search

mamba-org / mamba

The Fast Cross-Platform Package Manager
https://mamba.readthedocs.io
BSD 3-Clause "New" or "Revised" License
6.97k stars 359 forks source link

Cannot build package due to mamba build solver issue #2679

Open AlexSCFraser opened 1 year ago

AlexSCFraser commented 1 year ago

Troubleshooting docs

How did you install Mamba?

Mambaforge

Search tried in issue tracker

solver build

Latest version of Mamba

Tried in Conda?

I have this problem with Conda as well, without using Mamba

Describe your issue

I am trying to build an R package for distribution. Initially I tried using base conda build, but the conda solver literally never solves the dependency list. So I tried using mamba build (after installing boa) and conda mambabuild commands to try building the package instead. It at least gives me an error message that the environment can't be solved, but this makes no sense since I can install the entire dependency list into a fresh environment no problem. Reading through the output, one thing that stands out to me is that the r-base package seems to have gained a narrow range of outdated version somehow, which I'm not exactly sure has come from. So it may not be a problem with the solver as such, but perhaps somewhere in the build pipeline r-base gains an unnecessary dependency. I also tried updating conda to the latest version and enabling the libmamba solver for conda and I have the same issue as with mamba, it reports an unsatisfiable dependency error.

The dependency list in my meta.yaml:

  host:
    - r-base
  run:
    - r-base
    - r-jsonlite
    - r-ape
    - r-stringr
    - r-magicfor
    - r-knitr
    - r-dplyr
    - r-magrittr
    - r-rcolorbrewer
    - r-ggnewscale
    - r-ggplot2
    - bioconductor-ggtree

When I install these manually with mamba install r-base r-jsonlite r-ape r-stringr r-magicfor r-knitr r-dplyr r-magrittr r-rcolorbrewer r-ggnewscale r-ggplot2 bioconductor-ggtree in a fresh environment, it works normally, so I see no reason why the package build shouldn't be able to solve these dependencies.

The dependency list that is given as the one failed to solve by mamba build is:

 - r-magrittr
 - r-ape
 - r-knitr
 - r-dplyr
 - r-rcolorbrewer
 - r-stringr
 - r-ggnewscale
 - r-ggplot2
 - bioconductor-ggtree
 - r-base >=3.4,<3.5.0a0
 - r-magicfor
 - r-jsonlite

So I have no idea why r-base is now between 3.4 and 3.5, since this was not part of my requirements. And when I install these packages into a fresh environment, the version of r-base is r-base 3.6.3 hddad469_8 conda-forge in the environment list. So even if mamba build added a narrowing of the valid r-base versions, it shouldn't be so narrow. I've attached logs for mamba build and mamba mambabuild.

mamba info / micromamba info

__    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
        ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
        ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

        mamba (1.4.2) supported by @QuantStack

        GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████

     active environment : base
    active env location : C:\Users\sonic\mambaforge
            shell level : 1
       user config file : C:\Users\sonic\.condarc
 populated config files : C:\Users\sonic\mambaforge\.condarc
                          C:\Users\sonic\.condarc
          conda version : 23.1.0
    conda-build version : 3.25.0
         python version : 3.10.10.final.0
       virtual packages : __archspec=1=x86_64
                          __cuda=12.2=0
                          __win=0=0
       base environment : C:\Users\sonic\mambaforge  (writable)
      conda av data dir : C:\Users\sonic\mambaforge\etc\conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/bioconda/win-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://conda.anaconda.org/conda-forge/win-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/r/win-64
                          https://conda.anaconda.org/r/noarch
          package cache : C:\Users\sonic\mambaforge\pkgs
                          C:\Users\sonic\.conda\pkgs
                          C:\Users\sonic\AppData\Local\conda\conda\pkgs
       envs directories : C:\Users\sonic\mambaforge\envs
                          C:\Users\sonic\.conda\envs
                          C:\Users\sonic\AppData\Local\conda\conda\envs
               platform : win-64
             user-agent : conda/23.1.0 requests/2.28.2 CPython/3.10.10 Windows/10 Windows/10.0.19045
          administrator : False
             netrc file : None
           offline mode : False

Logs

(base) C:\Users\sonic\IdeaProjects\rsaccharis>mamba mambabuild .
Updating build index: C:\Users\sonic\mambaforge\conda-bld

