Conda installation fails

guillemmasfiol commented 2 years ago

Hi,

thank you for this interesting tool! I've been trying to install the software via the conda environment file in different Unix-based systems without success. The installation just keeps at "Solving environment" eternally, without ever concluding.

Are there any particularities of the python environment file to consider for installation? How can I overcome the issue?

thank you in advance!

guillemmasfiol commented 2 years ago

It seems the issue comes due to incompatibilities between packages:

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

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package openssl conflicts for: pip -> python[version='>=3.6'] -> openssl[version='1.0.|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1f,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=3.0.0,<4.0a0|>=1.1.1c,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.0.2n,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2l,<1.0.3a'] biopython=1.72 -> python[version='>=3.6,<3.7.0a0'] -> openssl[version='1.0.|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1f,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1l,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.0.2n,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2l,<1.0.3a|>=1.1.1b,<1.1.2a|>=3.0.0,<4.0a0|>=1.1.1i,<1.1.2a'] matplotlib -> python[version='>=3.9,<3.10.0a0'] -> openssl[version='1.0.*|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=3.0.0,<4.0a0|>=1.1.1d,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.1.1f,<1.1.2a|>=1.0.2n,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2l,<1.0.3a'] blast -> curl[version='>=7.77.0,<8.0a0'] -> openssl[version='>=1.1.1l,<1.1.2a|>=3.0.0,<4.0a0']

Package libgcc conflicts for: libwebp=0.5 -> giflib -> libgcc matplotlib -> pyqt -> libgcc blast -> libgcc circos -> perl-gd -> libgcc

Package libzlib conflicts for: circos -> perl-gd -> libzlib[version='>=1.2.11,<1.3.0a0'] matplotlib -> python[version='>=3.9,<3.10.0a0'] -> libzlib[version='1.2.11|1.2.11|>=1.2.11,<1.3.0a0',build='h36c2ea0_1012|h36c2ea0_1013'] pip -> python[version='>=3.6'] -> libzlib[version='>=1.2.11,<1.3.0a0'] blast -> curl[version='>=7.77.0,<8.0a0'] -> libzlib[version='1.2.11|1.2.11|>=1.2.11,<1.3.0a0',build='h36c2ea0_1012|h36c2ea0_1013'] biopython=1.72 -> python[version='>=3.6,<3.7.0a0'] -> libzlib[version='>=1.2.11,<1.3.0a0'] libwebp=0.5 -> libtiff -> libzlib[version='>=1.2.11,<1.3.0a0']

Package libstdcxx-ng conflicts for: pip -> python[version='>=3.6'] -> libstdcxx-ng[version='>=4.9|>=7.3.0|>=7.5.0|>=9.3.0|>=9.4.0|>=7.2.0'] libwebp=0.5 -> libtiff -> libstdcxx-ng[version='>=4.9|>=7.3.0|>=7.5.0|>=9.3.0|>=9.4.0|>=7.2.0'] blast -> pcre[version='>=8.41,<9.0a0'] -> libstdcxx-ng[version='>=7.2.0|>=9.4.0'] circos -> perl-gd -> libstdcxx-ng[version='>=4.9|>=7.3.0|>=9.4.0'] biopython=1.72 -> numpy -> libstdcxx-ng[version='>=4.9|>=7.3.0|>=9.4.0|>=9.3.0|>=7.5.0'] matplotlib -> libstdcxx-ng[version='>=7.2.0|>=7.3.0'] matplotlib -> matplotlib-base[version='>=3.5.1,<3.5.2.0a0'] -> libstdcxx-ng[version='>=4.9|>=7.5.0|>=9.4.0|>=9.3.0'] mummer -> libstdcxx-ng[version='>=7.3.0|>=9.3.0|>=9.4.0'] blast -> libstdcxx-ng[version='>=4.9|>=7.3.0|>=7.5.0|>=9.3.0'] biopython=1.72 -> libstdcxx-ng[version='>=7.2.0']

Package icu conflicts for: matplotlib -> icu[version='>=58.2,<59.0a0'] matplotlib -> matplotlib-base[version='>=3.3.0,<3.3.1.0a0'] -> icu[version='>=64.2,<65.0a0|>=67.1,<68.0a0'] blast -> boost=1.61 -> icu=56

Package python_abi conflicts for: matplotlib -> python_abi[version='3.10.|3.9.|3.7|3.7.|3.8.|3.6|3.6.',build='_cp39|_cp310|_pypy37_pp73|_cp37m|_cp38|_pypy36_pp73|_cp36m'] matplotlib -> matplotlib-base[version='>=2.2.5,<2.2.6.0a0'] -> python_abi=2.7[build=*_cp27mu]

Package zlib conflicts for: matplotlib -> zlib[version='>=1.2.11,<1.3.0a0'] matplotlib -> python[version='>=3.6,<3.7.0a0'] -> zlib[version='1.2.|1.2.11|1.2.8|1.2.11.']

