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Packages compatibility issue when creating an env using preprocessing.yml #270

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inaciomdrs opened this issue Apr 19, 2024 · 0 comments
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I tried to create a conda environment using preprocessing.yml file to run the codes from Quality Control chapter, however I get the following error message, regarding compatibility issues.

error libmamba Could not solve for environment specs
The following packages are incompatible
├─ anndata2ri 1.1* is not installable because it requires
│ └─ rpy2 >=3.4.3 , which conflicts with any installable versions previously reported;
├─ bioconductor-scdblfinder 1.8.0* is not installable because it requires
│ └─ bioconductor-scater >=1.22.0,<1.23.0 , which requires
│ └─ bioconductor-delayedmatrixstats >=1.16.0,<1.17.0 , which requires
│ └─ r-matrixstats >=0.60.0 , which conflicts with any installable versions previously reported;
├─ bioconductor-scran 1.22.1* is not installable because it requires
│ └─ r-dqrng but there are no viable options
│ ├─ r-dqrng [0.2.1|0.3.0|0.3.1|0.3.2] would require
│ │ └─ r-bh >=1.64.0_1 , which conflicts with any installable versions previously reported;
│ └─ r-dqrng [0.3.0|0.3.1] conflicts with any installable versions previously reported;
├─ bioconductor-scry 1.6.0* is not installable because it requires
│ └─ bioconductor-summarizedexperiment >=1.24.0,<1.25.0 , which requires
│ └─ bioconductor-matrixgenerics >=1.6.0,<1.7.0 , which requires
│ └─ r-base >=4.1,<4.2.0a0 but there are no viable options
│ ├─ r-base [4.1.0|4.1.1|4.1.2] would require
│ │ └─ libtiff >=4.3.0,<4.5.0a0 but there are no viable options
│ │ ├─ libtiff [4.4.0|4.5.0] would require
│ │ │ └─ libdeflate >=1.14,<1.15.0a0 , which conflicts with any installable versions previously reported;
│ │ ├─ libtiff 4.4.0 would require
│ │ │ └─ libdeflate >=1.12,<1.13.0a0 , which conflicts with any installable versions previously reported;
│ │ ├─ libtiff 4.4.0 would require
│ │ │ └─ libdeflate >=1.13,<1.14.0a0 , which conflicts with any installable versions previously reported;
│ │ ├─ libtiff [4.3.0|4.4.0] would require
│ │ │ └─ libdeflate >=1.10,<1.11.0a0 , which conflicts with any installable versions previously reported;
│ │ ├─ libtiff 4.4.0 conflicts with any installable versions previously reported;
│ │ ├─ libtiff 4.3.0 would require
│ │ │ └─ libdeflate >=1.8,<1.9.0a0 , which conflicts with any installable versions previously reported;
│ │ └─ libtiff 4.3.0 would require
│ │ └─ libdeflate >=1.7,<1.8.0a0 , which conflicts with any installable versions previously reported;
│ ├─ r-base 4.1.3 would require
│ │ ├─ libcurl >=7.82.0,<9.0a0 but there are no viable options
│ │ │ ├─ libcurl [7.82.0|7.83.0|...|8.4.0] would require
│ │ │ │ └─ libnghttp2 [>=1.47.0,<2.0a0 |>=1.51.0,<2.0a0 |>=1.52.0,<2.0a0 ] but there are no viable options
│ │ │ │ ├─ libnghttp2 1.58.0 would require
│ │ │ │ │ └─ c-ares >=1.21.0,<2.0a0 , which conflicts with any installable versions previously reported;
│ │ │ │ ├─ libnghttp2 1.58.0 would require
│ │ │ │ │ └─ c-ares >=1.23.0,<2.0a0 , which conflicts with any installable versions previously reported;
│ │ │ │ ├─ libnghttp2 [1.47.0|1.51.0|1.52.0] would require
│ │ │ │ │ └─ c-ares >=1.18.1,<2.0a0 , which conflicts with any installable versions previously reported;
│ │ │ │ ├─ libnghttp2 1.55.1 would require
│ │ │ │ │ └─ c-ares >=1.20.1,<2.0a0 , which conflicts with any installable versions previously reported;