No numpy version specified in conda_build_config.yaml.  Falling back to default numpy value of 1.22
WARNING:conda_build.metadata:No numpy version specified in conda_build_config.yaml.  Falling back to default numpy value of 1.22
Adding in variants from internal_defaults
INFO:conda_build.variants:Adding in variants from internal_defaults
Adding in variants from C:\Users\sonic\IdeaProjects\rsaccharis\conda-recipe\conda_build_config.yaml
INFO:conda_build.variants:Adding in variants from C:\Users\sonic\IdeaProjects\rsaccharis\conda-recipe\conda_build_config.yaml
Attempting to finalize metadata for rsaccharis
INFO:conda_build.metadata:Attempting to finalize metadata for rsaccharis
warning  libmamba Could not parse state file: Could not load cache state: [json.exception.type_error.302] type must be string, but is null
warning  libmamba Could not remove state file "C:\\Users\\sonic\\mambaforge\\pkgs\\cache\\33cd04cd.state.json": The process cannot access the file because it is being used by another process.
warning  libmamba Could not parse state file: Could not load cache state: [json.exception.type_error.302] type must be l
warning  libmamba Could not remove state file "C:\\Users\\sonic\\mambaforge\\pkgs\\cache\\2a957770.state.json": The pro.
warning  libmamba Could not parse state file: Could not load cache state: [json.exception.type_error.302] type must be l
warning  libmamba Could not remove state file "C:\\Users\\sonic\\mambaforge\\pkgs\\cache\\5afe41e9.state.json": The pro.
warning  libmamba Could not parse state file: Could not load cache state: [json.exception.type_error.302] type must be l
warning  libmamba Could not remove state file "C:\\Users\\sonic\\mambaforge\\pkgs\\cache\\09cdf8bf.state.json": The pro.
warning  libmamba Could not parse state file: Could not load cache state: [json.exception.type_error.302] type must be l
warning  libmamba Could not remove state file "C:\\Users\\sonic\\mambaforge\\pkgs\\cache\\3d1e1ba2.state.json": The pro.
warning  libmamba Could not parse state file: Could not load cache state: [json.exception.type_error.302] type must be l
warning  libmamba Could not remove state file "C:\\Users\\sonic\\mambaforge\\pkgs\\cache\\bcb51836.state.json": The pro.
bioconda/win-64                                    122.0 B @   1.4kB/s  0.1s
r/win-64                                           437.6kB @   1.7MB/s  0.3s
r/noarch                                           864.1kB @   1.8MB/s  0.5s
bioconda/noarch                                      4.5MB @   3.3MB/s  1.7s
conda-forge/noarch                                  13.3MB @   4.0MB/s  4.2s
conda-forge/win-64                                  21.2MB @   4.0MB/s  7.0s
Reloading output folder: C:\Users\sonic\mambaforge\conda-bld
file://C:/Users/sonic/mambaforge/conda-bld/win-64  127.0 B @ 198.7kB/s  0.0s
file://C:/Users/sonic/mambaforge/conda-bld/noarch  127.0 B @ 371.3kB/s  0.0s
Reloading output folder: C:\Users\sonic\mambaforge\conda-bld
file://C:/Users/sonic/mambaforge/conda-bld/win-64  127.0 B @ 228.4kB/s  0.0s
file://C:/Users/sonic/mambaforge/conda-bld/noarch  127.0 B @ 371.3kB/s  0.0s
Reloading output folder: C:\Users\sonic\mambaforge\conda-bld
file://C:/Users/sonic/mambaforge/conda-bld/win-64  127.0 B @ 284.8kB/s  0.0s
file://C:/Users/sonic/mambaforge/conda-bld/noarch  127.0 B @ 370.3kB/s  0.0s
BUILD START: ['rsaccharis-1.0.0-r34_0.tar.bz2']
Reloading output folder: C:\Users\sonic\mambaforge\conda-bld
file://C:/Users/sonic/mambaforge/conda-bld/win-64  127.0 B @ 253.0kB/s  0.0s
file://C:/Users/sonic/mambaforge/conda-bld/noarch  127.0 B @ 336.0kB/s  0.0s

## Package Plan ##

  environment location: C:\Users\sonic\mambaforge\conda-bld\rsaccharis_1689368957801\_h_env

The following NEW packages will be INSTALLED:

    _r-mutex:                1.0.1-anacondar_1    conda-forge
    m2w64-bwidget:           1.9.10-2             conda-forge
    m2w64-bzip2:             1.0.6-6              conda-forge
    m2w64-expat:             2.1.1-2              conda-forge
    m2w64-fftw:              3.3.4-6              conda-forge
    m2w64-flac:              1.3.1-3              conda-forge
    m2w64-gcc-libgfortran:   5.3.0-6              conda-forge
    m2w64-gcc-libs:          5.3.0-7              conda-forge
    m2w64-gcc-libs-core:     5.3.0-7              conda-forge
    m2w64-gettext:           0.19.7-2             conda-forge
    m2w64-gmp:               6.1.0-2              conda-forge
    m2w64-gsl:               2.1-2                conda-forge
    m2w64-libiconv:          1.14-6               conda-forge
    m2w64-libjpeg-turbo:     1.4.2-3              conda-forge
    m2w64-libogg:            1.3.2-3              conda-forge
    m2w64-libpng:            1.6.21-2             conda-forge
    m2w64-libsndfile:        1.0.26-2             conda-forge
    m2w64-libtiff:           4.0.6-2              conda-forge
    m2w64-libvorbis:         1.3.5-2              conda-forge
    m2w64-libwinpthread-git: 5.0.0.4634.697f757-2 conda-forge
    m2w64-libxml2:           2.9.3-3              conda-forge
    m2w64-mpfr:              3.1.4-4              conda-forge
    m2w64-pcre:              8.38-2               conda-forge
    m2w64-speex:             1.2rc2-3             conda-forge
    m2w64-speexdsp:          1.2rc3-3             conda-forge
    m2w64-tcl:               8.6.5-3              conda-forge
    m2w64-tk:                8.6.5-3              conda-forge
    m2w64-tktable:           2.10-5               conda-forge
    m2w64-wineditline:       2.101-5              conda-forge
    m2w64-xz:                5.2.2-2              conda-forge
    m2w64-zlib:              1.2.8-10             conda-forge
    msys2-conda-epoch:       20160418-1           conda-forge
    r-base:                  3.4.1-h8933c1f_8     conda-forge

