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gregversteeg / bio_corex

A flexible version of CorEx developed for bio-data challenges that handles missing data, continuous/discrete variables, multi-CPU, overlapping structure, and includes visualizations
Apache License 2.0
137 stars 30 forks source link

re graphviz on MacIntosh #25

Open paseman opened 3 years ago

paseman commented 3 years ago

I did 158 conda uninstall graphviz from https://brew.sh/ I did 159 /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)" giving Error: homebrew-core is a shallow clone. To brew update, first run: git -C /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core fetch --unshallow This command may take a few minutes to run due to the large size of the repository. This restriction has been made on GitHub's request because updating shallow clones is an extremely expensive operation due to the tree layout and traffic of Homebrew/homebrew-core and Homebrew/homebrew-cask. We don't do this for you automatically to avoid repeatedly performing an expensive unshallow operation in CI systems (which should instead be fixed to not use shallow clones). Sorry for the inconvenience! Failed during: /usr/local/bin/brew update --force --quiet

So, as the message said, I ran 160 git -C /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core fetch --unshallow followed by 161 brew install graphviz --with-gts giving Error: invalid option: --with-gts

The only thing I see that explains this is this medium article.
https://medium.com/@scrossoracle/building-graphviz-from-source-on-macos-b6a846d73949

Now, before I dive headlong into this crap, I'd like to make sure: Is this the correct direction? Thanks.

gregversteeg commented 3 years ago

Ha! I totally agree that this is a headache. Graphviz is only used for one thing in the visualization: to render a graph. The "with-gts" option is only required to make slightly prettier graphs. So I don't think it's worth the bother. You can just ignore the error about "triangulation library". To look at the graphs you can find the output graphs/tree.dot, etc. Those dot files specify a graph and they can be rendered using other, more modern software like OmniGraffle.

gregversteeg commented 3 years ago

(And I also hate using homebrew, and have no idea how it works. I vaguely remember that the last time I got this to work I did something like "brew install gts" and then "brew install graphviz" (without the option) and it got it right.)

paseman commented 3 years ago

"brew install gts" and then "brew install graphviz" (without the option) let's me run the baby example without triangulation errors. On to the next example. Thanks.