problem to install dependences

bochaoLin commented 4 months ago

Hi Oliver,

I'm currently in the process of reinstalling GenoPred, but I've hit a snag while trying to install its dependencies. Do you have any suggestions or insights on how to proceed? I'm utilizing a GPU node for the installation.

Thanks in advance!

(base) bash-4.4$ conda env remove --name genopred

Remove all packages in environment /hpc/hers_en/blin/program/miniconda3/envs/genopred:

(base) bash-4.4$ git clone https://github.com/opain/GenoPred.git Cloning into 'GenoPred'... remote: Enumerating objects: 5810, done. remote: Counting objects: 100% (328/328), done. remote: Compressing objects: 100% (147/147), done. remote: Total 5810 (delta 201), reused 221 (delta 179), pack-reused 5482 Receiving objects: 100% (5810/5810), 154.57 MiB | 31.02 MiB/s, done. Resolving deltas: 100% (2913/2913), done. Updating files: 100% (987/987), done. (base) bash-4.4$ conda env create -f GenoPred/pipeline/envs/pipeline.yaml Collecting package metadata (repodata.json): done Solving environment: done (base) bash-4.4$ conda activate genopred (genopred) bash-4.4$ cd GenoPred/pipeline/ (genopred) bash-4.4$ snakemake --restart-times 3 -j 1 --use-conda --conda-frontend mamba get_dependencies Initial version setup detected. Updating to v2.2. Building DAG of jobs... Creating conda environment envs/pgscatalog_utils.yaml... Downloading and installing remote packages. Environment for /hpc/hers_en/blin/program/GenoPred/pipeline/rules/../envs/pgscatalogutils.yaml created (location: .snakemake/conda/18794acb4f3a945abf441d2fbd22192c) Creating conda environment envs/analysis.yaml... Downloading and installing remote packages. CreateCondaEnvironmentException: Could not create conda environment from /hpc/hers_en/blin/program/GenoPred/pipeline/rules/../envs/analysis.yaml: Command: mamba env create --quiet --file "/hpc/hersen/blin/program/GenoPred/pipeline/.snakemake/conda/8d6f2661cc37d6e8f90394afa2603572.yaml" --prefix "/hpc/hersen/blin/program/GenoPred/pipeline/.snakemake/conda/8d6f2661cc37d6e8f90394afa2603572" Output: warning libmamba Cache file "/hpc/hers_en/blin/program/miniconda3/pkgs/cache/ffeee55f.json" was modified by another program warning libmamba Cache file "/hpc/hers_en/blin/program/miniconda3/pkgs/cache/2a957770.json" was modified by another program warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY Could not solve for environment specs The following packages are incompatible ├─ bcftools 1.18 is not installable because it requires │ └─ gsl >=2.7,<2.8.0a0 , which conflicts with any installable versions previously reported; ├─ bitarray 1.2.1 is installable with the potential options │ ├─ bitarray 1.2.1 would require │ │ └─ python_abi _cp27mu, which can be installed; │ ├─ bitarray 1.2.1 would require │ │ └─ python_abi _cp36m, which can be installed; │ ├─ bitarray 1.2.1 would require │ │ └─ python_abi 3.6. _cp36m, which conflicts with any installable versions previously reported; │ ├─ bitarray 1.2.1 would require │ │ └─ python_abi 3.6 _pypy36_pp73, which conflicts with any installable versions previously reported; │ ├─ bitarray 1.2.1 would require │ │ └─ python_abi _cp37m, which can be installed; │ ├─ bitarray 1.2.1 would require │ │ └─ python_abi 3.7. _cp37m, which conflicts with any installable versions previously reported; │ ├─ bitarray 1.2.1 would require │ │ └─ python_abi 3.8. _cp38, which conflicts with any installable versions previously reported; │ ├─ bitarray 1.2.1 would require │ │ └─ python_abi *_cp38, which can be installed; │ └─ bitarray 1.2.1 conflicts with any installable versions previously reported; ├─ c-ares 1.21.0 is not installable because it conflicts with any installable versions previously reported; ├─ cairo 1.18.0 is installable and it requires │ └─ icu >=73.2,<74.0a0 , which can be installed; ├─ futures 3.3.0 is installable with the potential options │ ├─ futures 3.3.0 would require │ │ └─ python_abi _cp27mu, which can be installed; │ ├─ futures 3.3.0 would require │ │ └─ python_abi 2.7. _cp27mu, which conflicts with any installable versions previously reported; │ └─ futures 3.3.0 conflicts with any installable versions previously reported; ├─ h5py 2.10.0 is installable with the potential options │ ├─ h5py 2.10.0 would require │ │ └─ python_abi _cp27mu, which can be installed; │ ├─ h5py 2.10.0 would require │ │ └─ hdf5 >=1.10.6,<1.10.7.0a0 mpimpich, which can be installed; │ ├─ h5py 2.10.0 would require │ │ └─ python_abi _cp36m, which can be installed; │ ├─ h5py 2.10.0 would require │ │ └─ python_abi _cp37m, which can be installed; │ ├─ h5py 2.10.0 would require │ │ └─ python_abi _cp38, which can be installed; │ ├─ h5py 2.10.0 would require │ │ └─ hdf5 >=1.10.6,<1.10.7.0a0 mpiopenmpi, which can be installed; │ ├─ h5py 2.10.0 would