-64::libopenblas-0.3.18-pthreads_h8fe5266_0
  libpng             conda-forge/linux-64::libpng-1.6.37-h21135ba_2
  libsanitizer       conda-forge/linux-64::libsanitizer-9.4.0-h79bfe98_12
  libssh2            conda-forge/linux-64::libssh2-1.10.0-ha35d2d1_2
  libstdcxx-devel_l~ conda-forge/linux-64::libstdcxx-devel_linux-64-9.4.0-hd854feb_12
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-11.2.0-he4da1e4_12
  libtiff            conda-forge/linux-64::libtiff-4.3.0-h542a066_3
  libuuid            conda-forge/linux-64::libuuid-2.32.1-h7f98852_1000
  libwebp-base       conda-forge/linux-64::libwebp-base-1.2.2-h7f98852_1
  libxcb             conda-forge/linux-64::libxcb-1.13-h7f98852_1004
  libxml2            conda-forge/linux-64::libxml2-2.9.12-h885dcf4_1
  libzlib            conda-forge/linux-64::libzlib-1.2.11-h36c2ea0_1013
  lz4-c              conda-forge/linux-64::lz4-c-1.9.3-h9c3ff4c_1
  make               conda-forge/linux-64::make-4.3-hd18ef5c_1
  ncurses            conda-forge/linux-64::ncurses-6.3-h9c3ff4c_0
  numpy              conda-forge/linux-64::numpy-1.22.2-py310h454958d_0
  openssl            conda-forge/linux-64::openssl-3.0.0-h7f98852_2
  pango              conda-forge/linux-64::pango-1.48.10-h54213e6_2
  pcre               conda-forge/linux-64::pcre-8.45-h9c3ff4c_0
  pcre2              conda-forge/linux-64::pcre2-10.37-h032f7d1_0
  pip                conda-forge/noarch::pip-22.0.3-pyhd8ed1ab_0
  pixman             conda-forge/linux-64::pixman-0.40.0-h36c2ea0_0
  pthread-stubs      conda-forge/linux-64::pthread-stubs-0.4-h36c2ea0_1001
  python             conda-forge/linux-64::python-3.10.2-hc74c709_3_cpython
  python_abi         conda-forge/linux-64::python_abi-3.10-2_cp310
  r-argparse         conda-forge/noarch::r-argparse-2.1.3-r41hc72bb7e_0
  r-assertthat       conda-forge/noarch::r-assertthat-0.2.1-r41hc72bb7e_2
  r-backports        conda-forge/linux-64::r-backports-1.4.1-r41hcfec24a_0
  r-base             conda-forge/linux-64::r-base-4.1.2-hde4fec0_0
  r-brio             conda-forge/linux-64::r-brio-1.1.3-r41hcfec24a_0
  r-callr            conda-forge/noarch::r-callr-3.7.0-r41hc72bb7e_0
  r-cli              conda-forge/linux-64::r-cli-3.2.0-r41h03ef668_0
  r-colorspace       conda-forge/linux-64::r-colorspace-2.0_2-r41hcfec24a_0
  r-crayon           conda-forge/noarch::r-crayon-1.5.0-r41hc72bb7e_0
  r-desc             conda-forge/noarch::r-desc-1.4.0-r41hc72bb7e_0
  r-diffobj          conda-forge/linux-64::r-diffobj-0.3.5-r41hcfec24a_0
  r-digest           conda-forge/linux-64::r-digest-0.6.29-r41h03ef668_0
  r-ellipsis         conda-forge/linux-64::r-ellipsis-0.3.2-r41hcfec24a_0
  r-evaluate         conda-forge/noarch::r-evaluate-0.14-r41hc72bb7e_2
  r-fansi            conda-forge/linux-64::r-fansi-1.0.2-r41hcfec24a_0
  r-farver           conda-forge/linux-64::r-farver-2.1.0-r41h03ef668_0
  r-findpython       conda-forge/noarch::r-findpython-1.0.7-r41hc72bb7e_0
  r-ggplot2          conda-forge/noarch::r-ggplot2-3.3.5-r41hc72bb7e_0
  r-glue             conda-forge/linux-64::r-glue-1.6.1-r41hcfec24a_0
  r-gridextra        conda-forge/noarch::r-gridextra-2.3-r41hc72bb7e_1003
  r-gtable           conda-forge/noarch::r-gtable-0.3.0-r41hc72bb7e_3
  r-isoband          conda-forge/linux-64::r-isoband-0.2.5-r41h03ef668_0
  r-jsonlite         conda-forge/linux-64::r-jsonlite-1.7.3-r41hcfec24a_0
  r-labeling         conda-forge/noarch::r-labeling-0.4.2-r41hc72bb7e_1
  r-lattice          conda-forge/linux-64::r-lattice-0.20_45-r41hcfec24a_0
  r-lifecycle        conda-forge/noarch::r-lifecycle-1.0.1-r41hc72bb7e_0
  r-magrittr         conda-forge/linux-64::r-magrittr-2.0.2-r41hcfec24a_0
  r-mass             conda-forge/linux-64::r-mass-7.3_55-r41hcfec24a_0
  r-matrix           conda-forge/linux-64::r-matrix-1.4_0-r41he454529_0
  r-mgcv             conda-forge/linux-64::r-mgcv-1.8_38-r41he454529_0
  r-munsell          conda-forge/noarch::r-munsell-0.5.0-r41hc72bb7e_1004
  r-nlme             conda-forge/linux-64::r-nlme-3.1_155-r41h859d828_0
  r-pillar           conda-forge/noarch::r-pillar-1.7.0-r41hc72bb7e_0
  r-pkgconfig        conda-forge/noarch::r-pkgconfig-2.0.3-r41hc72bb7e_1
  r-pkgload          conda-forge/linux-64::r-pkgload-1.2.4-r41h03ef668_0
