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EulerProject / EulerX

Euler is an open source logic toolkit for aligning taxonomies and visualizing the results; see http://sysbio.oxfordjournals.org/cgi/reprint/syw023? ijkey=a0EkUEzzS2tpSL3&keytype=ref Demonstration videos are here: https://vimeo.com/126527661 and here: http://www2.cs.uic.edu/~tdang/ProvenanceMatrix/video.mp4
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GraphViz failing #21

Open camwebb opened 6 years ago

camwebb commented 6 years ago

All graphviz (dot) conversions are failing due to rank=source in the Legend. If I edit this out, or use rank=min or rank=max they run just fine. Using graphviz version 2.40.1. Thanks.

shizhuoyu commented 6 years ago

It seems to me it is the issue of Graphviz software instead of Euler. Could you please show me more details: what operating system you were using? Did you build from source or just use Graphviz binary directly? A few screenshots may help if possible. FYI, I am using MacOS(10.9) but I am using an older version graphviz.app (2.36.0) since newer versions somehow does not work according to the website of Graphviz software (http://www.graphviz.org/Download_macos.php). Maybe you could try an older version of Graphviz as a walk-around.

camwebb commented 6 years ago

Agree it's graphviz. Opened an issue there: https://github.com/ellson/graphviz/issues/1273. I can work around the bug until fixed. Thanks!

camwebb commented 6 years ago

This bug in Graphviz is not getting fixed, so any new install of EulerX will fail to be able to make PDFs. I've installed one several new machines recently, and each time I have to add a hack to the code to pass the y2d output through sed 's/=source/=max/g'. Annoying for you, I know, but could you add a temporary patch?

camwebb commented 6 years ago

More... stable graphviz is still being released at version 2.40.1, which is broken (see here). I can confirm that dev version (graphviz-2.41.20171026.1811) works fine on EulerX files using rank=source. So whether you want to patch eulerx will depend on when we expect graphviz 2.41 to be released and incorporated into repos.

RoronoaZoro0895 commented 3 years ago

I am facing the same issue on ubuntu bionic(18.04)... any plans for future release?