require │ │ └─ hdf5 >=1.10.6,<1.10.7.0a0 , which can be installed; │ └─ h5py 2.10.0 conflicts with any installable versions previously reported; ├─ hdf5 1.10.5 is not installable because it conflicts with any installable versions previously reported; ├─ icu 73.2 is requested and can be installed; ├─ krb5 1.21.2 is requested and can be installed; ├─ libdeflate 1.19 is not installable because it conflicts with any installable versions previously reported; ├─ libffi 3.4.2 is requested and can be installed; ├─ libgfortran-ng 13.2.0 is requested and can be installed; ├─ libopenblas 0.3.21 is installable with the potential options │ ├─ libopenblas 0.3.21 would require │ │ └─ openblas >=0.3.21,<0.3.22.0a0 , which can be installed; │ └─ libopenblas 0.3.21 conflicts with any installable versions previously reported; ├─ libsodium 1.0.18 is requested and can be installed; ├─ nbconvert 4.2.0 is installable with the potential options │ ├─ nbconvert 4.2.0 would require │ │ └─ python_abi _cp27mu, which can be installed; │ ├─ nbconvert 4.2.0 would require │ │ └─ python 3.4 , which requires │ │ └─ openssl [1.0 |1.0. ], which can be installed; │ └─ nbconvert 4.2.0 would require │ └─ python 3.5 with the potential options │ ├─ python [3.4.5|3.5.1|...|3.5.5], which can be installed (as previously explained); │ ├─ python 3.5.5 would require │ │ └─ openssl >=1.0.2o,<1.0.3a , which can be installed; │ └─ python [3.5.4|3.5.5|3.5.6] conflicts with any installable versions previously reported; ├─ openssl 3.1.4 is not installable because it conflicts with any installable versions previously reported; ├─ pcre2 10.40 is requested and can be installed; ├─ python 2.7.18 is installable with the potential options │ ├─ python [2.7.15|2.7.18|...|3.7.8] would require │ │ └─ libffi [>=3.2.1,<3.3.0a0 |>=3.2.1,<3.3a0 ], which conflicts with any installable versions previously reported; │ ├─ python [2.7.18|3.6.11|...|3.7.9] would require │ │ └─ libffi >=3.3,<3.4.0a0 , which conflicts with any installable versions previously reported; │ └─ python 2.7.18, which can be installed; ├─ python_abi 2.7 is not installable because it conflicts with any installable versions previously reported; ├─ pyyaml 5.3.1 is installable with the potential options │ ├─ pyyaml 5.3.1 would require │ │ └─ python >=2.7,<2.8.0a0 with the potential options │ │ ├─ python [2.7.15|2.7.18|...|3.7.8], which cannot be installed (as previously explained); │ │ ├─ python [2.7.18|3.6.11|...|3.7.9], which cannot be installed (as previously explained); │ │ ├─ python 2.7.18, which can be installed; │ │ ├─ python [2.7.12|2.7.13|...|3.6.3] would require │ │ │ └─ sqlite 3.13. , which can be installed; │ │ ├─ python [2.7.14|2.7.15|3.6.3|3.6.4|3.6.5] would require │ │ │ └─ sqlite 3.20. , which can be installed; │ │ ├─ python [2.7.15|3.6.6|...|3.7.3] would require │ │ │ └─ readline >=7.0,<8.0a0 , which can be installed; │ │ └─ python [2.7.13|2.7.14|2.7.15|2.7.16|2.7.17] conflicts with any installable versions previously reported; │ ├─ pyyaml 5.3.1 would require │ │ └─ python_abi 3.6 _pypy36_pp73, which conflicts with any installable versions previously reported; │ ├─ pyyaml 5.3.1 would require │ │ └─ python_abi 3.6. _cp36m, which conflicts with any installable versions previously reported; │ ├─ pyyaml 5.3.1 would require │ │ └─ python_abi 3.7. _cp37m, which conflicts with any installable versions previously reported; │ ├─ pyyaml 5.3.1 would require │ │ └─ python_abi 3.7 _pypy37_pp73, which conflicts with any installable versions previously reported; │ ├─ pyyaml 5.3.1 would require │ │ └─ python_abi 3.8. _cp38, which conflicts with any installable versions previously reported; │ ├─ pyyaml 5.3.1 would require │ │ └─ python_abi 3.9. _cp39, which conflicts with any installable versions previously reported; │ └─ pyyaml 5.3.1 conflicts with any installable versions previously reported; ├─ pyzmq 18.1.0 is not installable because there are no viable options │ ├─ pyzmq 18.1.0 would require │ │ └─ libsodium >=1.0.17,<1.0.18.0a0 , which conflicts with any installable versions previously reported; │ └─ pyzmq 18.1.0 conflicts with any installable versions previously reported; ├─ r-abind 1.4_5 is not installable because it conflicts with any installable versions previously reported; ├─ r-bit 4.0.5 is not installable because it conflicts with any installable versions previously reported; ├─ r-bit64 4.0.5 is not installable because it conflicts with any installable versions previously reported; ├─ r-brio 1.1.3 is not installable because it conflicts with any installable versions previously reported; ├─ r-car 3.1_2 is not installable because it conflicts with any installable versions previously reported; ├─ r-catools 1.18.2 is not installable because it conflicts with any installable versions previously