I'm pretty new to using the Terminal and command lines but I've been trying to follow the install instructions for Sourcetracker2. When I run the command:
Package hdf5 conflicts for:
biom-format -> h5py -> hdf5[version='1.10.1|1.10.1.|1.10.2.|>=1.10.3,<1.10.4.0a0|>=1.10.4,<1.10.5.0a0|>=1.10.4,<1.10.5.0a0|>=1.10.4,<1.10.5.0a0|>=1.10.5,<1.10.6.0a0|>=1.10.5,<1.10.6.0a0|>=1.10.5,<1.10.6.0a0|>=1.10.6,<1.10.7.0a0|>=1.10.6,<1.10.7.0a0|>=1.10.6,<1.10.7.0a0|>=1.12.1,<1.12.2.0a0|>=1.10.2,<1.10.3.0a0|1.8.18|1.8.18.|1.8.17|1.8.17.|1.8.17.|1.8.15.|>=1.8.20,<1.9.0a0|>=1.8.18,<1.8.19.0a0|>=1.10.1,<1.10.2.0a0',build='mpimpich|mpiopenmpi|mpimpich|mpiopenmpi|mpimpich|mpiopenmpi|mpimpich|mpiopenmpi']
hdf5The following specifications were found to be incompatible with your system:
Hi,
I'm pretty new to using the Terminal and command lines but I've been trying to follow the install instructions for Sourcetracker2. When I run the command:
conda create -n st2 -c biocore python=3.5 numpy scipy scikit-bio biom-format h5py hdf5 seaborn
It just hangs and doesn't do anything.
So after some googling I ran the command:
conda config --set channel_priority strict
I then retry to create the environment again but get conflicts below, any help would be greatly appreciated!
~$ conda create -n st2 -c biocore python=3.5 numpy scipy scikit-bio biom-format h5py hdf5 seaborn Collecting package metadata (current_repodata.json): done Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: \ Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. Examining conflict for scikit-bio biom-format python seaborn: : 14it [03:13, 14.Examining conflict for scikit-bio biom-format python seaborn: : 15it [03:13, 15.Examining conflict for scikit-bio seaborn: : 15it [03:19, 15.38s/it] failed
UnsatisfiableError: The following specifications were found to be incompatible with each other:
Output in format: Requested package -> Available versions
Package _libgcc_mutex conflicts for: numpy -> libgcc-ng[version='>=9.4.0'] -> _libgcc_mutex[version='|0.1',build='main|conda_forge|main'] biom-format -> libgcc-ng[version='>=7.5.0'] -> _libgcc_mutex[version='|0.1|0.1',build='main|conda_forge|main'] scikit-bio -> libgcc-ng[version='>=7.5.0'] -> _libgcc_mutex[version='|0.1|0.1',build='main|conda_forge|main'] python=3.5 -> libgcc-ng[version='>=4.9'] -> _libgcc_mutex[version='|0.1|0.1',build='main|conda_forge|main'] hdf5 -> libgcc-ng[version='>=9.4.0'] -> _libgcc_mutex[version='|0.1',build='main|conda_forge|main'] h5py -> libgcc-ng[version='>=9.4.0'] -> _libgcc_mutex[version='|0.1',build='main|conda_forge|main'] scipy -> libgcc-ng[version='>=9.4.0'] -> _libgcc_mutex[version='*|0.1',build='main|conda_forge|main']
