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VisDunneRight / jovi-benchmark-sets

https://visdunneright.github.io/jovi-benchmark-sets/
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Running quarto publish or quarto render gives warnings we should address #6

Open codydunne opened 3 months ago

codydunne commented 3 months ago

All the warnings below are shown by quarto preview and quarto publish.

These seem to be a dataset issue... @picorana did you miss them in a search & replace or something?

WARN: Unable to resolve link target: data/Benchmark sets 0cc6b5e454304aec98f3b59b1a720476/Literature ad87f14e7097454fb2f784e2c8a2797a/Literature - Algorithm 12e01bfc60a84007aa7d2d34293e123d/Edge-Path Bundling A Less Ambiguous Edge Bundling  fcfa5882e692481298cbee906e005c30.md
WARN: Unable to resolve link target: data/Benchmark sets 0cc6b5e454304aec98f3b59b1a720476/Literature ad87f14e7097454fb2f784e2c8a2797a/Literature - Algorithm 12e01bfc60a84007aa7d2d34293e123d/Visualizing Co-phylogenetic Reconciliations fd4b98c0071f4e96924bacd938e706b5.md
WARN: Unable to resolve link target: data/Benchmark sets 0cc6b5e454304aec98f3b59b1a720476/Literature ad87f14e7097454fb2f784e2c8a2797a/Literature - Algorithm 12e01bfc60a84007aa7d2d34293e123d/Design Considerations for Optimizing Storyline Vis 0a518ed402154bdcb136759d50e09b1b.md
WARN: Unable to resolve link target: data/Benchmark sets 0cc6b5e454304aec98f3b59b1a720476/Literature ad87f14e7097454fb2f784e2c8a2797a/Literature - Algorithm 12e01bfc60a84007aa7d2d34293e123d/StoryFlow Tracking the Evolution of Stories 85d6352e70a54f3e8840adcfea70363a.md
WARN: Unable to resolve link target: data/Benchmark sets 0cc6b5e454304aec98f3b59b1a720476/Literature ad87f14e7097454fb2f784e2c8a2797a/Literature - Algorithm 12e01bfc60a84007aa7d2d34293e123d/Drawing Directed Acyclic Graphs An Experimental St 1677531652194663b7fdf25025c61cc6.md
WARN: Unable to resolve link target: data/Benchmark sets 0cc6b5e454304aec98f3b59b1a720476/Literature ad87f14e7097454fb2f784e2c8a2797a/Literature - Algorithm 12e01bfc60a84007aa7d2d34293e123d/Layer-Free Upward Crossing Minimization 676f8a507ff343b5ae83c34446796fb5.md
WARN: Unable to resolve link target: data/Benchmark sets 0cc6b5e454304aec98f3b59b1a720476/Literature ad87f14e7097454fb2f784e2c8a2797a/Literature - Algorithm 12e01bfc60a84007aa7d2d34293e123d/Drawing Dynamic Graphs Without Timeslices 4da7155eac4b4979ae165f3b0f1d2b1b.md
WARN: Unable to resolve link target: data/Benchmark sets 0cc6b5e454304aec98f3b59b1a720476/Literature ad87f14e7097454fb2f784e2c8a2797a/Literature - Algorithm 12e01bfc60a84007aa7d2d34293e123d/Computing Stable Demers Cartograms fb418899e13f45f4b6b3c6296e07a599.md
WARN: Unable to resolve link target: data/Benchmark sets 0cc6b5e454304aec98f3b59b1a720476/Literature ad87f14e7097454fb2f784e2c8a2797a/Literature - Algorithm 12e01bfc60a84007aa7d2d34293e123d/Drawing Dynamic Graphs Without Timeslices 4da7155eac4b4979ae165f3b0f1d2b1b.md
WARN: Unable to resolve link target: data/Benchmark sets 0cc6b5e454304aec98f3b59b1a720476/Literature ad87f14e7097454fb2f784e2c8a2797a/Literature - Algorithm 12e01bfc60a84007aa7d2d34293e123d/GION Interactively Untangling Large Graphs on Wall 774568ebdd114a8790c026bfa0b125f0.md
WARN: Unable to resolve link target: data/Benchmark sets 0cc6b5e454304aec98f3b59b1a720476/Literature ad87f14e7097454fb2f784e2c8a2797a/Literature - Algorithm 12e01bfc60a84007aa7d2d34293e123d/Rapid Graph Layout Using Space Filling Curves 10601cd6078a4ea18b17c7d40eda0041.md
WARN: Unable to resolve link target: data/Benchmark sets 0cc6b5e454304aec98f3b59b1a720476/Literature ad87f14e7097454fb2f784e2c8a2797a/Literature - Algorithm 12e01bfc60a84007aa7d2d34293e123d/Edge-Path Bundling A Less Ambiguous Edge Bundling  fcfa5882e692481298cbee906e005c30.md

I'm not sure what is causing these but it seems to work in the end...:

WARNING (/opt/quarto/share/filters/main.lua:13900) Unable to resolve crossref @sec-collection-process
WARNING (/opt/quarto/share/filters/main.lua:13900) Unable to resolve crossref @sec-data-processing
WARNING (/opt/quarto/share/filters/main.lua:13900) Unable to resolve crossref @sec-established-network-repositories
WARNING (/opt/quarto/share/filters/main.lua:13900) Unable to resolve crossref @sec-uniform-benchmark-datasets
WARNING (/opt/quarto/share/filters/main.lua:13900) Unable to resolve crossref @sec-lost
WARNING (/opt/quarto/share/filters/main.lua:13900) Unable to resolve crossref @sec-collection-process
WARNING (/opt/quarto/share/filters/main.lua:13900) Unable to resolve crossref @sec-data-processing

I already fixed these, which are due to (1) needing new labels and (2) cross-references in quarto not going to inside collapsed blocks. You have to crossref the block, not any headings inside:

WARNING (/opt/quarto/share/filters/main.lua:13900) Unable to resolve crossref @sec-research-statements
WARNING (/opt/quarto/share/filters/main.lua:13900) Unable to resolve crossref @sec-authorship

I also fixed this, due to a capitalization issue 🤦 .

[WARNING] Citeproc: citation Dang2016 not found
picorana commented 3 months ago

The crossref errors are due to things being referenced before they appear in the body of the paper. I can't do much, they work in the end.

The "unable to resolve link target" is due to quarto including in the compilation a number of sub-files we have for the datasets, which do not end up being used in the final render. I would like to keep the files there because those are part of the general export we do from notion, and would be again exported with the same broken references whenever we update the data.