reported; ├─ r-corrplot 0.92 is not installable because it conflicts with any installable versions previously reported; ├─ r-cowplot 1.1.1 is not installable because it conflicts with any installable versions previously reported; ├─ r-data.table 1.14.8 is not installable because it conflicts with any installable versions previously reported; ├─ r-dendextend 1.17.1 is not installable because it conflicts with any installable versions previously reported; ├─ r-deoptimr 1.1_3 is not installable because it conflicts with any installable versions previously reported; ├─ r-diagram 1.6.5 is not installable because it conflicts with any installable versions previously reported; ├─ r-digest 0.6.33 is not installable because it conflicts with any installable versions previously reported; ├─ r-dorng 1.8.6 is not installable because it conflicts with any installable versions previously reported; ├─ r-dplyr 1.1.3 is not installable because it conflicts with any installable versions previously reported; ├─ r-dt 0.28 is not installable because it conflicts with any installable versions previously reported; ├─ r-e1071 1.7_13 is not installable because it conflicts with any installable versions previously reported; ├─ r-ellipse 0.5.0 is not installable because it conflicts with any installable versions previously reported; ├─ r-factominer 2.9 is not installable because it conflicts with any installable versions previously reported; ├─ r-ff 4.0.9 is not installable because it conflicts with any installable versions previously reported; ├─ r-fields 15.2 is not installable because it conflicts with any installable versions previously reported; ├─ r-flashclust 1.01_2* is not installable because there are no viable options │ ├─ r-flashclust 1.01_2 would require │ │ └─ r-base 3.3.2 but there are no viable options │ │ ├─ r-base 3.3.2 would require │ │ │ └─ icu 56. , which conflicts with any installable versions previously reported; │ │ ├─ r-base [3.3.2|3.4.1] would require │ │ │ └─ icu 58. , which conflicts with any installable versions previously reported; │ │ └─ r-base [3.3.1|3.3.2|3.4.1] would require │ │ └─ icu 54. , which does not exist (perhaps a missing channel); │ ├─ r-flashclust 1.01_2 would require │ │ └─ r-base 3.3.1 , which cannot be installed (as previously explained); │ └─ r-flashclust 1.01_2 conflicts with any installable versions previously reported; ├─ r-future 1.33.0 is not installable because it conflicts with any installable versions previously reported; ├─ r-ggally 2.1.2 is not installable because it conflicts with any installable versions previously reported; ├─ r-ggplot2 3.4.4 is not installable because it conflicts with any installable versions previously reported; ├─ r-ggrepel 0.9.4 is not installable because it conflicts with any installable versions previously reported; ├─ r-ggsignif 0.6.4 is not installable because it conflicts with any installable versions previously reported; ├─ r-globals 0.16.2 is not installable because it conflicts with any installable versions previously reported; ├─ r-gplots 3.1.3 is not installable because it conflicts with any installable versions previously reported; ├─ r-htmltools 0.5.7 is not installable because it conflicts with any installable versions previously reported; ├─ r-htmlwidgets 1.6.2 is not installable because it conflicts with any installable versions previously reported; ├─ r-jsonlite 1.8.7 is not installable because it conflicts with any installable versions previously reported; ├─ r-knitr 1.45 is not installable because it conflicts with any installable versions previously reported; ├─ r-leaps 3.1 is not installable because it conflicts with any installable versions previously reported; ├─ r-listenv 0.9.0 is not installable because it conflicts with any installable versions previously reported; ├─ r-magrittr 2.0.3 is not installable because it conflicts with any installable versions previously reported; ├─ r-matrixstats 1.0.0 is not installable because it conflicts with any installable versions previously reported; ├─ r-nabor 0.5.0 is not installable because there are no viable options │ ├─ r-nabor 0.5.0 would require │ │ └─ r-base >=3.4.1,<3.4.2.0a0 but there are no viable options │ │ ├─ r-base [3.3.2|3.4.1], which cannot be installed (as previously explained); │ │ ├─ r-base [3.3.1|3.3.2|3.4.1], which cannot be installed (as previously explained); │ │ └─ r-base [3.4.1|3.5.1] would require │ │ └─ gsl >=2.2.1,<2.3.0a0 , which conflicts with any installable versions previously reported; │ ├─ r-nabor 0.5.0 would require │ │ └─ r-base >=3.5.1,<3.5.2.0a0 but there are no viable options │ │ ├─ r-base [3.4.1|3.5.1], which cannot be installed (as previously explained); │ │ ├─ r-base [3.5.1|3.6.1|3.6.2] would require │ │ │ └─ gsl >=2.5,<2.6.0a0 , which conflicts