mob-suite
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Published
20 hours ago •
phac-nml
phac-nml
Error Installing mob suite from conda
Hi, I tried to install MOB SUITE. I got the error.
Here is the traceback.
conda install -c bioconda mob_suite
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /home/yichen/anaconda3
added / updated specs:
- mob_suite
The following packages will be downloaded:
package | build
---------------------------|-----------------
blast-2.12.0 | pl5262h3289130_0 22.4 MB bioconda
capnproto-0.6.1 | hfc679d8_1 2.7 MB conda-forge
conda-build-3.22.0 | py39hf3d152e_2 563 KB conda-forge
entrez-direct-16.2 | he881be0_1 7.5 MB bioconda
ete3-3.1.2 | pyh9f0ad1d_0 1.8 MB conda-forge
gsl-1.16 | 0 6.9 MB conda-forge
mash-2.0 | gsl1.16_1 223 KB bioconda
mob_suite-3.0.0 | py_1 184 KB bioconda
patch-2.7.6 | h7f98852_1002 121 KB conda-forge
perl-5.26.2 | h36c2ea0_1008 15.4 MB conda-forge
perl-archive-tar-2.18 | 1 27 KB bioconda
perl-common-sense-3.74 | pl526_2 11 KB bioconda
perl-json-4.02 | pl526_0 52 KB bioconda
perl-json-xs-2.34 | pl526_1 61 KB bioconda
perl-list-moreutils-0.15 | pl526_1 13 KB bioconda
xorg-libsm-1.2.2 | h470a237_5 24 KB conda-forge
------------------------------------------------------------
Total: 57.9 MB
The following NEW packages will be INSTALLED:
blast bioconda/linux-64::blast-2.12.0-pl5262h3289130_0
capnproto conda-forge/linux-64::capnproto-0.6.1-hfc679d8_1
entrez-direct bioconda/linux-64::entrez-direct-16.2-he881be0_1
ete3 conda-forge/noarch::ete3-3.1.2-pyh9f0ad1d_0
gsl conda-forge/linux-64::gsl-1.16-0
libgcc conda-forge/linux-64::libgcc-7.2.0-h69d50b8_2
mash bioconda/linux-64::mash-2.0-gsl1.16_1
mob_suite bioconda/noarch::mob_suite-3.0.0-py_1
patch conda-forge/linux-64::patch-2.7.6-h7f98852_1002
perl conda-forge/linux-64::perl-5.26.2-h36c2ea0_1008
perl-archive-tar bioconda/linux-64::perl-archive-tar-2.18-1
perl-common-sense bioconda/linux-64::perl-common-sense-3.74-pl526_2
perl-json bioconda/linux-64::perl-json-4.02-pl526_0
perl-json-xs bioconda/linux-64::perl-json-xs-2.34-pl526_1
perl-list-moreuti~ bioconda/linux-64::perl-list-moreutils-0.15-pl526_1
xorg-kbproto conda-forge/linux-64::xorg-kbproto-1.0.7-h7f98852_1002
xorg-libice conda-forge/linux-64::xorg-libice-1.0.10-h7f98852_0
xorg-libsm conda-forge/linux-64::xorg-libsm-1.2.2-h470a237_5
xorg-libx11 conda-forge/linux-64::xorg-libx11-1.7.2-h7f98852_0
xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.9-h7f98852_0
xorg-libxdmcp conda-forge/linux-64::xorg-libxdmcp-1.1.3-h7f98852_0
xorg-libxext conda-forge/linux-64::xorg-libxext-1.3.4-h7f98852_1
xorg-libxrender conda-forge/linux-64::xorg-libxrender-0.9.10-h7f98852_1003
xorg-renderproto conda-forge/linux-64::xorg-renderproto-0.11.1-h7f98852_1002
xorg-xextproto conda-forge/linux-64::xorg-xextproto-7.3.0-h7f98852_1002
xorg-xproto conda-forge/linux-64::xorg-xproto-7.0.31-h7f98852_1007
The following packages will be UPDATED:
conda-build pkgs/main::conda-build-3.21.5-py39h06~ --> conda-forge::conda-build-3.22.0-py39hf3d152e_2
Proceed ([y]/n)? y
Downloading and Extracting Packages
entrez-direct-16.2 | 7.5 MB | ##################################### | 100%
conda-build-3.22.0 | 563 KB | ##################################### | 100%
mob_suite-3.0.0 | 184 KB | ##################################### | 100%
xorg-libsm-1.2.2 | 24 KB | ##################################### | 100%
perl-5.26.2 | 15.4 MB | ##################################### | 100%
blast-2.12.0 | 22.4 MB | ##################################### | 100%
capnproto-0.6.1 | 2.7 MB | ##################################### | 100%
perl-json-4.02 | 52 KB | ##################################### | 100%
perl-list-moreutils- | 13 KB | ##################################### | 100%
perl-common-sense-3. | 11 KB | ##################################### | 100%
gsl-1.16 | 6.9 MB | ##################################### | 100%
mash-2.0 | 223 KB | ##################################### | 100%
perl-archive-tar-2.1 | 27 KB | ##################################### | 100%
perl-json-xs-2.34 | 61 KB | ##################################### | 100%
ete3-3.1.2 | 1.8 MB | ##################################### | 100%
patch-2.7.6 | 121 KB | ##################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
ERROR conda.core.link:_execute(730): An error occurred while installing package 'bioconda::mob_suite-3.0.0-py_1'.
Rolling back transaction: done
LinkError: post-link script failed for package bioconda::mob_suite-3.0.0-py_1
location of failed script: /home/yichen/anaconda3/bin/.mob_suite-post-link.sh
==> script messages <==
<None>
==> script output <==
stdout:
stderr: Traceback (most recent call last):
File "/home/yichen/anaconda3/bin/mob_init", line 7, in <module>
from mob_suite.mob_init import main
File "/home/yichen/anaconda3/lib/python3.9/site-packages/mob_suite/mob_init.py", line 8, in <module>
from mob_suite.blast import BlastRunner
File "/home/yichen/anaconda3/lib/python3.9/site-packages/mob_suite/blast/__init__.py", line 9, in <module>
from pandas.io.common import EmptyDataError
ImportError: cannot import name 'EmptyDataError' from 'pandas.io.common' (/home/yichen/anaconda3/lib/python3.9/site-packages/pandas/io/common.py)
return code: 1
()
Hi, you are installing version of MOB-Suite 3.0.0-py_1 that had no restriction to pandas version upper bound. You can simply install conda install pandas==1.0.5 and then install mob-suite again. The subsequent versions 3.0.3 and 3.1.0 did not have this issue. For more info see https://github.com/phac-nml/mob-suite/issues/63
