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Cannot build package due to mamba build solver issue
Troubleshooting docs
- [X] My problem is not solved in the Troubleshooting docs
How did you install Mamba?
Mambaforge
Search tried in issue tracker
solver build
Latest version of Mamba
- [X] My problem is not solved with the latest version
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through the output, one thing that stands out to me is that the r-base package seems to have gained a narrow range of outdated version somehow, which I'm not exactly sure has come from.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
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mamba (1.4.2) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
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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
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.
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
