Check updates to vegan (2.0-4), picante (1.4-1), and ape (3.0-5) for compatibility

joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:

http://joey711.github.io/phyloseq/

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Check updates to vegan (2.0-4), picante (1.4-1), and ape (3.0-5) for compatibility #141

Closed joey711 closed 11 years ago

joey711 commented 12 years ago

Hopefully functionality remains consistent enough. Check that updating those packages causes no issues, and if any enhancements in those packages can result in gains for phyloseq.

This is separate from updates to welcome updates from ggplot2 and related packages.

Also still need to check if reshape2 package is appropriate (and better) for phyloseq than original reshape package.

joey711 commented 11 years ago

Just ran a check after installing the latest picante, ape, and vegan (listed above), and R CMD check phyloseq gave no problems. This issue is closed, as of commit:

04d4d9ff27c80caf52e1dd68dde2aa42fe562424