│ │ │ │ └─ libnghttp2 [1.52.0|1.57.0] conflicts with any installable versions previously reported;
│ │ │ ├─ libcurl [8.5.0|8.6.0|8.7.1] would require
│ │ │ │ └─ libnghttp2 >=1.58.0,<2.0a0 , which cannot be installed (as previously explained);
│ │ │ ├─ libcurl 7.82.0 conflicts with any installable versions previously reported;
│ │ │ ├─ libcurl 7.84.0 conflicts with any installable versions previously reported;
│ │ │ ├─ libcurl 7.85.0 conflicts with any installable versions previously reported;
│ │ │ ├─ libcurl [7.86.0|7.87.0|7.88.1] conflicts with any installable versions previously reported;
│ │ │ ├─ libcurl 8.1.1 conflicts with any installable versions previously reported;
│ │ │ ├─ libcurl 8.2.1 conflicts with any installable versions previously reported;
│ │ │ └─ libcurl [8.4.0|8.5.0] conflicts with any installable versions previously reported;
│ │ └─ libtiff >=4.3.0,<4.5.0a0 but there are no viable options
│ │ ├─ libtiff [4.4.0|4.5.0], which cannot be installed (as previously explained);
│ │ ├─ libtiff 4.4.0, which cannot be installed (as previously explained);
│ │ ├─ libtiff 4.4.0, which cannot be installed (as previously explained);
│ │ ├─ libtiff [4.3.0|4.4.0], which cannot be installed (as previously explained);
│ │ ├─ libtiff 4.4.0 conflicts with any installable versions previously reported;
│ │ ├─ libtiff 4.3.0, which cannot be installed (as previously explained);
│ │ └─ libtiff 4.3.0, which cannot be installed (as previously explained);
│ ├─ r-base 4.1.3 would require
│ │ ├─ libcurl >=7.85.0,<9.0a0 but there are no viable options
│ │ │ ├─ libcurl [7.82.0|7.83.0|...|8.4.0], which cannot be installed (as previously explained);
│ │ │ ├─ libcurl [8.5.0|8.6.0|8.7.1], which cannot be installed (as previously explained);
│ │ │ ├─ libcurl 7.85.0 conflicts with any installable versions previously reported;
│ │ │ ├─ libcurl [7.86.0|7.87.0|7.88.1] conflicts with any installable versions previously reported;
│ │ │ ├─ libcurl 8.1.1 conflicts with any installable versions previously reported;
│ │ │ ├─ libcurl 8.2.1 conflicts with any installable versions previously reported;
│ │ │ └─ libcurl [8.4.0|8.5.0] conflicts with any installable versions previously reported;
│ │ └─ libtiff >=4.4.0,<4.5.0a0 but there are no viable options
│ │ ├─ libtiff [4.4.0|4.5.0], which cannot be installed (as previously explained);
│ │ ├─ libtiff 4.4.0, which cannot be installed (as previously explained);
│ │ ├─ libtiff 4.4.0, which cannot be installed (as previously explained);
│ │ ├─ libtiff [4.3.0|4.4.0], which cannot be installed (as previously explained);
│ │ └─ libtiff 4.4.0 conflicts with any installable versions previously reported;
│ ├─ r-base 4.1.3 would require
│ │ ├─ libcurl >=7.83.1,<9.0a0 but there are no viable options
│ │ │ ├─ libcurl [7.82.0|7.83.0|...|8.4.0], which cannot be installed (as previously explained);
│ │ │ ├─ libcurl [8.5.0|8.6.0|8.7.1], which cannot be installed (as previously explained);
│ │ │ ├─ libcurl 7.84.0 conflicts with any installable versions previously reported;
│ │ │ ├─ libcurl 7.85.0 conflicts with any installable versions previously reported;
│ │ │ ├─ libcurl [7.86.0|7.87.0|7.88.1] conflicts with any installable versions previously reported;
│ │ │ ├─ libcurl 8.1.1 conflicts with any installable versions previously reported;
│ │ │ ├─ libcurl 8.2.1 conflicts with any installable versions previously reported;
│ │ │ └─ libcurl [8.4.0|8.5.0] conflicts with any installable versions previously reported;
│ │ └─ libtiff >=4.4.0,<4.5.0a0 but there are no viable options