Package scipy conflicts for: biom-format -> scipy[version='>=0.13.0|>=1.3.1'] scipy scikit-bio -> scipy[version='>=0.13.0|>=0.15.1|>=1.3.0'] seaborn -> scipy[version='>=0.15.2|>=1.0.1|>=1.0'] scikit-bio -> scikit-learn[version='>=0.19.1'] -> scipy[version='>=0.19.1'] seaborn -> statsmodels[version='>=0.8.0'] -> scipy[version='>=0.14|>=1.2|>=1.3']
Package python conflicts for: scikit-bio -> cachecontrol[version='>=0.11.5'] -> python[version='3.7.|3.9.|>=2.7,<2.8.0a0|>=3.5|>=3.6|>=3.8.0a,<3.9.0a0|>=3.7.1,<3.8.0a0|3.8.'] scipy -> python[version='2.7.|3.5.|3.6.|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.9,<3.10.0a0|>=3.8,<3.9.0a0|>=3.5,<3.6.0a0|3.4.'] scipy -> python_abi=3.9[build=_cp39] -> python[version='3.7.|3.8.|3.9.'] biom-format -> python[version='2.7.|3.5.|3.6.|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=3.9,<3.10.0a0|>=3.8,<3.9.0a0|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|3.4.'] numpy -> python[version='2.7.|3.5.|3.6.|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.9,<3.10.0a0|>=3.8,<3.9.0a0|>=3.5,<3.6.0a0|3.4.'] numpy -> python_abi=3.9[build=_cp39] -> python[version='3.7.|3.8.|3.9.'] python=3.5 biom-format -> click -> python[version='3.7.|>=3.10,<3.11.0a0|>=3.7.1,<3.8.0a0|>=3|>=3.6|3.9.|3.8.|<3'] seaborn -> python[version='2.7.|3.5.|3.6.|>=3.6|3.4.|>=3.5,<3.6.0a0|>=3.7,<3.8.0a0|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0'] scikit-bio -> python[version='2.7.|3.4.|3.5.|>=3.9,<3.10.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=3.8,<3.9.0a0|>=3.5,<3.6.0a0|3.6.'] seaborn -> statsmodels[version='>=0.8.0'] -> python[version='>=3.7.1,<3.8.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0']
Package libgfortran-ng conflicts for: h5py -> hdf5[version='>=1.12.1,<1.12.2.0a0'] -> libgfortran-ng[version='>=4.9|>=7,<8.0a0|>=7.2.0,<8.0a0'] seaborn -> numpy[version='>=1.13.3'] -> libgfortran-ng[version='>=4.9|>=7,<8.0a0|>=7.2.0,<8.0a0'] scipy -> numpy[version='>=1.9.3,<2.0a0'] -> libgfortran-ng[version='>=4.9|>=8,<9.0a0'] hdf5 -> libgfortran-ng[version='>=7,<8.0a0|>=7.2.0,<8.0a0'] scikit-bio -> numpy[version='>=1.9.2'] -> libgfortran-ng[version='>=4.9|>=7,<8.0a0|>=7.2.0,<8.0a0'] biom-format -> numpy[version='>=1.3.0'] -> libgfortran-ng[version='>=4.9|>=7,<8.0a0|>=7.2.0,<8.0a0'] numpy -> libgfortran-ng[version='>=4.9|>=7,<8.0a0|>=7.2.0,<8.0a0'] hdf5 -> openmpi[version='>=3.1,<3.2.0a0'] -> libgfortran-ng[version='>=4.9'] scipy -> libgfortran-ng[version='>=7,<8.0a0|>=7.2.0,<8.0a0'] numpy -> libblas[version='>=3.8.0,<4.0a0'] -> libgfortran-ng[version='>=8,<9.0a0']
