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I'm working through this tutorial: https://joey711.github.io/phyloseq/plot_ordination-examples.html

In Ubuntu 16.04, I'm getting errors any time I try to use one of the ordination functions.

Update: It does work for me in Windows 10, R 3.3.2

What's wrong with my Ubuntu 16.04, R 3.4.1 setup

> GP.ord <- ordinate(GP1, "NMDS", "bray")
Square root transformation
Wisconsin double standardization
Error in .C("veg_distance", x = as.double(x), nr = N, nc = ncol(x), d = double(N *  : 
  "veg_distance" not available for .C() for package "vegan"

> ordinate(physeq = phylo)
Error in .C("data2hill", as.double(veg), mi = as.integer(nr), n = as.integer(nc),  :
  "data2hill" not available for .C() for package "vegan" 

> R.version
               _
platform       x86_64-pc-linux-gnu
arch           x86_64
os             linux-gnu
system         x86_64, linux-gnu
status
major          3
minor          4.1
year           2017
month          06
day            30
svn rev        72865
language       R
version.string R version 3.4.1 (2017-06-30)
nickname       Single Candle

> temp <- installed.packages()
> temp[rownames(temp) %in% c("phyloseq", "vegan") , ]
         Package LibPath                                        Version  Priority
phyloseq "phyloseq" "/usr/local/lib/R/site-library"                "1.19.1" NA
vegan    "vegan" "/usr/lib/R/site-library"                      "2.4-3"  NA
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Mark Miller
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  • maybe https://github.com/vegandevs/vegan/commit/5338303bce058054518e41721a93ef97ce24494e ? – Ben Bolker Aug 17 '17 at 23:45
  • works for me with same package versions on MacOS, R 3.4.0. (Doubt 3.4.0 -> 3.4.1 would make a difference?) – Ben Bolker Aug 17 '17 at 23:52
  • hmm. Also works for me on Ubuntu 16.04, R-devel (3.5.0), vegan 2.4.3/phyloseq 1.19.1 ... – Ben Bolker Aug 18 '17 at 00:11
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    just googled. I think it's https://stackoverflow.com/questions/44010681/resolve-metamds-error-veg-distance-not-available-for-c-for-package-vegan ? (re-install `vegan`) ... – Ben Bolker Aug 18 '17 at 00:12
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    @BenBolker thanks, removing all vegan libraries in any location and reinstalling it did work. Would you believe that I did Google the `data2hill` missing error, but not the `veg_distance` error? embarrassing. – Mark Miller Aug 18 '17 at 00:23

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