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ropensci / RNeXML

Implementing semantically rich NeXML I/O in R
https://docs.ropensci.org/RNeXML
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Updated rendering of README markdown file #153

Closed hlapp closed 8 years ago

hlapp commented 8 years ago

Right now there are two commits here:

  1. dc1ba90c4822e82f0bce9f1b8d44637110d15249 fixes a missing badge and a failing image include, mistakes that must have been there for a while.
  2. a2dd8a9f2e478c4442386c9543cdc22b2d5e077c updates the rest of the file with the output that executing the R code chunks currently yields, with the most recent version of this and its dependent packages. (The exception to this is the update of the output of geiger::fitDiscrete() which is not included - see #151 for why.)

Some of the changes in a2dd8a9f2e478c4442386c9543cdc22b2d5e077c are a little concerning because they seem to be indicative of as of yet undiagnosed issues with the package code. I'm going to add line notes to point those out - perhaps they are entirely expected, or harmless. If they suggest problems in the package code that need to be fixed, I'm willing to separate them out into their own PR, so feel free to advise accordingly.

I also didn't know whether the package root-level figure/ directory created by the code chunk that creates the tree plot is truly the desired location, but there also didn't seem to be a more obvious one. I can relocate that file (and change the directory specification in README.Rmd accordingly) if you want to make a recommendation.

cboettig commented 8 years ago

Thanks, those two issues do smell like bugs -- I think I should merge this but open issues to address them.