connectomicslab/connectomemapper3

BUG: environment.yml fails to setup broken dependency obspy (Ubuntu 18, Connectomemapper RC4)

jwirsich opened this issue · 2 comments

jwirsich commented

Encountered issue

Creating the conda environment for cmpbidasappmanager fails because of broken dependency:

conda env create -f environment.yml
C compiler: gcc -pthread -B /home/jwirsich/miniconda3/envs/py37cmp-gui/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC

creating build/temp.linux-x86_64-3.7/obspy
creating build/temp.linux-x86_64-3.7/obspy/io
creating build/temp.linux-x86_64-3.7/obspy/io/gse2
creating build/temp.linux-x86_64-3.7/obspy/io/gse2/src
creating build/temp.linux-x86_64-3.7/obspy/io/gse2/src/GSE_UTI

OS: Ubuntu 18.04
CMP3 version: v3.0.0-RC4

Workaround

Manually setup obspy (conda install -c conda-forge obspy) and uncomment it in environment.yml

sebastientourbier commented

I am closing this issue as this should have been fixed in release v3.0.0 but feel free to reopen the issue if this happens again.

  • 👍1
jwirsich commented

Still a problem with cmp3.1/python3.9 both on Ubuntu 18 and OS 12.6.1, but workaround still works