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Reloading output folder: C:\Users\sonic\mambaforge\conda-bld
file://C:/Users/sonic/mambaforge/conda-bld/win-64  127.0 B @ 296.7kB/s  0.0s
file://C:/Users/sonic/mambaforge/conda-bld/noarch  127.0 B @ 351.8kB/s  0.0s
Reloading output folder: C:\Users\sonic\mambaforge\conda-bld
file://C:/Users/sonic/mambaforge/conda-bld/win-64  127.0 B @ 307.5kB/s  0.0s
file://C:/Users/sonic/mambaforge/conda-bld/noarch  127.0 B @ 388.4kB/s  0.0s
Mamba failed to solve:
 - r-ggnewscale
 - r-ape
 - r-stringr
 - r-magrittr
 - r-dplyr
 - r-knitr
 - r-jsonlite
 - r-base >=3.4,<3.5.0a0
 - r-magicfor
 - r-ggplot2
 - bioconductor-ggtree
 - r-rcolorbrewer

with channels:

The reported errors are:
- Encountered problems while solving:
-   - nothing provides r-base >=4.2,<4.3.0a0 needed by r-ggnewscale-0.4.8-r42hc72bb7e_1
-

Leaving build/test directories:
  Work:
 C:\Users\sonic\mambaforge\conda-bld\work
  Test:
 C:\Users\sonic\mambaforge\conda-bld\test_tmp
Leaving build/test environments:
  Test:
source activate  C:\Users\sonic\mambaforge\conda-bld\_test_env
  Build:
source activate  C:\Users\sonic\mambaforge\conda-bld\_build_env

Traceback (most recent call last):
  File "C:\Users\sonic\mambaforge\lib\site-packages\boa\cli\mambabuild.py", line 141, in mamba_get_install_actions
    solution = solver.solve_for_action(_specs, prefix)
  File "C:\Users\sonic\mambaforge\lib\site-packages\boa\core\solver.py", line 244, in solve_for_action
    t = self.solve(specs)
  File "C:\Users\sonic\mambaforge\lib\site-packages\boa\core\solver.py", line 234, in solve
    raise RuntimeError("Solver could not find solution." + error_string)
RuntimeError: Solver could not find solution.Mamba failed to solve:
 - r-ggnewscale
 - r-ape
 - r-stringr
 - r-magrittr
 - r-dplyr
 - r-knitr
 - r-jsonlite
 - r-base >=3.4,<3.5.0a0
 - r-magicfor
 - r-ggplot2
 - bioconductor-ggtree
 - r-rcolorbrewer

with channels:

The reported errors are:
- Encountered problems while solving:
-   - nothing provides r-base >=4.2,<4.3.0a0 needed by r-ggnewscale-0.4.8-r42hc72bb7e_1
-

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Users\sonic\mambaforge\Scripts\conda-mambabuild-script.py", line 9, in <module>
    sys.exit(main())
  File "C:\Users\sonic\mambaforge\lib\site-packages\boa\cli\mambabuild.py", line 256, in main
    call_conda_build(action, config)
  File "C:\Users\sonic\mambaforge\lib\site-packages\boa\cli\mambabuild.py", line 228, in call_conda_build
    result = api.build(
  File "C:\Users\sonic\mambaforge\lib\site-packages\conda_build\api.py", line 253, in build
    return build_tree(
  File "C:\Users\sonic\mambaforge\lib\site-packages\conda_build\build.py", line 3799, in build_tree
    packages_from_this = build(
  File "C:\Users\sonic\mambaforge\lib\site-packages\conda_build\build.py", line 2572, in build
    create_build_envs(top_level_pkg, notest)
  File "C:\Users\sonic\mambaforge\lib\site-packages\conda_build\build.py", line 2406, in create_build_envs
    raise e
  File "C:\Users\sonic\mambaforge\lib\site-packages\conda_build\build.py", line 2377, in create_build_envs
    environ.get_install_actions(
  File "C:\Users\sonic\mambaforge\lib\site-packages\boa\cli\mambabuild.py", line 150, in mamba_get_install_actions
    raise err
conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform win-64: {MatchSpec("r-ggne}

(base) C:\Users\sonic\IdeaProjects\rsaccharis>mamba build .
No numpy version specified in conda_build_config.yaml.  Falling back to default numpy value of 1.22
WARNING:conda_build.metadata:No numpy version specified in conda_build_config.yaml.  Falling back to default numpy value of 1.22
Adding in variants from internal_defaults
INFO:conda_build.variants:Adding in variants from internal_defaults
Adding in variants from C:\Users\sonic\IdeaProjects\rsaccharis\conda-recipe\conda_build_config.yaml
INFO:conda_build.variants:Adding in variants from C:\Users\sonic\IdeaProjects\rsaccharis\conda-recipe\conda_build_config.yaml
Attempting to finalize metadata for rsaccharis
INFO:conda_build.metadata:Attempting to finalize metadata for rsaccharis
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
BUILD START: ['rsaccharis-1.0.0-r34_0.tar.bz2']
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: C:\Users\sonic\mambaforge\conda-bld\rsaccharis_1689363748531\_h_env

The following NEW packages will be INSTALLED:

