unable to create conda environment

[zihhuafang]

Hi,

I was trying to install PhenoSV following the instruction in README but have encountered the issue to create conda environment when running conda env create --name phenosv --file phenosv.yml It seems like the packages in the phenosv.yml are incompatible.

Solving environment: - Found conflicts! Looking for incompatible packages. Could not solve for environment specs The following packages are incompatible ├─ pybedtools 0.9.0 is installable with the potential options │ ├─ pybedtools 0.9.0 would require │ │ └─ libgcc-ng >=12 , which conflicts with any installable versions previously reported; │ ├─ pybedtools 0.9.0 would require │ │ └─ python >=3.6,<3.7.0a0 with the potential options │ │ ├─ python [3.6.0|3.6.1|...|3.6.9], which can be installed; │ │ └─ python [3.6.7|3.7.1] would require │ │ └─ openssl >=1.1.1,<1.1.2.0a0 , which does not exist (perhaps a missing channel); │ ├─ pybedtools 0.9.0 would require │ │ └─ python >=3.7,<3.8.0a0 with the potential options │ │ ├─ python [3.6.7|3.7.1], which cannot be installed (as previously explained); │ │ └─ python [3.7.0|3.7.1|...|3.7.9], which can be installed; │ ├─ pybedtools 0.9.0 would require │ │ └─ python >=3.8,<3.9.0a0 , which can be installed; │ └─ pybedtools 0.9.0 would require │ └─ python >=3.9,<3.10.0a0 , which can be installed; ├─ pysam 0.19.1 is uninstallable because there are no viable options │ ├─ pysam 0.19.1 would require │ │ └─ libdeflate >=1.13,<1.14.0a0 , which conflicts with any installable versions previously reported; │ └─ pysam 0.19.1 would require │ └─ libdeflate >=1.10,<1.11.0a0 , which conflicts with any installable versions previously reported; ├─ python 3.10.4 is uninstallable because it conflicts with any installable versions previously reported; ├─ pytorch-lightning 1.6.4 is uninstallable because it conflicts with any installable versions previously reported; ├─ tensorboard 2.10.1 is uninstallable because it conflicts with any installable versions previously reported; └─ torchmetrics 0.10.0 is uninstallable because it conflicts with any installable versions previously reported.

I attached a more detailed log of the package conflicts here. conda.log

Is there a possible fix for the version of packages? Thank you. Zih-Hua

[kaichop]

Are you using Apple M1 chip? It is not supported because many packages do not have binary for M1. Also you may want to upgrade your conda environment and see if it solves the problem.

On Wed, Dec 13, 2023 at 9:00 AM Zih-Hua Fang @.***> wrote:

Hi,

I was trying to install PhenoSV following the instruction in README but have encountered the issue to create conda environment when running conda env create --name phenosv --file phenosv.yml It seems like the packages in the phenosv.yml are incompatible.

Solving environment: - Found conflicts! Looking for incompatible packages. Could not solve for environment specs The following packages are incompatible ├─ pybedtools 0.9.0** is installable with the potential options │ ├─ pybedtools 0.9.0 would require │ │ └─ libgcc-ng >=12 , which conflicts with any installable versions previously reported; │ ├─ pybedtools 0.9.0 would require │ │ └─ python >=3.6,<3.7.0a0 with the potential options │ │ ├─ python [3.6.0|3.6.1|...|3.6.9], which can be installed; │ │ └─ python [3.6.7|3.7.1] would require │ │ └─ openssl

=1.1.1,<1.1.2.0a0 , which does not exist (perhaps a missing channel); │ ├─ pybedtools 0.9.0 would require │ │ └─ python >=3.7,<3.8.0a0 with the potential options │ │ ├─ python [3.6.7|3.7.1], which cannot be installed (as previously explained); │ │ └─ python [3.7.0|3.7.1|...|3.7.9], which can be installed; │ ├─ pybedtools 0.9.0 would require │ │ └─ python =3.8,<3.9.0a0 , which can be installed; │ └─ pybedtools 0.9.0 would require │ └─ python >=3.9,<3.10.0a0 , which can be installed; ├─ pysam 0.19.1 is uninstallable because there are no viable options │ ├─ pysam 0.19.1 would require │ │ └─ libdeflate >=1.13,<1.14.0a0 , which conflicts with any installable versions previously reported; │ └─ pysam 0.19.1 would require │ └─ libdeflate >=1.10,<1.11.0a0 , which conflicts with any installable versions previously reported; ├─ python 3.10.4 is uninstallable because it conflicts with any installable versions previously reported; ├─ pytorch-lightning 1.6.4 is uninstallable because it conflicts with any installable versions previously reported; ├─ tensorboard 2.10.1 is uninstallable because it conflicts with any installable versions previously reported; └─ torchmetrics 0.10.0** is uninstallable because it conflicts with any installable versions previously reported.

I attached a more detailed log of the package conflicts here. conda.log https://github.com/WGLab/PhenoSV/files/13661408/conda.log

Is there a possible fix for the version of packages? Thank you. Zih-Hua

— Reply to this email directly, view it on GitHub https://github.com/WGLab/PhenoSV/issues/1, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OFEXTCMEQ2ZGZ453MTYJGYGVAVCNFSM6AAAAABATG2H7CVHI2DSMVQWIX3LMV43ASLTON2WKOZSGAZTSNZXGY4DQNA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[zihhuafang]

No, it's Linux environment.

I have tried freshly installed miniconda based on README, but it returned the same error. wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh bash Miniconda3-latest-Linux-x86_64.sh conda env create --name phenosv --file phenosv.yml

I also tried conda update by running conda update conda followed by conda env create --name phenosv --file phenosv.yml

Any other suggestions for the fix or troubleshooting? Thank you very much.

[kaichop]

The log file seems to show that your conda version is 2.28. The current most updated version is 23.11. Are you sure you have updated conda to the latest version? The version 2.28 is really old.

[zihhuafang]

My conda version was 23.11.0 after I freshly installed miniconda as I checked by conda -V. I figured out the problem was conda channel priority. After I ran conda config --set channel_priority true, I was able to create conda environment by running conda env create --name phenosv --file phenosv.yml

[kaichop]

Thank you!

On Wed, Dec 20, 2023 at 5:16 AM Zih-Hua Fang @.***> wrote:

Closed #1 https://github.com/WGLab/PhenoSV/issues/1 as completed.

— Reply to this email directly, view it on GitHub https://github.com/WGLab/PhenoSV/issues/1#event-11300540216, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OBJPAWPNGG5ASDKRW3YKK3JHAVCNFSM6AAAAABATG2H7CVHI2DSMVQWIX3LMV45UABCJFZXG5LFIV3GK3TUJZXXI2LGNFRWC5DJN5XDWMJRGMYDANJUGAZDCNQ . You are receiving this because you commented.Message ID: @.***>