Package pip conflicts for: biopython=1.72 -> python[version='>=3.6,<3.7.0a0'] -> pip matplotlib -> python[version='>=3.9,<3.10.0a0'] -> pip pip

Package mkl conflicts for: biopython=1.72 -> numpy -> mkl[version='>=2018.0.0,<2019.0a0|>=2018.0.1,<2019.0a0|>=2018.0.2,<2019.0a0|>=2018.0.3,<2019.0a0|>=2019.1,<2021.0a0|>=2019.3,<2021.0a0|>=2019.4,<2021.0a0|>=2021.2.0,<2022.0a0|>=2021.3.0,<2022.0a0|>=2021.4.0,<2022.0a0|>=2019.4,<2020.0a0'] matplotlib -> numpy=1.11 -> mkl[version='>=2018.0.0,<2019.0a0|>=2018.0.1,<2019.0a0|>=2018.0.2,<2019.0a0|>=2018.0.3,<2019.0a0|>=2019.1,<2021.0a0|>=2019.4,<2021.0a0|>=2021.4.0,<2022.0a0|>=2021.3.0,<2022.0a0|>=2021.2.0,<2022.0a0|>=2019.3,<2021.0a0|>=2019.4,<2020.0a0']

Package perl-app-cpanminus conflicts for: blast -> perl-list-moreutils -> perl-app-cpanminus circos -> perl-list-moreutils -> perl-app-cpanminus

Package perl-threaded conflicts for: circos -> perl-gd -> perl-threaded[version='>=5.22.0'] circos -> perl-threaded mummer -> perl-threaded blast -> entrez-direct -> perl-threaded

Package numpy conflicts for: matplotlib -> numpy[version='1.10.|1.11.|>=1.14.6,<2.0a0'] matplotlib -> matplotlib-base[version='>=3.5.1,<3.5.2.0a0'] -> numpy[version='>=1.11.3,<2.0a0|>=1.15.4,<2.0a0|>=1.16.5,<2.0a0|>=1.16.6,<2.0a0|>=1.17|>=1.19.5,<2.0a0|>=1.21.4,<2.0a0|>=1.18.5,<2.0a0|>=1.21.2,<2.0a0|>=1.19.2,<2.0a0|>=1.17.5,<2.0a0|>=1.19.4,<2.0a0|>=1.9.3,<2.0a0'] blast -> boost[version='>=1.68.0,<1.68.1.0a0'] -> numpy[version='1.11.|1.12.|1.13.*|>=1.11|>=1.8|>=1.9.3,<2.0a0|>=1.9|>=1.7|>=1.19.5,<2.0a0|>=1.18.5,<2.0a0|>=1.21.4,<2.0a0|>=1.17.5,<2.0a0|>=1.16.6,<2.0a0|>=1.16.5,<2.0a0|>=1.19.4,<2.0a0|>=1.19.2,<2.0a0|>=1.14.6,<2.0a0'] biopython=1.72 -> numpy[version='>=1.11.3,<2.0a0|>=1.8']

Package pypy3.7 conflicts for: matplotlib -> python[version='>=3.7,<3.8.0a0'] -> pypy3.7[version='7.3.|7.3.3.|7.3.4.|7.3.5.|7.3.7.*'] matplotlib -> pypy3.7[version='>=7.3.3|>=7.3.4|>=7.3.5|>=7.3.7']

Package tzdata conflicts for: pip -> python[version='>=3.6'] -> tzdata matplotlib -> python[version='>=3.9,<3.10.0a0'] -> tzdata

Package libgcc-ng conflicts for: matplotlib -> libgcc-ng[version='>=7.2.0|>=7.3.0'] matplotlib -> matplotlib-base[version='>=3.5.1,<3.5.2.0a0'] -> libgcc-ng[version='>=4.9|>=7.5.0|>=9.4.0|>=9.3.0']

Package python conflicts for: matplotlib -> python[version='2.7.|3.4.|3.5.|>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.9,<3.10.0a0|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0'] matplotlib -> pyqt -> python[version='3.10.|3.6.|3.9.|3.7.|3.8.|>=3.6|>=3|<3']

Package perl conflicts for: blast -> entrez-direct -> perl[version='>=5.26.2,<5.27.0a0|>=5.32.1,<6.0a0',build=_perl5] blast -> perl[version='5.22.0.|>=5.26.2,<5.26.3.0a0']