    _r-mutex:                1.0.1-anacondar_1    conda-forge
    m2w64-bwidget:           1.9.10-2             conda-forge
    m2w64-bzip2:             1.0.6-6              conda-forge
    m2w64-expat:             2.1.1-2              conda-forge
    m2w64-fftw:              3.3.4-6              conda-forge
    m2w64-flac:              1.3.1-3              conda-forge
    m2w64-gcc-libgfortran:   5.3.0-6              conda-forge
    m2w64-gcc-libs:          5.3.0-7              conda-forge
    m2w64-gcc-libs-core:     5.3.0-7              conda-forge
    m2w64-gettext:           0.19.7-2             conda-forge
    m2w64-gmp:               6.1.0-2              conda-forge
    m2w64-gsl:               2.1-2                conda-forge
    m2w64-libiconv:          1.14-6               conda-forge
    m2w64-libjpeg-turbo:     1.4.2-3              conda-forge
    m2w64-libogg:            1.3.2-3              conda-forge
    m2w64-libpng:            1.6.21-2             conda-forge
    m2w64-libsndfile:        1.0.26-2             conda-forge
    m2w64-libtiff:           4.0.6-2              conda-forge
    m2w64-libvorbis:         1.3.5-2              conda-forge
    m2w64-libwinpthread-git: 5.0.0.4634.697f757-2 conda-forge
    m2w64-libxml2:           2.9.3-3              conda-forge
    m2w64-mpfr:              3.1.4-4              conda-forge
    m2w64-pcre:              8.38-2               conda-forge
    m2w64-speex:             1.2rc2-3             conda-forge
    m2w64-speexdsp:          1.2rc3-3             conda-forge
    m2w64-tcl:               8.6.5-3              conda-forge
    m2w64-tk:                8.6.5-3              conda-forge
    m2w64-tktable:           2.10-5               conda-forge
    m2w64-wineditline:       2.101-5              conda-forge
    m2w64-xz:                5.2.2-2              conda-forge
    m2w64-zlib:              1.2.8-10             conda-forge
    msys2-conda-epoch:       20160418-1           conda-forge
    r-base:                  3.4.1-h8933c1f_8     conda-forge

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... WARNING conda.models.version:get_matcher(546): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.*, but conda is ignoring the .* and treating it as 1
WARNING conda.models.version:get_matcher(546): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 2.*, but conda is ignoring the .* and treating it as 2
WARNING conda.models.version:get_matcher(546): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 3.*, but conda is ignoring the .* and treating it as 3
WARNING conda.models.version:get_matcher(546): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 3.6.*, but conda is ignoring the .* and treating it as 3.6
WARNING conda.models.version:get_matcher(546): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 2.*, but conda is ignoring the .* and treating it as 2
WARNING conda.models.version:get_matcher(546): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 4.*, but conda is ignoring the .* and treating it as 4
WARNING conda.models.version:get_matcher(546): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 0.23.*, but conda is ignoring the .* and treating it as 0.23
WARNING conda.models.version:get_matcher(546): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 3.*, but conda is ignoring the .* and treating it as 3

Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed

Leaving build/test directories:
  Work:
 C:\Users\sonic\mambaforge\conda-bld\work
  Test:
 C:\Users\sonic\mambaforge\conda-bld\test_tmp
Leaving build/test environments:
  Test:
source activate  C:\Users\sonic\mambaforge\conda-bld\_test_env
  Build:
source activate  C:\Users\sonic\mambaforge\conda-bld\_build_env

Traceback (most recent call last):
  File "C:\Users\sonic\mambaforge\lib\site-packages\conda_build\environ.py", line 900, in get_install_actions
    actions = install_actions(prefix, index, specs, force=True)
  File "C:\Users\sonic\mambaforge\lib\site-packages\conda\common\io.py", line 84, in decorated
    return f(*args, **kwds)
  File "C:\Users\sonic\mambaforge\lib\site-packages\conda\plan.py", line 470, in install_actions
    txn = solver.solve_for_transaction(prune=prune, ignore_pinned=not pinned)
  File "C:\Users\sonic\mambaforge\lib\site-packages\conda\core\solve.py", line 132, in solve_for_transaction
    unlink_precs, link_precs = self.solve_for_diff(update_modifier, deps_modifier,
  File "C:\Users\sonic\mambaforge\lib\site-packages\conda\core\solve.py", line 175, in solve_for_diff
    final_precs = self.solve_final_state(update_modifier, deps_modifier, prune, ignore_pinned,
  File "C:\Users\sonic\mambaforge\lib\site-packages\conda\core\solve.py", line 299, in solve_final_state
    ssc = self._run_sat(ssc)
  File "C:\Users\sonic\mambaforge\lib\site-packages\conda\common\io.py", line 84, in decorated
    return f(*args, **kwds)
  File "C:\Users\sonic\mambaforge\lib\site-packages\conda\core\solve.py", line 847, in _run_sat
    ssc.solution_precs = ssc.r.solve(tuple(final_environment_specs),
  File "C:\Users\sonic\mambaforge\lib\site-packages\conda\common\io.py", line 84, in decorated
    return f(*args, **kwds)
  File "C:\Users\sonic\mambaforge\lib\site-packages\conda\resolve.py", line 1324, in solve
    self.find_conflicts(specs, specs_to_add, history_specs)
  File "C:\Users\sonic\mambaforge\lib\site-packages\conda\resolve.py", line 350, in find_conflicts
    raise UnsatisfiableError(bad_deps, strict=strict_channel_priority)
conda.exceptions.UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package m2w64-gcc-libs-core conflicts for:
r-ggnewscale -> r-base[version='>=4.1,<4.2.0a0'] -> m2w64-gcc-libs-core
r-dplyr -> m2w64-gcc-libs-core
r-ggplot2 -> r-cli -> m2w64-gcc-libs-core
r-magrittr -> m2w64-gcc-libs-core
r-rcolorbrewer -> r-base[version='>=4.1,<4.2.0a0'] -> m2w64-gcc-libs-core
r-stringr -> r-cli -> m2w64-gcc-libs-core
r-base[version='>=3.4,<3.5.0a0'] -> m2w64-gcc-libs -> m2w64-gcc-libs-core
r-knitr -> r-xfun[version='>=0.34'] -> m2w64-gcc-libs-core
r-jsonlite -> m2w64-gcc-libs-core
bioconductor-ggtree -> r-ape -> m2w64-gcc-libs-core
r-ape -> m2w64-gcc-libs-core

