preliminary microbio.me/qiime API. incomplete

Missing unit tests, example data, and some kind of issue with tar.gz
files but not .zip files. The server appears to have both kinds...
fixed .tgz new-directory issue. Problems with subsetted test files...
v1.5.10 fix error showing in psmelt, derived from tax_table extraction

Needs checks. Updated validity method to throw more informative error
int he future, explains which taxonomy_table columns are now empty
(which violates the "validity" definition for taxonomyTable class)
v1.5.10 fixed further issue in taxonomyTable validity method
Still some issue with trimming empty tax_table columns by default...
added cache/* to .gitignore for gh-pages hangover
failed merge_taxa unit test. Need to figure out why. But then in good shape.

  Running ‘testthat-phyloseq.R’
 ERROR
Running the tests in ‘tests/testthat-phyloseq.R’ failed.
Last 13 lines of output:
  5: attr.all.equal(target, current, tolerance = tolerance, scale =
scale, ...)
  6: mode(current)
  7: ntaxa(n1)

  4. Failure: merge_taxa() replaces disagreements in taxonomy with NA
------------
  sum(is.na(t951)) not equal to 1L
  Mean relative difference: 1

  5. Failure: merge_taxa() replaces disagreements in taxonomy with NA
------------
  is.na(t951[length(rank_names(n8))]) not equal to expected
  1 element mismatch
  Error: Test failures
v1.5.10 fix psmelt() bug when tax_table has empty columns
Merge branch 'empty-taxtable' into microbio_me_qiime
v1.5.11 microbio.me/qiime support

See tutorial at:
http://joey711.github.io/phyloseq/download-microbio.me.html
Merge pull request #203 from joey711/microbio_me_qiime

Microbio.me/qiime
https://github.com/joey711/phyloseq/issues/202

See tutorial
http://joey711.github.io/phyloseq/download-microbio.me.html