with any installable versions previously reported; │ │ ├─ r-base 3.5.1 would require │ │ │ └─ gsl >=2.4,<2.5.0a0 , which conflicts with any installable versions previously reported; │ │ ├─ r-base 3.5.1 would require │ │ │ └─ krb5 >=1.16.2,<1.17.0a0 , which conflicts with any installable versions previously reported; │ │ └─ r-base 3.5.1 conflicts with any installable versions previously reported; │ ├─ r-nabor 0.5.0 would require │ │ └─ r-base >=3.6,<3.7.0a0 but there are no viable options │ │ ├─ r-base [3.5.1|3.6.1|3.6.2], which cannot be installed (as previously explained); │ │ ├─ r-base [3.6.2|3.6.3] would require │ │ │ └─ gsl >=2.6,<2.7.0a0 , which conflicts with any installable versions previously reported; │ │ └─ r-base [3.6.0|3.6.1] conflicts with any installable versions previously reported; │ ├─ r-nabor 0.5.0 would require │ │ └─ r-base >=4.0,<4.1.0a0 but there are no viable options │ │ ├─ r-base 4.0.0 would require │ │ │ ├─ gsl >=2.6,<2.7.0a0 , which conflicts with any installable versions previously reported; │ │ │ └─ pcre2 >=10.34,<10.35.0a0 , which conflicts with any installable versions previously reported; │ │ ├─ r-base [4.0.1|4.0.2] would require │ │ │ ├─ gsl >=2.6,<2.7.0a0 , which conflicts with any installable versions previously reported; │ │ │ └─ pcre2 >=10.35,<10.36.0a0 , which conflicts with any installable versions previously reported; │ │ ├─ r-base [4.0.3|4.0.5] would require │ │ │ ├─ gsl >=2.6,<2.7.0a0 , which conflicts with any installable versions previously reported; │ │ │ └─ pcre2 >=10.36,<10.37.0a0 , which conflicts with any installable versions previously reported; │ │ ├─ r-base 4.0.5 would require │ │ │ ├─ krb5 >=1.19.3,<1.20.0a0 , which conflicts with any installable versions previously reported; │ │ │ └─ pcre2 >=10.37,<10.38.0a0 , which conflicts with any installable versions previously reported; │ │ ├─ r-base 4.0.5 would require │ │ │ ├─ gsl >=2.6,<2.7.0a0 , which conflicts with any installable versions previously reported; │ │ │ └─ pcre2 >=10.37,<10.38.0a0 , which conflicts with any installable versions previously reported; │ │ ├─ r-base 4.0.5 would require │ │ │ ├─ krb5 >=1.19.3,<1.20.0a0 , which conflicts with any installable versions previously reported; │ │ │ └─ libtiff >=4.4.0,<4.5.0a0 but there are no viable options │ │ │ ├─ 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 4.4.0 would require │ │ │ │ └─ libdeflate >=1.10,<1.11.0a0 , which conflicts with any installable versions previously reported; │ │ │ ├─ libtiff 4.4.0 would require │ │ │ │ └─ libdeflate >=1.14,<1.15.0a0 , which conflicts with any installable versions previously reported; │ │ │ └─ libtiff 4.4.0 conflicts with any installable versions previously reported; │ │ └─ r-base 4.0.5 would require │ │ ├─ krb5 >=1.19.2,<1.20.0a0 , which conflicts with any installable versions previously reported; │ │ └─ pcre2 >=10.37,<10.38.0a0 , which conflicts with any installable versions previously reported; │ └─ r-nabor 0.5.0 conflicts with any installable versions previously reported; ├─ r-nloptr 2.0.3 is not installable because there are no viable options │ ├─ r-nloptr 2.0.3 would require │ │ └─ r-base >=4.0,<4.1.0a0 , which cannot be installed (as previously explained); │ ├─ r-nloptr 2.0.3 would require │ │ └─ nlopt >=2.7.1,<2.8.0a0 but there are no viable options │ │ ├─ nlopt 2.7.1 would require │ │ │ └─ python_abi 3.10. _cp310, which conflicts with any installable versions previously reported; │ │ ├─ nlopt 2.7.1 would require │ │ │ └─ python_abi 3.11. _cp311, which conflicts with any installable versions previously reported; │ │ ├─ nlopt 2.7.1 would require │ │ │ └─ python_abi 3.7. _cp37m, which conflicts with any installable versions previously reported; │ │ ├─ nlopt 2.7.1 would require │ │ │ └─ python_abi 3.8 _pypy38_pp73, which conflicts with any installable versions previously reported; │ │ ├─ nlopt 2.7.1 would require │ │ │ └─ python_abi 3.8. _cp38, which conflicts with any installable versions previously reported; │ │ ├─ nlopt 2.7.1 would require │ │ │ └─ python_abi 3.9. _cp39, which conflicts with any installable versions previously reported; │ │ ├─ nlopt 2.7.1 would require │ │ │ └─ python_abi 3.9 _pypy39_pp73, which conflicts with any installable versions previously reported; │ │ ├─ nlopt 2.7.1 would require │ │ │ └─ python_abi 3.12. _cp312, which conflicts with any installable versions previously reported; │ │ └─ nlopt 2.7.1 conflicts with any installable versions previously reported; │ └─ r-nloptr 2.0.3 conflicts with any installable versions previously reported; ├─ r-optparse 1.7.3 is not installable because it conflicts with any installable versions previously reported; ├─ r-png 0.1_8 is not installable because it conflicts with any installable versions previously reported; ├─ r-polynom 1.4_1 is