Package r-stringr conflicts for:
bioconductor-ggtree -> r-tidyr -> r-stringr[version='>=1.5.0']
r-knitr -> r-stringr[version='>=0.6']
r-stringr
r-knitr -> r-evaluate[version='>=0.10'] -> r-stringr[version='>=0.6.2']
r-ggplot2 -> r-reshape2 -> r-stringr

Package r-glue conflicts for:
r-knitr -> r-stringr[version='>=0.6'] -> r-glue[version='>=1.2.0|>=1.6.1']
r-ggnewscale -> r-ggplot2[version='>=3.0.0'] -> r-glue
r-ggplot2 -> r-glue
r-stringr -> r-glue[version='>=1.2.0|>=1.6.1']
r-dplyr -> r-glue[version='>=1.1.1|>=1.3.0|>=1.3.2']
bioconductor-ggtree -> r-cli -> r-glue[version='>=1.1.1|>=1.3.0|>=1.3.2']

Package r conflicts for:
bioconductor-ggtree -> r-tidyr -> r=3.1.3
r-jsonlite -> r=3.1.3
r-stringr -> r-stringi[version='>=0.4.1'] -> r=3.1.3
r-knitr -> r=3.1.3

Package r-base conflicts for:
bioconductor-ggtree -> r-ape -> r-base[version='3.2.4.*|3.3.0.*|3.3.1.*|3.3.2.*|3.4.1.*|>=3.4.1,<3.4.2.0a0|>=3.5,<3.6.0a0|>=3.4.3,<3.4.4.0a0|>=3.4.2,<3.4.3a0']
r-stringr -> r-base[version='3.2.4.*|3.3.0.*|3.3.1.*|3.3.2.*|3.4.1.*|>=3.4.1,<3.4.2.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=4.0,<4.1.0a0|>=4.1,<4.2.0a0|>=4.2,<4.3.0a0|>=4.3,<4.4.0a0|>=3.5.1,<3.5.2.0a0|>=3.4.3,<3.4.4.0a0|>=3.4.2,<3.4.3a0']
r-ggplot2 -> r-base[version='3.2.4.*|3.3.0.*|3.3.1.*|3.3.2.*|3.4.1.*|>=3.4.1,<3.4.2.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=4.0,<4.1.0a0|>=4.1,<4.2.0a0|>=4.2,<4.3.0a0|>=4.3,<4.4.0a0|>=3.5.1,<3.5.2.0a0|>=3.4.3,<3.4.4.0a0|>=3.4.2,<3.4.3a0']
r-ape -> r-base[version='3.2.4.*|3.3.0.*|3.3.1.*|3.3.2.*|3.4.1.*|>=3.4.1,<3.4.2.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=4.0,<4.1.0a0|>=4.1,<4.2.0a0|>=3.5.1,<3.5.2.0a0|>=3.4.3,<3.4.4.0a0|>=3.4.2,<3.4.3a0']
r-jsonlite -> r-base[version='3.2.4.*|3.3.0.*|3.3.1.*|3.3.2.*|3.4.1.*|>=3.4.1,<3.4.2.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=4.0,<4.1.0a0|>=4.1,<4.2.0a0|>=3.5.1,<3.5.2.0a0|>=3.4.3,<3.4.4.0a0|>=3.4.2,<3.4.3a0']
r-knitr -> r-base[version='3.2.4.*|3.3.0.*|3.3.1.*|3.3.2.*|3.4.1.*|>=3.4.1,<3.4.2.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=4.0,<4.1.0a0|>=4.1,<4.2.0a0|>=4.2,<4.3.0a0|>=4.3,<4.4.0a0|>=3.5.1,<3.5.2.0a0|>=3.4.3,<3.4.4.0a0|>=3.4.2,<3.4.3a0']
bioconductor-ggtree -> r-base[version='>=3.5.1,<3.5.2.0a0|>=3.6,<3.7.0a0|>=4.0,<4.1.0a0|>=4.1,<4.2.0a0|>=4.2,<4.3.0a0|>=4.3,<4.4.0a0']
r-base[version='>=3.4,<3.5.0a0']
r-magicfor -> r-base[version='>=3.6,<3.7.0a0|>=4.2,<4.3.0a0']
r-dplyr -> r-generics -> r-base[version='>=4.2,<4.3.0a0|>=4.3,<4.4.0a0']
r-dplyr -> r-base[version='3.2.4.*|3.3.0.*|3.3.1.*|3.3.2.*|3.4.1.*|>=3.4.1,<3.4.2.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=4.0,<4.1.0a0|>=4.1,<4.2.0a0|>=3.5.1,<3.5.2.0a0|>=3.4.3,<3.4.4.0a0|>=3.4.2,<3.4.3a0']
r-rcolorbrewer -> r-base[version='3.2.4.*|3.3.0.*|3.3.1.*|3.3.2.*|3.4.1.*|>=3.4.1,<3.4.2.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=4.0,<4.1.0a0|>=4.1,<4.2.0a0|>=4.2,<4.3.0a0|>=4.3,<4.4.0a0|>=3.5.1,<3.5.2.0a0|>=3.4.3,<3.4.4.0a0|>=3.4.2,<3.4.3a0']
r-magrittr -> r-base[version='3.2.4.*|3.3.0.*|3.3.1.*|3.3.2.*|3.4.1.*|>=3.4.1,<3.4.2.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=4.0,<4.1.0a0|>=4.1,<4.2.0a0|>=3.5.1,<3.5.2.0a0|>=3.4.3,<3.4.4.0a0|>=3.4.2,<3.4.3a0']