  r-praise           conda-forge/noarch::r-praise-1.0.0-r41hc72bb7e_1005
  r-processx         conda-forge/linux-64::r-processx-3.5.2-r41hcfec24a_0
  r-ps               conda-forge/linux-64::r-ps-1.6.0-r41hcfec24a_0
  r-r6               conda-forge/noarch::r-r6-2.5.1-r41hc72bb7e_0
  r-rcolorbrewer     conda-forge/noarch::r-rcolorbrewer-1.1_2-r41h785f33e_1003
  r-rcpp             conda-forge/linux-64::r-rcpp-1.0.8-r41h03ef668_0
  r-rematch2         conda-forge/noarch::r-rematch2-2.1.2-r41hc72bb7e_1
  r-rlang            conda-forge/linux-64::r-rlang-0.4.12-r41hcfec24a_0
  r-rprojroot        conda-forge/noarch::r-rprojroot-2.0.2-r41hc72bb7e_0
  r-rstudioapi       conda-forge/noarch::r-rstudioapi-0.13-r41hc72bb7e_0
  r-scales           conda-forge/noarch::r-scales-1.1.1-r41hc72bb7e_0
  r-testthat         conda-forge/linux-64::r-testthat-3.1.2-r41h03ef668_0
  r-tibble           conda-forge/linux-64::r-tibble-3.1.6-r41hcfec24a_0
  r-utf8             conda-forge/linux-64::r-utf8-1.2.2-r41hcfec24a_0
  r-vctrs            conda-forge/linux-64::r-vctrs-0.3.8-r41hcfec24a_1
  r-viridis          conda-forge/noarch::r-viridis-0.6.2-r41hc72bb7e_0
  r-viridislite      conda-forge/noarch::r-viridislite-0.4.0-r41hc72bb7e_0
  r-waldo            conda-forge/noarch::r-waldo-0.3.1-r41hc72bb7e_0
  r-withr            conda-forge/noarch::r-withr-2.4.3-r41hc72bb7e_0
  readline           conda-forge/linux-64::readline-8.1-h46c0cb4_0
  scipy              conda-forge/linux-64::scipy-1.8.0-py310hea5193d_1
  sed                conda-forge/linux-64::sed-4.8-he412f7d_0
  setuptools         conda-forge/linux-64::setuptools-60.9.1-py310hff52083_0
  smudgeplot         bioconda/linux-64::smudgeplot-0.2.4-py310r41h779adbc_2
  sqlite             conda-forge/linux-64::sqlite-3.37.0-h9cd32fc_0
  sysroot_linux-64   conda-forge/noarch::sysroot_linux-64-2.12-he073ed8_15
  tk                 conda-forge/linux-64::tk-8.6.11-h27826a3_1
  tktable            conda-forge/linux-64::tktable-2.10-hb7b940f_3
  tzdata             conda-forge/noarch::tzdata-2021e-he74cb21_0
  wheel              conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
  xorg-kbproto       conda-forge/linux-64::xorg-kbproto-1.0.7-h7f98852_1002
  xorg-libice        conda-forge/linux-64::xorg-libice-1.0.10-h7f98852_0
  xorg-libsm         conda-forge/linux-64::xorg-libsm-1.2.3-hd9c2040_1000
  xorg-libx11        conda-forge/linux-64::xorg-libx11-1.7.2-h7f98852_0
  xorg-libxau        conda-forge/linux-64::xorg-libxau-1.0.9-h7f98852_0
  xorg-libxdmcp      conda-forge/linux-64::xorg-libxdmcp-1.1.3-h7f98852_0
  xorg-libxext       conda-forge/linux-64::xorg-libxext-1.3.4-h7f98852_1
  xorg-libxrender    conda-forge/linux-64::xorg-libxrender-0.9.10-h7f98852_1003
  xorg-libxt         conda-forge/linux-64::xorg-libxt-1.2.1-h7f98852_2
  xorg-renderproto   conda-forge/linux-64::xorg-renderproto-0.11.1-h7f98852_1002
  xorg-xextproto     conda-forge/linux-64::xorg-xextproto-7.3.0-h7f98852_1002
  xorg-xproto        conda-forge/linux-64::xorg-xproto-7.0.31-h7f98852_1007
  xz                 conda-forge/linux-64::xz-5.2.5-h516909a_1
  zlib               conda-forge/linux-64::zlib-1.2.11-h36c2ea0_1013
  zstd               conda-forge/linux-64::zstd-1.5.2-ha95c52a_0

DryRunExit: Dry run. Exiting.

If that does not work which conda version are you using?

neoformit commented 2 years ago

Thanks @bgruening - yes I can confirm that works - it installs and run without error :smiley: Can you explain how this now works?

When I just run conda create -n smudgeplot -c bioconda python=3.10 smudgeplot --dry it lists this smudgeplot instead:

smudgeplot         bioconda/linux-64::smudgeplot-0.2.3-r36h516909a_0

My only concern is whether Galaxy will install and run the correct version - I'll post back here when I know the answer to that.

bgruening commented 2 years ago

Your channel priorities are probably incorrect. With my command I made sure they are correct. Don't worry about Galaxy they set up the correct channel priority and use the similar command that I used above.

https://bioconda.github.io/user/install.html#set-up-channels

neoformit commented 2 years ago

Great, that makes sense! Thanks a lot for your time on this.

bgruening commented 2 years ago

Sure thing, thanks for your patients.