not installable because it conflicts with any installable versions previously reported; ├─ r-prettyunits 1.2.0 is not installable because it conflicts with any installable versions previously reported; ├─ r-progress 1.2.2 is not installable because it conflicts with any installable versions previously reported; ├─ r-proxy 0.4_27 is not installable because it conflicts with any installable versions previously reported; ├─ r-r.methodss3 1.8.2 is not installable because it conflicts with any installable versions previously reported; ├─ r-r.oo 1.25.0 is not installable because it conflicts with any installable versions previously reported; ├─ r-r.utils 2.12.2 is not installable because it conflicts with any installable versions previously reported; ├─ r-rappdirs 0.3.3 is not installable because it conflicts with any installable versions previously reported; ├─ r-readr 2.1.4 is not installable because it conflicts with any installable versions previously reported; ├─ r-rematch2 2.1.2 is not installable because it conflicts with any installable versions previously reported; ├─ r-reshape 0.8.9 is not installable because it conflicts with any installable versions previously reported; ├─ r-rmarkdown 2.25 is not installable because it conflicts with any installable versions previously reported; ├─ r-rocr 1.0_11 is not installable because it conflicts with any installable versions previously reported; ├─ r-scales 1.2.1 is not installable because it conflicts with any installable versions previously reported; ├─ r-scatterplot3d 0.3_44 is not installable because it conflicts with any installable versions previously reported; ├─ r-shape 1.4.6 is not installable because it conflicts with any installable versions previously reported; ├─ r-spam 2.10_0 is not installable because it conflicts with any installable versions previously reported; ├─ r-statmod 1.5.0 is not installable because it conflicts with any installable versions previously reported; ├─ r-stringr 1.5.0 is not installable because it conflicts with any installable versions previously reported; ├─ r-testthat 3.2.0 is not installable because it conflicts with any installable versions previously reported; ├─ r-tibble 3.2.1 is not installable because it conflicts with any installable versions previously reported; ├─ r-viridis 0.6.4 is not installable because it conflicts with any installable versions previously reported; ├─ r-yaml 2.3.7 is not installable because it conflicts with any installable versions previously reported; ├─ scipy 1.2.0 is installable with the potential options │ ├─ scipy 1.2.0 would require │ │ └─ openblas >=0.3.3,<0.3.4.0a0 but there are no viable options │ │ ├─ openblas 0.3.3 would require │ │ │ └─ libgfortran-ng >=7,<8.0a0 , which conflicts with any installable versions previously reported; │ │ └─ openblas 0.3.3 conflicts with any installable versions previously reported; │ ├─ scipy 1.2.0 would require │ │ └─ libgfortran-ng >=7,<8.0a0 , which conflicts with any installable versions previously reported; │ ├─ scipy 1.2.0 would require │ │ └─ python >=3.6,<3.7.0a0 with the potential options │ │ ├─ python [2.7.15|2.7.18|...|3.7.8], which cannot be installed (as previously explained); │ │ ├─ python [2.7.18|3.6.11|...|3.7.9], which cannot be installed (as previously explained); │ │ ├─ python [2.7.12|2.7.13|...|3.6.3], which can be installed (as previously explained); │ │ ├─ python [3.6.12|3.6.9] would require │ │ │ └─ python_abi 3.6 _pypy36_pp73, which conflicts with any installable versions previously reported; │ │ ├─ python [3.6.10|3.6.12|...|3.6.9] conflicts with any installable versions previously reported; │ │ ├─ python [2.7.14|2.7.15|3.6.3|3.6.4|3.6.5], which can be installed (as previously explained); │ │ └─ python [2.7.15|3.6.6|...|3.7.3], which can be installed (as previously explained); │ ├─ scipy 1.2.0 would require │ │ └─ python >=3.7,<3.8.0a0 with the potential options │ │ ├─ python [2.7.15|2.7.18|...|3.7.8], which cannot be installed (as previously explained); │ │ ├─ python [2.7.18|3.6.11|...|3.7.9], which cannot be installed (as previously explained); │ │ ├─ python [2.7.15|3.6.6|...|3.7.3], which can be installed (as previously explained); │ │ ├─ python [3.7.10|3.7.12|3.7.9] would require │ │ │ └─ python_abi 3.7 _pypy37_pp73, which conflicts with any installable versions previously reported; │ │ └─ python [3.7.0|3.7.1|...|3.7.9] conflicts with any installable versions previously reported; │ └─ scipy 1.2.0 conflicts with any installable versions previously reported; ├─ sqlite 3.44.0 is not installable because it requires │ └─ readline >=8.2,<9.0a0 , which conflicts with any installable versions previously reported; └─ xmltodict 0.12.0** is not installable because it conflicts with any installable versions previously reported.