Package libpng conflicts for: libwebp=0.5 -> libpng matplotlib -> freetype=2.6 -> libpng[version='1.6.*|>=1.6.21,<1.7|>=1.6.32,<1.6.35'] matplotlib -> libpng[version='>=1.6.23,<1.7|>=1.6.37,<1.7.0a0|>=1.6.36,<1.7.0a0|>=1.6.35,<1.7.0a0|>=1.6.34,<1.7.0a0|>=1.6.32,<1.7.0a0']

Package xz conflicts for: biopython=1.72 -> python[version='>=3.6,<3.7.0a0'] -> xz[version='5.0.|5.2.|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0'] matplotlib -> python[version='>=3.9,<3.10.0a0'] -> xz[version='5.0.|5.2.|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0'] libwebp=0.5 -> libtiff -> xz[version='5.0.|5.2.|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0'] pip -> python[version='>=3.6'] -> xz[version='5.0.|5.2.|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0']

Package pypy3.6 conflicts for: matplotlib -> pypy3.6[version='>=7.3.2|>=7.3.3'] matplotlib -> tornado -> pypy3.6[version='7.3.|7.3.0.|7.3.1.|7.3.2.|7.3.3.*|>=7.3.1']The following specifications were found to be incompatible with your system:

feature:/linux-64::__glibc==2.31=0
feature:|@/linux-64::__glibc==2.31=0
biopython=1.72 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
blast -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
matplotlib -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
mummer -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.31

Note that strict channel priority may have removed packages required for satisfiability.`

tpillone commented 2 years ago

Hi,

For the never ending "Solving environment" problem, I would recommend using mamba to solve complex environments (https://github.com/mamba-org/mamba). It's a reimplementation of the conda package manager.

I could not reproduce the conflicting installation, it might be due to your specific conda installation. Could you try to remove the constrain on the biopython version in the env.yaml (biopython=1.72)?
mummer2circos will not work properly with the latest versions of biopython, but I can update it if it's a source of conflict.

guillemmasfiol commented 2 years ago

Hi,

thanks for the recommendation of mamba! it actually appears to have successfully bypassed the issue.

Here are the steps I followed for succesfful installation:


# install mamba from conda: 
    conda install mamba -n base -c conda-forge

# add conda-forge channel:
    mamba install xtensor-r -c  conda-forge

# install mummer2circos from provided environment file:
            mamba env create -f env.yaml

# activate conda activate mummer2circos:
                         conda activate mummer2circos
                        mummer2circos --help

Yixiangzhang1996 commented 2 years ago

hi there is a problem. pip it works,but not work in installing dependencies for mummer2circos. can not find a solution...

` Summary:

Install: 133 packages

Total download: 0 B

────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

Preparing transaction: done Verifying transaction: done Executing transaction: done Installing pip dependencies: | Ran pip subprocess with arguments: ['/miniconda3/envs/mummer2circos/bin/python', '-m', 'pip', 'install', '-U', '-r', '/mummer2circos/condaenv.xef6uwg3.requirements.txt'] Pip subprocess output: Collecting git+https://github.com/metagenlab/mummer2circos.git (from -r /mummer2circos/condaenv.xef6uwg3.requirements.txt (line 1)) Cloning https://github.com/metagenlab/mummer2circos.git to /tmp/pip-req-build-wiymfu4_

Pip subprocess error: Running command git clone --quiet https://github.com/metagenlab/mummer2circos.git /tmp/pip-req-build-wiymfu4_ fatal: unable to access 'https://github.com/metagenlab/mummer2circos.git/': Encountered end of file error: subprocess-exited-with-error

× git clone --quiet https://github.com/metagenlab/mummer2circos.git /tmp/pip-req-build-wiymfu4_ did not run successfully. │ exit code: 128 ╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip. error: subprocess-exited-with-error

× git clone --quiet https://github.com/metagenlab/mummer2circos.git /tmp/pip-req-build-wiymfu4_ did not run successfully. │ exit code: 128 ╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip. failed

CondaEnvException: Pip failed `

guillemmasfiol commented 2 years ago

@Yixiangzhang1996 Hi, did you try installing with mamba?

Yixiangzhang1996 commented 2 years ago

@Yixiangzhang1996 Hi, did you try installing with mamba?

Yes,when I ran the step of "mamba env create -f env.yaml" it comes wrong at the installing dependencies as I pasted above.

Yixiangzhang1996 commented 2 years ago

@Yixiangzhang1996 Hi, did you try installing with mamba?

metagenlab / mummer2circos

Conda installation fails #6