Package libgcc-ng conflicts for: seaborn -> statsmodels[version='>=0.8.0'] -> libgcc-ng[version='>=4.9|>=7.3.0|>=7.5.0|>=9.3.0|>=9.4.0|>=7.2.0'] biom-format -> libgcc-ng[version='>=4.9|>=7.3.0|>=7.5.0'] python=3.5 -> libgcc-ng[version='>=4.9|>=7.5.0|>=7.3.0|>=7.2.0'] scikit-bio -> libgcc-ng[version='>=4.9|>=7.3.0|>=7.5.0|>=7.2.0'] h5py -> libgcc-ng[version='>=4.9|>=7.3.0|>=7.5.0|>=9.3.0|>=9.4.0|>=7.2.0'] scikit-bio -> numpy[version='>=1.9.2'] -> libgcc-ng[version='>=9.3.0|>=9.4.0'] hdf5 -> libgcc-ng[version='>=4.9|>=7.3.0|>=7.5.0|>=9.3.0|>=9.4.0|>=7.2.0'] scipy -> libopenblas[version='>=0.3.2,<0.3.3.0a0'] -> libgcc-ng[version='>=8.2.0'] python=3.5 -> bzip2[version='>=1.0.6,<2.0a0'] -> libgcc-ng[version='>=9.3.0|>=9.4.0'] numpy -> libopenblas[version='>=0.3.2,<0.3.3.0a0'] -> libgcc-ng[version='>=8.2.0'] scipy -> libgcc-ng[version='>=4.9|>=7.3.0|>=7.5.0|>=9.3.0|>=9.4.0|>=7.2.0'] numpy -> libgcc-ng[version='>=4.9|>=7.3.0|>=7.5.0|>=9.3.0|>=9.4.0|>=7.2.0'] biom-format -> h5py -> libgcc-ng[version='>=7.2.0|>=9.3.0|>=9.4.0']
Package matplotlib-base conflicts for: scikit-bio -> matplotlib[version='>=1.4.3'] -> matplotlib-base[version='2.1.2|2.1.2|2.1.2|2.2.3|2.2.3|2.2.3|2.2.4|2.2.4|2.2.4|2.2.4|2.2.4|2.2.4|2.2.4|2.2.4|2.2.4|2.2.4|3.0.1|3.0.2|3.0.2|3.0.2|3.0.2|3.0.2|3.0.3|3.0.3|3.0.3|3.0.3|3.1.0|3.1.0|3.1.0|3.1.0|3.1.1|3.1.1|3.1.1|3.1.1|3.1.1|3.1.1|3.1.1|3.1.1|3.1.2|3.1.2|3.1.2|3.1.2|3.1.2|3.1.2|3.1.3|3.1.3|3.1.3|>=3.2.0,<3.2.1.0a0|>=3.2.1,<3.2.2.0a0|>=3.2.2,<3.2.3.0a0|>=3.3.0,<3.3.1.0a0|>=3.3.1,<3.3.2.0a0|>=3.3.2,<3.3.3.0a0|>=3.3.3,<3.3.4.0a0|>=3.3.4,<3.3.5.0a0|>=3.4.1,<3.4.2.0a0|>=3.4.2,<3.4.3.0a0|>=3.4.3,<3.4.4.0a0|>=2.2.5,<2.2.6.0a0|3.1.3|3.1.3|3.1.3|3.1.2|3.1.2|3.1.2',build='py37hef1b27d_1|py38hef1b27d_1|py36hef1b27d_1|py36hef1b27d_0|py37h250f245_1|py27h250f245_1|py36h250f245_1|py27h60b886d_1|py37h60b886d_1|py37hfd891ef_0|py27hfd891ef_0|py36hfd891ef_0|py37h250f245_1|py36h250f245_1|py27h250f245_1|py27h250f245_2|py37h250f245_2|py38h250f245_2|py36h167e16e_1001|py36h167e16e_0|py37h5f35d83_1|py37h5f35d83_0|py36hfd891ef_0|py37hfd891ef_0|py37he7580a8_1|py38h250f245_1|py38h250f245_2|py36h250f245_2|py38h250f245_0|py37h250f245_1|py38h250f245_1|py38h250f245_0|py37h250f245_0|py36h250f245_0|py36h250f245_1|py36h250f245_0|py37h250f245_0|py37h250f245_2|py36he7580a8_1|py36hfd891ef_1|py37hfd891ef_1|py36h5f35d83_0|py36h5f35d83_1|py37h167e16e_0|py36h167e16e_1002|py37h167e16e_1002|py37h167e16e_1001|py36h167e16e_1000|py37hc2fb212_1001|py36h250f245_2|py36h60b886d_1|py37hef1b27d_0|py38hef1b27d_0'] scikit-bio -> matplotlib-base[version='>=1.4.3']