Traceback (most recent call last): File "/hpc/hers_en/blin/program/miniconda3/envs/genopred/lib/python3.8/weakref.py", line 642, in _exitfunc f() File "/hpc/hers_en/blin/program/miniconda3/envs/genopred/lib/python3.8/weakref.py", line 566, in call return info.func(*info.args, **(info.kwargs or {})) File "/hpc/hers_en/blin/program/miniconda3/envs/genopred/lib/python3.8/tempfile.py", line 826, in _cleanup cls._rmtree(name) File "/hpc/hers_en/blin/program/miniconda3/envs/genopred/lib/python3.8/tempfile.py", line 822, in _rmtree _shutil.rmtree(name, onerror=onerror) File "/hpc/hers_en/blin/program/miniconda3/envs/genopred/lib/python3.8/shutil.py", line 718, in rmtree _rmtree_safe_fd(fd, path, onerror) File "/hpc/hers_en/blin/program/miniconda3/envs/genopred/lib/python3.8/shutil.py", line 655, in _rmtree_safe_fd _rmtree_safe_fd(dirfd, fullname, onerror) File "/hpc/hers_en/blin/program/miniconda3/envs/genopred/lib/python3.8/shutil.py", line 655, in _rmtree_safe_fd _rmtree_safe_fd(dirfd, fullname, onerror) File "/hpc/hers_en/blin/program/miniconda3/envs/genopred/lib/python3.8/shutil.py", line 655, in _rmtree_safe_fd _rmtree_safe_fd(dirfd, fullname, onerror) [Previous line repeated 4 more times] File "/hpc/hers_en/blin/program/miniconda3/envs/genopred/lib/python3.8/shutil.py", line 659, in _rmtree_safe_fd onerror(os.rmdir, fullname, sys.exc_info()) File "/hpc/hers_en/blin/program/miniconda3/envs/genopred/lib/python3.8/shutil.py", line 657, in _rmtree_safe_fd os.rmdir(entry.name, dir_fd=topfd) OSError: [Errno 39] Directory not empty: 'envs'