Package r-magrittr conflicts for:
r-knitr -> r-stringr[version='>=0.6'] -> r-magrittr
r-ggplot2 -> r-tibble -> r-magrittr
r-stringr -> r-magrittr
bioconductor-ggtree -> r-magrittr
r-dplyr -> r-magrittr[version='>=1.5']
bioconductor-ggtree -> r-dplyr -> r-magrittr[version='>=1.5']
r-magrittr

Package r-digest conflicts for:
r-stringr -> r-vctrs -> r-digest
r-ape -> r-digest
r-ggnewscale -> r-ggplot2[version='>=3.0.0'] -> r-digest
bioconductor-ggtree -> r-ape -> r-digest
r-dplyr -> r-vctrs[version='>=0.3.5'] -> r-digest
r-knitr -> r-digest
r-ggplot2 -> r-digest

Package r-labeling conflicts for:
r-ggplot2 -> r-scales[version='>=1.2.0'] -> r-labeling
bioconductor-ggtree -> r-scales -> r-labeling

Package r-crayon conflicts for:
r-dplyr -> r-pillar[version='>=1.5.1'] -> r-crayon[version='>=1.3.4']
r-stringr -> r-cli -> r-crayon[version='>=1.3.4']
r-ggplot2 -> r-cli -> r-crayon[version='>=1.3.4']
bioconductor-ggtree -> r-cli -> r-crayon[version='>=1.3.4']

Package m2w64-pcre2 conflicts for:
r-rcolorbrewer -> r-base[version='>=4.1,<4.2.0a0'] -> m2w64-pcre2
r-ape -> r-base[version='>=4.1,<4.2.0a0'] -> m2w64-pcre2
r-knitr -> r-base[version='>=4.1,<4.2.0a0'] -> m2w64-pcre2
r-dplyr -> r-base[version='>=4.1,<4.2.0a0'] -> m2w64-pcre2
r-ggnewscale -> r-base[version='>=4.1,<4.2.0a0'] -> m2w64-pcre2
r-ggplot2 -> r-base[version='>=4.1,<4.2.0a0'] -> m2w64-pcre2
r-magrittr -> r-base[version='>=4.1,<4.2.0a0'] -> m2w64-pcre2
r-jsonlite -> r-base[version='>=4.1,<4.2.0a0'] -> m2w64-pcre2
bioconductor-ggtree -> r-base[version='>=4.1,<4.2.0a0'] -> m2w64-pcre2
r-stringr -> r-base[version='>=4.1,<4.2.0a0'] -> m2w64-pcre2

Package m2w64-libwinpthread-git conflicts for:
r-jsonlite -> m2w64-gcc-libs -> m2w64-libwinpthread-git
r-magrittr -> m2w64-gcc-libs -> m2w64-libwinpthread-git
r-base[version='>=3.4,<3.5.0a0'] -> m2w64-gcc-libs -> m2w64-libwinpthread-git
r-ape -> m2w64-gcc-libs -> m2w64-libwinpthread-git
r-dplyr -> m2w64-gcc-libs -> m2w64-libwinpthread-git

Package r-jsonlite conflicts for:
r-jsonlite
bioconductor-ggtree -> bioconductor-treeio[version='>=1.24.0,<1.25.0'] -> r-jsonlite

Package r-lazyeval conflicts for:
r-ggplot2 -> r-lazyeval
r-ggplot2 -> r-tibble -> r-lazyeval[version='>=0.1.10']
bioconductor-ggtree -> r-dplyr -> r-lazyeval[version='>=0.1.10|>=0.2.0']
r-dplyr -> r-lazyeval[version='>=0.1.10']
r-ggnewscale -> r-ggplot2[version='>=3.0.0'] -> r-lazyeval

Package liblapack conflicts for:
bioconductor-ggtree -> r-ape -> liblapack[version='>=3.8.0,<4.0.0a0|>=3.8.0,<4.0a0|>=3.9.0,<4.0a0']
r-dplyr -> r-base[version='>=4.1,<4.2.0a0'] -> liblapack[version='>=3.8.0,<4.0.0a0|>=3.8.0,<4.0a0|>=3.9.0,<4.0a0']
r-ape -> liblapack[version='>=3.8.0,<4.0.0a0|>=3.8.0,<4.0a0|>=3.9.0,<4.0a0']
r-jsonlite -> r-base[version='>=4.1,<4.2.0a0'] -> liblapack[version='>=3.8.0,<4.0.0a0|>=3.8.0,<4.0a0|>=3.9.0,<4.0a0']
r-ggnewscale -> r-base[version='>=4.1,<4.2.0a0'] -> liblapack[version='>=3.8.0,<4.0.0a0|>=3.8.0,<4.0a0|>=3.9.0,<4.0a0']
r-knitr -> r-base[version='>=4.1,<4.2.0a0'] -> liblapack[version='>=3.8.0,<4.0.0a0|>=3.8.0,<4.0a0|>=3.9.0,<4.0a0']
r-stringr -> r-base[version='>=4.1,<4.2.0a0'] -> liblapack[version='>=3.8.0,<4.0.0a0|>=3.8.0,<4.0a0|>=3.9.0,<4.0a0']
r-magicfor -> r-base[version='>=3.6,<3.7.0a0'] -> liblapack[version='>=3.8.0,<4.0.0a0|>=3.8.0,<4.0a0']
r-magrittr -> r-base[version='>=4.1,<4.2.0a0'] -> liblapack[version='>=3.8.0,<4.0.0a0|>=3.8.0,<4.0a0|>=3.9.0,<4.0a0']
r-ggplot2 -> r-mgcv -> liblapack[version='>=3.8.0,<4.0.0a0|>=3.8.0,<4.0a0|>=3.9.0,<4.0a0']
r-rcolorbrewer -> r-base[version='>=4.1,<4.2.0a0'] -> liblapack[version='>=3.8.0,<4.0.0a0|>=3.8.0,<4.0a0|>=3.9.0,<4.0a0']