Package pytz conflicts for: seaborn -> matplotlib-base[version='>=2.1.2'] -> pytz[version='>=2017.2|>=2017.3'] biom-format -> pandas -> pytz[version='>=2017.2|>=2017.3'] scikit-bio -> matplotlib[version='>=1.4.3'] -> pytz[version='>=2017.2|>=2017.3']
Package liblapacke conflicts for: scipy -> blas=[build=openblas] -> liblapacke[version='3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.9.0|3.9.0|3.9.0|3.9.0|3.9.0|3.9.0|3.9.0|3.9.0|3.9.0|3.9.0|3.9.0|3.9.0',build='5_mkl|9_mkl|10_mkl|13_mkl|14_mkl|16_mkl|21_mkl|6_mkl|7_mkl|10_mkl|11_linux64_mkl|12_linux64_mkl|0_openblas|2_openblas|8_openblas|9_openblas|12_openblas|15_openblas|16_openblas|12_linux64_openblas|11_linux64_openblas|10_openblas|9_openblas|8_openblas|7_openblas|6_openblas|5_openblas|17_openblas|14_openblas|13_openblas|11_openblas|10_openblas|7_openblas|6_openblas|5_openblas|4_openblas|3_openblas|9_mkl|8_mkl|5_mkl|20_mkl|19_mkl|18_mkl|15_mkl|12_mkl|11_mkl|8_mkl|7_mkl|6_mkl|4_mkl'] numpy -> blas=[build=openblas] -> liblapacke[version='3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.9.0|3.9.0|3.9.0|3.9.0|3.9.0|3.9.0|3.9.0|3.9.0|3.9.0|3.9.0|3.9.0|3.9.0',build='5_mkl|9_mkl|10_mkl|13_mkl|14_mkl|16_mkl|21_mkl|6_mkl|7_mkl|10_mkl|11_linux64_mkl|12_linux64_mkl|0_openblas|2_openblas|8_openblas|9_openblas|12_openblas|15_openblas|16_openblas|12_linux64_openblas|11_linux64_openblas|10_openblas|9_openblas|8_openblas|7_openblas|6_openblas|5_openblas|17_openblas|14_openblas|13_openblas|11_openblas|10_openblas|7_openblas|6_openblas|5_openblas|4_openblas|3_openblas|9_mkl|8_mkl|5_mkl|20_mkl|19_mkl|18_mkl|15_mkl|12_mkl|11_mkl|8_mkl|7_mkl|6_mkl|4_mkl']
Package future conflicts for: scikit-bio -> future[version='>=0.14.3'] biom-format -> future[version='>=0.14.3|>=0.15.0|>=0.16.0']
Package icu conflicts for: scikit-bio -> matplotlib[version='>=1.4.3'] -> icu[version='>=58.2,<59.0a0|>=64.2,<65.0a0|>=67.1,<68.0a0'] seaborn -> matplotlib-base[version='>=2.1.2'] -> icu[version='>=58.2,<59.0a0|>=64.2,<65.0a0|>=67.1,<68.0a0']
Package setuptools conflicts for: biom-format -> setuptools seaborn -> matplotlib-base[version='>=2.1.2'] -> setuptools scikit-bio -> ipython[version='>=3.2.0'] -> setuptools[version='>=18.5|>=40.0'] python=3.5 -> pip -> setuptools