│ │ ├─ libtiff [4.4.0|4.5.0], which cannot be installed (as previously explained);
│ │ ├─ libtiff 4.4.0, which cannot be installed (as previously explained);
│ │ ├─ libtiff 4.4.0, which cannot be installed (as previously explained);
│ │ ├─ libtiff [4.3.0|4.4.0], which cannot be installed (as previously explained);
│ │ └─ libtiff 4.4.0 conflicts with any installable versions previously reported;
│ ├─ r-base 4.1.3 would require
│ │ ├─ libcurl [>=8.0.1,<9.0a0 |>=8.1.0,<9.0a0 ] but there are no viable options
│ │ │ ├─ libcurl [7.82.0|7.83.0|...|8.4.0], which cannot be installed (as previously explained);
│ │ │ ├─ libcurl [8.5.0|8.6.0|8.7.1], which cannot be installed (as previously explained);
│ │ │ ├─ libcurl 8.1.1 conflicts with any installable versions previously reported;
│ │ │ ├─ libcurl 8.2.1 conflicts with any installable versions previously reported;
│ │ │ └─ libcurl [8.4.0|8.5.0] conflicts with any installable versions previously reported;
│ │ └─ libtiff >=4.5.0,<4.6.0a0 but there are no viable options
│ │ ├─ libtiff [4.5.0|4.5.1|4.6.0] would require
│ │ │ └─ libdeflate >=1.18,<1.19.0a0 , which conflicts with any installable versions previously reported;
│ │ ├─ libtiff 4.5.1 conflicts with any installable versions previously reported;
│ │ ├─ libtiff 4.5.0 would require
│ │ │ └─ libdeflate >=1.17,<1.18.0a0 , which conflicts with any installable versions previously reported;
│ │ ├─ libtiff [4.4.0|4.5.0], which cannot be installed (as previously explained);
│ │ ├─ libtiff 4.5.0 would require
│ │ │ └─ libdeflate >=1.16,<1.17.0a0 , which conflicts with any installable versions previously reported;
│ │ └─ libtiff 4.5.0 conflicts with any installable versions previously reported;
│ ├─ r-base 4.1.3 would require
│ │ ├─ libcurl >=8.3.0,<9.0a0 but there are no viable options
│ │ │ ├─ libcurl [7.82.0|7.83.0|...|8.4.0], which cannot be installed (as previously explained);
│ │ │ ├─ libcurl [8.5.0|8.6.0|8.7.1], which cannot be installed (as previously explained);
│ │ │ └─ libcurl [8.4.0|8.5.0] conflicts with any installable versions previously reported;
│ │ └─ libtiff >=4.6.0,<4.7.0a0 but there are no viable options
│ │ ├─ libtiff 4.6.0 would require
│ │ │ └─ libdeflate >=1.20,<1.21.0a0 , which conflicts with any installable versions previously reported;
│ │ ├─ libtiff 4.6.0 would require
│ │ │ └─ libdeflate >=1.19,<1.20.0a0 , which conflicts with any installable versions previously reported;
│ │ └─ libtiff [4.5.0|4.5.1|4.6.0], which cannot be installed (as previously explained);
│ ├─ r-base 4.1.3 would require
│ │ ├─ libcurl >=7.86.0,<9.0a0 but there are no viable options
│ │ │ ├─ libcurl [7.82.0|7.83.0|...|8.4.0], which cannot be installed (as previously explained);
│ │ │ ├─ libcurl [8.5.0|8.6.0|8.7.1], which cannot be installed (as previously explained);
│ │ │ ├─ libcurl [7.86.0|7.87.0|7.88.1] conflicts with any installable versions previously reported;
│ │ │ ├─ libcurl 8.1.1 conflicts with any installable versions previously reported;
│ │ │ ├─ libcurl 8.2.1 conflicts with any installable versions previously reported;
│ │ │ └─ libcurl [8.4.0|8.5.0] conflicts with any installable versions previously reported;
│ │ └─ libtiff >=4.5.0,<4.6.0a0 but there are no viable options
│ │ ├─ libtiff [4.5.0|4.5.1|4.6.0], which cannot be installed (as previously explained);
│ │ ├─ libtiff 4.5.1 conflicts with any installable versions previously reported;
│ │ ├─ libtiff 4.5.0, which cannot be installed (as previously explained);
│ │ ├─ libtiff [4.4.0|4.5.0], which cannot be installed (as previously explained);