Package r-rcpp conflicts for:
r-ape -> r-rcpp[version='>=0.12.0']
r-dplyr -> r-bindrcpp[version='>=0.2.0.9000'] -> r-rcpp[version='>=0.12.16|>=0.12.3']
r-ggplot2 -> r-isoband -> r-rcpp[version='>=0.11.0|>=0.12.3']
r-dplyr -> r-rcpp[version='>=0.12.0|>=0.12.15|>=0.12.19|>=1.0.0|>=1.0.1|>=0.12.6|>=0.12.7']
bioconductor-ggtree -> r-ape -> r-rcpp[version='>=0.12.0|>=1.0.1|>=1.0.0|>=0.12.19|>=0.12.15|>=0.12.6|>=0.12.7|>=0.12.3']

Package r-ape conflicts for:
r-ape
bioconductor-ggtree -> r-ape

Package r-r6 conflicts for:
bioconductor-ggtree -> r-dplyr -> r-r6[version='>=2.2.2']
r-dplyr -> r-r6[version='>=2.2.2']
r-ggplot2 -> r-scales[version='>=1.2.0'] -> r-r6

Package r-ggplot2 conflicts for:
bioconductor-ggtree -> r-aplot -> r-ggplot2
bioconductor-ggtree -> r-ggplot2[version='>3.3.6|>=3.0.0']
r-ggplot2

Package r-backports conflicts for:
r-dplyr -> r-vctrs[version='>=0.3.5'] -> r-backports
r-stringr -> r-vctrs -> r-backports

Package r-stringi conflicts for:
r-stringr -> r-stringi[version='>=0.4.1|>=1.1.6|>=1.1.7|>=1.5.3']
bioconductor-ggtree -> r-tidyr -> r-stringi
r-knitr -> r-stringr[version='>=0.6'] -> r-stringi[version='>=0.4.1|>=1.1.6|>=1.1.7|>=1.5.3']

Package r-dplyr conflicts for:
bioconductor-ggtree -> r-dplyr
r-dplyr
bioconductor-ggtree -> r-tidyr -> r-dplyr[version='>=0.2|>=0.4|>=0.7.0|>=0.8.2|>=1.0.0|>=1.0.10']

Package m2-texinfo-tex conflicts for:
r-ape -> r-base=3.3.2 -> m2-texinfo-tex
r-stringr -> r-base=3.3.2 -> m2-texinfo-tex
r-dplyr -> r-base=3.3.2 -> m2-texinfo-tex
r-rcolorbrewer -> r-base=3.3.2 -> m2-texinfo-tex
r-ggplot2 -> r-base=3.3.2 -> m2-texinfo-tex
r-knitr -> r-base=3.3.2 -> m2-texinfo-tex
r-jsonlite -> r-base=3.3.2 -> m2-texinfo-tex
r-magrittr -> r-base=3.3.2 -> m2-texinfo-tex

Package r-rcolorbrewer conflicts for:
r-ggplot2 -> r-scales[version='>=1.2.0'] -> r-rcolorbrewer
bioconductor-ggtree -> r-scales -> r-rcolorbrewer
r-rcolorbrewer

Package r-nlme conflicts for:
bioconductor-ggtree -> r-ape -> r-nlme
r-ggplot2 -> r-mgcv -> r-nlme[version='>=3.1|>=3.1_64']
r-ape -> r-nlme

Package r-pkgconfig conflicts for:
r-dplyr -> r-tibble[version='>=2.1.3'] -> r-pkgconfig[version='>=2.0.2']
r-dplyr -> r-pkgconfig[version='>=2.0.1']

Package r-pillar conflicts for:
r-dplyr -> r-pillar[version='>=1.5.1']
r-dplyr -> r-tibble[version='>=2.1.3'] -> r-pillar[version='>=1.1.0|>=1.3.1|>=1.4.3|>=1.5.0|>=1.8.1']

Package r-ellipsis conflicts for:
r-dplyr -> r-ellipsis
r-dplyr -> r-pillar[version='>=1.5.1'] -> r-ellipsis[version='>=0.2.0|>=0.3.2']

