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pachterlab / kb_python

A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
https://www.kallistobus.tools/
BSD 2-Clause "Simplified" License
141 stars 24 forks source link

Installation Error #166

Closed FionaMoon closed 2 years ago

FionaMoon commented 2 years ago

Hi, I got trouble when I try to install kb_python. I can't install it either by pip or by conda. It seems that the porblem is caused by pysam.

      collect2: error: ld returned 1 exit status
      error: command '/xtdisk/fangxd_group/liangyue/miniconda/bin/x86_64-conda-linux-gnu-cc' failed with exit code 1
      [end of output]

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

× Encountered error while trying to install package.
╰─> pysam

note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.

Thank you inadvance!

Fiona

Lioscro commented 2 years ago

Hi, @FionaMoon,

A few questions for you first. What Python version, OS, and CPU architecture are you using? Seems like something is misconfigured such that pysam can not be compiled (probably due to samtools compilation).

What is the output if you try to install pysam directly?

pip install pysam

or

conda install pysam
FionaMoon commented 2 years ago

Hi, Thank you for you reply!

I have python 3.8.13 & 3.9.10 environments. My operating system is GNU/Linux CPU Architecture: x86_64

When I try to install pysam directly by pip install pysam:

error: legacy-install-failure

× Encountered error while trying to install package.
╰─> pysam

note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.
Lioscro commented 2 years ago

This seems like an issue on pysam's side. I'm not very knowledgeable on their internals, I would recommend submitting an issue on their Github (https://github.com/pysam-developers/pysam).

FionaMoon commented 2 years ago

Thank you for your reply ! I'll ask pysam side .

@.***

@.*** |

---- Replied Message ---- | From | Joseph @.> | | Date | 06/06/2022 21:24 | | To | @.> | | Cc | @.**@.> | | Subject | Re: [pachterlab/kb_python] Installation Error (Issue #166) |

This seems like an issue on pysam's side. I'm not very knowledgeable on their internals, I would recommend submitting an issue on their Github (https://github.com/pysam-developers/pysam).

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

FionaMoon commented 2 years ago

Hi All， I've solved this question by install the newest version of conda.