│ │ ├─ libtiff 4.5.0, which cannot be installed (as previously explained);
│ │ └─ libtiff 4.5.0 conflicts with any installable versions previously reported;
│ ├─ r-base 4.1.3 would require
│ │ ├─ libcurl >=8.1.2,<9.0a0 but there are no viable options
│ │ │ ├─ libcurl [7.82.0|7.83.0|...|8.4.0], which cannot be installed (as previously explained);
│ │ │ ├─ libcurl [8.5.0|8.6.0|8.7.1], which cannot be installed (as previously explained);
│ │ │ ├─ libcurl 8.2.1 conflicts with any installable versions previously reported;
│ │ │ └─ libcurl [8.4.0|8.5.0] conflicts with any installable versions previously reported;
│ │ └─ libtiff >=4.5.1,<4.6.0a0 but there are no viable options
│ │ ├─ libtiff [4.5.0|4.5.1|4.6.0], which cannot be installed (as previously explained);
│ │ └─ libtiff 4.5.1 conflicts with any installable versions previously reported;
│ └─ r-base 4.1.3 would require
│ ├─ libcurl >=7.86.0,<9.0a0 but there are no viable options
│ │ ├─ libcurl [7.82.0|7.83.0|...|8.4.0], which cannot be installed (as previously explained);
│ │ ├─ libcurl [8.5.0|8.6.0|8.7.1], which cannot be installed (as previously explained);
│ │ ├─ libcurl [7.86.0|7.87.0|7.88.1] conflicts with any installable versions previously reported;
│ │ ├─ libcurl 8.1.1 conflicts with any installable versions previously reported;
│ │ ├─ libcurl 8.2.1 conflicts with any installable versions previously reported;
│ │ └─ libcurl [8.4.0|8.5.0] conflicts with any installable versions previously reported;
│ └─ libtiff >=4.4.0,<4.5.0a0 but there are no viable options
│ ├─ libtiff [4.4.0|4.5.0], which cannot be installed (as previously explained);
│ ├─ libtiff 4.4.0, which cannot be installed (as previously explained);
│ ├─ libtiff 4.4.0, which cannot be installed (as previously explained);
│ ├─ libtiff [4.3.0|4.4.0], which cannot be installed (as previously explained);
│ └─ libtiff 4.4.0 conflicts with any installable versions previously reported;
├─ leidenalg 0.9.1* is not installable because it requires
│ └─ igraph >=0.10.2,<0.11.0a0 , which requires
│ └─ glpk >=5.0,<6.0a0 , which conflicts with any installable versions previously reported;
├─ r-base 4.1.3* , which cannot be installed (as previously explained);
├─ r-sctransform 0.3.3* is not installable because it requires
│ └─ r-future.apply but there are no viable options
│ ├─ r-future.apply [0.1.0|0.2.0|1.0.0] would require
│ │ └─ r-future >=1.6.2 , which conflicts with any installable versions previously reported;
│ ├─ r-future.apply 1.0.1 would require
│ │ └─ r-future >=1.9.0 , which conflicts with any installable versions previously reported;
│ ├─ r-future.apply 1.1.0 would require
│ │ └─ r-future >=1.10.0 , which conflicts with any installable versions previously reported;
│ ├─ r-future.apply [1.10.0|1.11.0|...|1.9.1] would require
│ │ └─ r-future >=1.13.0 , which conflicts with any installable versions previously reported;
│ └─ r-future.apply [1.11.0|1.9.0] conflicts with any installable versions previously reported;
├─ r-soupx 1.6.1* is not installable because it requires
│ └─ r-seurat >=3.2.2 , which conflicts with any installable versions previously reported;
└─ scanpy 1.9.3* is not installable because it conflicts with any installable versions previously reported.
critical libmamba Could not solve for environment specs

To Reproduce

I've tried to create the environment using either conda 23.7.4 either mamba 1.5.8 with the command [conda/mamba] env create -f preprocessing.yml

@inaciomdrs inaciomdrs added the bug Something isn't working label Apr 19, 2024
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