opain commented 4 months ago

Hi,

Thanks for the reporting the issue. I have not had this problem before.

It looks like it might be related to some cache. It could be worth clearing the cache for conda and mamba:

conda clean --all mamba clean --all

If the issue persists, you could try building the analysis.yaml directly in case it provides a more informative error:

mamba env create -f analysis.yaml --verbose

Let me know if that helps!

bochaoLin commented 4 months ago

Hi Oliver, Thanks for the response. I have delete the caches, however, the issue persist: bash-4.4$ cd /hpc/hers_en/blin/program/GenoPred/pipeline/ bash-4.4$ conda activate genopred (genopred) bash-4.4$ conda clean --all Will remove 576 (1.10 GB) tarball(s). Proceed ([y]/n)? y

Will remove 1 index cache(s). Proceed ([y]/n)? y

Will remove 195 (1.29 GB) package(s). Proceed ([y]/n)? There are no tempfile(s) to remove. There are no logfile(s) to remove. (genopred) bash-4.4$ mamba clean --all There are no unused tarball(s) to remove. Will remove 1 index cache(s). Proceed ([y]/n)? y

There are no unused package(s) to remove. There are no tempfile(s) to remove. There are no logfile(s) to remove. (genopred) bash-4.4$ mamba env create -f analysis.yaml --verbose

EnvironmentFileNotFound: '/hpc/hers_en/blin/program/GenoPred/pipeline/analysis.yaml' file not found