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Users\sonic\mambaforge\Scripts\conda-build-script.py", line 10, in <module>
    sys.exit(main())
  File "C:\Users\sonic\mambaforge\lib\site-packages\conda_build\cli\main_build.py", line 593, in main
    execute(sys.argv[1:])
  File "C:\Users\sonic\mambaforge\lib\site-packages\conda_build\cli\main_build.py", line 573, in execute
    outputs = api.build(
  File "C:\Users\sonic\mambaforge\lib\site-packages\conda_build\api.py", line 253, in build
    return build_tree(
  File "C:\Users\sonic\mambaforge\lib\site-packages\conda_build\build.py", line 3799, in build_tree
    packages_from_this = build(
  File "C:\Users\sonic\mambaforge\lib\site-packages\conda_build\build.py", line 2572, in build
    create_build_envs(top_level_pkg, notest)
  File "C:\Users\sonic\mambaforge\lib\site-packages\conda_build\build.py", line 2406, in create_build_envs
    raise e
  File "C:\Users\sonic\mambaforge\lib\site-packages\conda_build\build.py", line 2377, in create_build_envs
    environ.get_install_actions(
  File "C:\Users\sonic\mambaforge\lib\site-packages\conda_build\environ.py", line 902, in get_install_actions
    raise DependencyNeedsBuildingError(exc, subdir=subdir)
conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform win-64: {"r-stringr[version='>=1.5.0']", "r-magrittr[version='>=1.5']", "r-r6[version='>=2.2.2']", "r-base[version='3.2.4.*|3.3.0.*|3.3.1.*|3.3.2.*|3.4.1.*|>=3.4.1,<3.4.2.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=4.0,<4.1.0a0|>=4.1,<4.2.0a0|>=4.2,<4.3.0a0|>=4.3,<4.4.0a0|>=3.5.1,<3.5.2.0a0|>=3.4.3,<3.4.4.0a0|>=3.4.2,<3.4.3a0']", 'r-stringr', "r-ggplot2[version='>3.3.6|>=3.0.0']", "r-base[version='>=4.2,<4.3.0a0|>=4.3,<4.4.0a0']", "r-stringr[version='>=0.6']", "r-rcpp[version='>=0.12.16|>=0.12.3']", "r-rcpp[version='>=0.12.0|>=1.0.1|>=1.0.0|>=0.12.19|>=0.12.15|>=0.12.6|>=0.12.7|>=0.12.3']", 'r=3.1.3', 'r-jsonlite', 'r-backports', 'm2w64-libwinpthread-git', "r-pkgconfig[version='>=2.0.2']", 'r-ggplot2', "r-base[version='3.2.4.*|3.3.0.*|3.3.1.*|3.3.2.*|3.4.1.*|>=3.4.1,<3.4.2.0a0|>=3.5,<3.6.0a0|>=3.4.3,<3.4.4.0a0|>=3.4.2,<3.4.3a0']", "r-crayon[version='>=1.3.4']", "r-rcpp[version='>=0.12.0|>=0.12.15|>=0.12.19|>=1.0.0|>=1.0.1|>=0.12.6|>=0.12.7']", "r-glue[version='>=1.2.0|>=1.6.1']", 'm2w64-pcre2', "r-base[version='>=3.5.1,<3.5.2.0a0|>=3.6,<3.7.0a0|>=4.0,<4.1.0a0|>=4.1,<4.2.0a0|>=4.2,<4.3.0a0|>=4.3,<4.4.0a0']", "r-stringi[version='>=0.4.1|>=1.1.6|>=1.1.7|>=1.5.3']", "r-dplyr[version='>=0.2|>=0.4|>=0.7.0|>=0.8.2|>=1.0.0|>=1.0.10']", "r-pillar[version='>=1.5.1']", "r-ellipsis[version='>=0.2.0|>=0.3.2']", "r-glue[version='>=1.1.1|>=1.3.0|>=1.3.2']", "r-stringr[version='>=0.6.2']", "r-rcpp[version='>=0.11.0|>=0.12.3']", 'r-dplyr', 'r-glue', "r-base[version='>=3.6,<3.7.0a0|>=4.2,<4.3.0a0']", 'r-nlme', 'r-r6', "liblapack[version='>=3.8.0,<4.0.0a0|>=3.8.0,<4.0a0']", 'm2w64-gcc-libs-core', 'r-ellipsis', 'm2-texinfo-tex', "liblapack[version='>=3.8.0,<4.0.0a0|>=3.8.0,<4.0a0|>=3.9.0,<4.0a0']", 'r-digest', "r-nlme[version='>=3.1|>=3.1_64']", 'r-magrittr', 'r-ape', "r-lazyeval[version='>=0.1.10']", "r-lazyeval[version='>=0.1.10|>=0.2.0']", "r-pkgconfig[version='>=2.0.1']", 'r-labeling', 'r-rcolorbrewer', "r-base[version='3.2.4.*|3.3.0.*|3.3.1.*|3.3.2.*|3.4.1.*|>=3.4.1,<3.4.2.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=4.0,<4.1.0a0|>=4.1,<4.2.0a0|>=3.5.1,<3.5.2.0a0|>=3.4.3,<3.4.4.0a0|>=3.4.2,<3.4.3a0']", "r-pillar[version='>=1.1.0|>=1.3.1|>=1.4.3|>=1.5.0|>=1.8.1']", 'r-stringi', "r-rcpp[version='>=0.12.0']", 'r-lazyeval'}

environment.yml

No response

~/.condarc

channels:
  - bioconda
  - conda-forge
  - r
jonashaag commented 1 year ago

Conda-build and boa will restrict R to some old version. You can change that with the command line or maybe by adding a lower pin. The reason is that packages are generally built multiple times for multiple R versions. Same with NumPy, Python, maybe others. Those are all packages that are special cased.

AlexSCFraser commented 1 month ago

So a note to anyone with a similar issue, I solved this by specifying the r_base version in my conda build config, as below.

conda_build_config.yaml

r_base:
  - 3.6.3

I'm not sure this should be closed though, because to me this seems like it should be unnecessary and that the solver should be able to override the special case and choose a compatible version of r_base when there is a solver error because of some hardcoded r_base version being incompatible with a set of r packages. I understand there are probably reasons for the special case of r_base versions to exist, but