Package numpy conflicts for: numpy scipy -> numpy[version='1.10.|1.11.|1.12.|1.13.|>=1.11|>=1.11.3,<2.0a0|>=1.14.6,<2.0a0|>=1.16.5,<2.0a0|>=1.16.6,<2.0a0|>=1.17.5,<2.0a0|>=1.18.5,<2.0a0|>=1.19.5,<2.0a0|>=1.19.4,<2.0a0|>=1.19.2,<2.0a0|>=1.18.1,<2.0a0|>=1.9.3,<2.0a0|>=1.9|>=1.15.1,<2.0a0'] biom-format -> h5py -> numpy[version='1.10.|1.11.|1.12.|1.13.|>=1.16.6,<2.0a0|>=1.17.5,<2.0a0|>=1.18.5,<2.0a0|>=1.19.5,<2.0a0|>=1.8|>=1.8,<1.14|>=1.11.3,<2.0a0|>=1.15.4,<2.0a0|>=1.18.4,<2.0a0|>=1.18.1,<2.0a0|>=1.12.1,<2.0a0|>=1.11.|>=1.9.|>=1.11|>=1.9|>=1.7|>=1.20.3,<2.0a0|>=1.20.2,<2.0a0|>=1.13.3,<2.0a0|>=1.15.1,<2.0a0'] seaborn -> statsmodels[version='>=0.8.0'] -> numpy[version='1.10.|1.11.|1.12.|1.13.|>=1.11.|>=1.11.3,<2.0a0|>=1.11|>=1.14.6,<2.0a0|>=1.15.4,<2.0a0|>=1.16.5,<2.0a0|>=1.16.6,<2.0a0|>=1.18.5,<2.0a0|>=1.19.5,<2.0a0|>=1.19.2,<2.0a0|>=1.18.1,<2.0a0|>=1.17.5,<2.0a0|>=1.9.3,<2.0a0|>=1.17.0,<2.0a0|>=1.19.1,<2.0a0|>=1.19.4,<2.0a0|>=1.18.4,<2.0a0|>=1.12.1,<2.0a0|>=1.9.|>=1.20.3,<2.0a0|>=1.20.2,<2.0a0|>=1.13.3,<2.0a0|>=1.9|>=1.15.1,<2.0a0|>=1.8|>=1.7|>=1.4.0'] scikit-bio -> matplotlib[version='>=1.4.3'] -> numpy[version='1.11.|>=1.19.5,<2.0a0|>=1.18.5,<2.0a0|>=1.17.5,<2.0a0|>=1.19.2,<2.0a0|>=1.15.4,<2.0a0|>=1.18.4,<2.0a0|>=1.18.1,<2.0a0|>=1.12.1,<2.0a0|>=1.11.|>=1.9.|>=1.11|>=1.9|>=1.8|>=1.7|1.13.|>=1.20.3,<2.0a0|>=1.20.2,<2.0a0|>=1.13.3,<2.0a0|>=1.15.1,<2.0a0'] scikit-bio -> numpy[version='1.10.|>=1.14.6,<2.0a0|>=1.16.5,<2.0a0|>=1.19.4,<2.0a0|>=1.9.2|>=1.9.3,<2.0a0|>=1.9.2,<1.14.0|1.12.|>=1.16.6,<2.0a0|>=1.11.3,<2.0a0'] seaborn -> numpy[version='>=1.13.3|>=1.9.3|>=1.15'] biom-format -> numpy[version='>=1.14.6,<2.0a0|>=1.16.5,<2.0a0|>=1.3.0|>=1.19.4,<2.0a0|>=1.19.2,<2.0a0|>=1.9.3,<2.0a0']
Package h5py conflicts for: h5py biom-format -> h5py[version='>=2.2.0']
Package libcurl conflicts for: h5py -> hdf5[version='>=1.12.1,<1.12.2.0a0'] -> libcurl[version='>=7.71.1,<8.0a0|>=7.77.0,<8.0a0|>=7.79.1,<8.0a0|>=7.76.0,<8.0a0'] hdf5 -> libcurl[version='>=7.71.1,<8.0a0|>=7.76.0,<8.0a0|>=7.77.0,<8.0a0|>=7.79.1,<8.0a0']
Package mpfr conflicts for: scipy -> libgcc -> mpfr[version='>=2.4.0'] biom-format -> libgcc -> mpfr[version='>=2.4.0']
Package hdf5 conflicts for: biom-format -> h5py -> hdf5[version='1.10.1|1.10.1.|1.10.2.|>=1.10.3,<1.10.4.0a0|>=1.10.4,<1.10.5.0a0|>=1.10.4,<1.10.5.0a0|>=1.10.4,<1.10.5.0a0|>=1.10.5,<1.10.6.0a0|>=1.10.5,<1.10.6.0a0|>=1.10.5,<1.10.6.0a0|>=1.10.6,<1.10.7.0a0|>=1.10.6,<1.10.7.0a0|>=1.10.6,<1.10.7.0a0|>=1.12.1,<1.12.2.0a0|>=1.10.2,<1.10.3.0a0|1.8.18|1.8.18.|1.8.17|1.8.17.|1.8.17.|1.8.15.|>=1.8.20,<1.9.0a0|>=1.8.18,<1.8.19.0a0|>=1.10.1,<1.10.2.0a0',build='mpimpich|mpiopenmpi|mpimpich|mpiopenmpi|mpimpich|mpiopenmpi|mpimpich|mpiopenmpi'] hdf5The following specifications were found to be incompatible with your system:
Your installed version is: 2.31
Note that strict channel priority may have removed packages required for satisfiability.