(genopred) bash-4.4$ snakemake --restart-times 3 -j 1 --use-conda --conda-frontend mamba get_dependencies Building DAG of jobs... Creating conda environment envs/analysis.yaml... Downloading and installing remote packages. CreateCondaEnvironmentException: Could not create conda environment from /hpc/hers_en/blin/program/GenoPred/pipeline/rules/../envs/analysis.yaml: Command: mamba env create --quiet --file "/hpc/hersen/blin/program/GenoPred/pipeline/.snakemake/conda/8d6f2661cc37d6e8f90394afa2603572.yaml" --prefix "/hpc/hersen/blin/program/GenoPred/pipeline/.snakemake/conda/8d6f2661cc37d6e8f90394afa2603572" Output: warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY Traceback (most recent call last): File "/hpc/hers_en/blin/program/miniconda3/envs/genopred/lib/python3.8/weakref.py", line 642, in _exitfunc f() File "/hpc/hers_en/blin/program/miniconda3/envs/genopred/lib/python3.8/weakref.py", line 566, in call return info.func(*info.args, **(info.kwargs or {})) File "/hpc/hers_en/blin/program/miniconda3/envs/genopred/lib/python3.8/tempfile.py", line 826, in _cleanup cls._rmtree(name) File "/hpc/hers_en/blin/program/miniconda3/envs/genopred/lib/python3.8/tempfile.py", line 822, in _rmtree _shutil.rmtree(name, onerror=onerror) File "/hpc/hers_en/blin/program/miniconda3/envs/genopred/lib/python3.8/shutil.py", line 718, in rmtree _rmtree_safe_fd(fd, path, onerror) File "/hpc/hers_en/blin/program/miniconda3/envs/genopred/lib/python3.8/shutil.py", line 655, in _rmtree_safe_fd _rmtree_safe_fd(dirfd, fullname, onerror) File "/hpc/hers_en/blin/program/miniconda3/envs/genopred/lib/python3.8/shutil.py", line 655, in _rmtree_safe_fd _rmtree_safe_fd(dirfd, fullname, onerror) File "/hpc/hers_en/blin/program/miniconda3/envs/genopred/lib/python3.8/shutil.py", line 655, in _rmtree_safe_fd _rmtree_safe_fd(dirfd, fullname, onerror) [Previous line repeated 4 more times] File "/hpc/hers_en/blin/program/miniconda3/envs/genopred/lib/python3.8/shutil.py", line 659, in _rmtree_safe_fd onerror(os.rmdir, fullname, sys.exc_info()) File "/hpc/hers_en/blin/program/miniconda3/envs/genopred/lib/python3.8/shutil.py", line 657, in _rmtree_safe_fd os.rmdir(entry.name, dir_fd=topfd) OSError: [Errno 39] Directory not empty: 'envs'

opain commented 4 months ago

Thank you for trying those suggestions.

You are starting with a fresh copy of GenoPred, so this probably isn’t the answer, but check that their aren’t any temporary conda environments, and if so remove them.

rm -rf /hpc/hers_en/blin/program/GenoPred/pipeline/.snakemake/conda/

Your attempt to build the environment outside of snakemake failed because the wrong path to the analysis.yaml was specified. Try:

mamba env create --file /hpc/hers_en/blin/program/GenoPred/pipeline/envs/analysis.yaml --prefix /hpc/hers_en/blin/program/GenoPred/pipeline/.snakemake/conda/test_env

If the error persists, it is probably worth updating conda and mamba (after activating genopred environment:

conda update conda conda install mamba -c conda-forge

Not sure why this is happening though. If these solutions do not work, it is also possible to run the pipeline within a container (docker or singularity): https://opain.github.io/GenoPred/running_offline.html. I set this up for running the pipeline in an offline environment, but it can also be used to have even tighter control of the software environment.

opain commented 4 months ago

Resolving the GenoPred Issue

A colleague of mine ran into the same issue and has kindly documented how they resolved it. It is not totally clear which of these steps were required for it to run as it should, but it now works as it should.

Step-by-Step Instructions

Delete the GenoPred Folder:
```
rm -r GenoPred
```
Remove GenoPred Environment:
```
conda env remove --name genopred
```

Remove Any Leftover Conda Environment Folders:

rm -r ~/.conda/pkgs
rm -r ~/.conda/envs/.conda_envs_dir_test
rm -r ~/.conda_build_locks/
rm -r ~/.condarc

Clear Cache from Conda:
```
conda clean --all -y
```
Follow installation instructions for GenoPred again. Use Conda Instead of Mamba When Running the get_dependencies Command:
```
snakemake --restart-times 3 -j 1 --use-conda --conda-frontend conda get_dependencies
```

Additional Notes

Ensure that you have the correct permissions to delete the folders and files listed.
Replace GenoPred, and other paths with the correct paths if they differ in your setup.
The conda clean --all -y command will remove unused packages and caches, which helps in freeing up space and resolving potential conflicts.
Using snakemake with the --use-conda and --conda-frontend conda options ensures that the dependencies are managed correctly.

Following these steps should help resolve the issues you are encountering with GenoPred.

unchowdhury commented 4 months ago

Thank you Oliver for providing the solution, it resolved the issue and the installation has been done successfully. I skipped deleting Miniconda though.

opain commented 4 months ago

Thank you @unchowdhury for the feedback. Really useful to hear this resolved the issue for you as well, and that deleting miniconda was not necessary (I will update my response above to exclude this step).

opain / GenoPred