PacificBiosciences / pbbioconda

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
BSD 3-Clause Clear License
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Segmentation fault (core dumped) when installing ilma. #683

Closed JiaLonghao1997 closed 1 month ago

JiaLonghao1997 commented 2 months ago

I got the error 'Segmentation fault (core dumped)' when installing ilma.

(pacbio) [jialh@amdnode3 MM_10Plex_42MB_SEQUENCING_DATA_EXPRESS2.0]$ mamba install bioconda::lima

Looking for: ['bioconda::lima']

conda-forge/linux-64                                        Using cache
conda-forge/noarch                                          Using cache
bioconda/linux-64                                           Using cache
bioconda/noarch                                             Using cache
bioconda/linux-64                                           Using cache
bioconda/noarch                                             Using cache
pkgs/main/noarch                                              No change
pkgs/main/linux-64                                            No change
pkgs/r/linux-64                                               No change
pkgs/r/noarch                                                 No change
lima: overriding channel, version and build from installed packages due to --force-reinstall.

Pinned packages:
  - python 2.7.*

Transaction

  Prefix: /home1/jialh/tools/anaconda3/envs/mamba/envs/pacbio

  Updating specs:

   - bioconda::lima

  Package  Version  Build       Channel        Size
─────────────────────────────────────────────────────
  Reinstall:
─────────────────────────────────────────────────────

  o lima     2.9.0  h9ee0642_1  bioconda     Cached

  Summary:

  Reinstall: 1 packages

  Total download: 0 B

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

Confirm changes: [Y/n] Y

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(pacbio) [jialh@amdnode3 MM_10Plex_42MB_SEQUENCING_DATA_EXPRESS2.0]$ lima
Segmentation fault (core dumped)
(pacbio) [jialh@amdnode3 MM_10Plex_42MB_SEQUENCING_DATA_EXPRESS2.0]$ python
Python 2.7.15 | packaged by conda-forge | (default, Mar  5 2020, 14:56:06) 
[GCC 7.3.0] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> exit()
(pacbio) [jialh@amdnode3 MM_10Plex_42MB_SEQUENCING_DATA_EXPRESS2.0]$ cat /proc/version
Linux version 3.10.0-1062.el7.x86_64 (mockbuild@kbuilder.bsys.centos.org) (gcc version 4.8.5 20150623 (Red Hat 4.8.5-36) (GCC) ) #1 SMP Wed Aug 7 18:08:02 UTC 2019
armintoepfer commented 1 month ago

Please retry on a OS that is not end of life.