Vegan and Phyloseq

[sfeds]

Hi,

I just wrote this in another thread but then realized that the topic was closed, so I'll open a new one just in case, my apologies if it wasn't necessary.

I'm having issues with vegan and phyloseq when calling the function "distance".
I have been reading in the issues tracker for vegan, and also here, but I'm still unsure of the solution.
I have updated both packages (phyloseq also from source code).

As a recap, I have:

library("vegan") ; packageVersion("vegan")
[1] ‘2.5.1’
library("phyloseq") ; packageVersion("phyloseq")
[1] ‘1.22.3’

GPdist <- phyloseq::distance(pseq_ra, "bray")
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"

Any tips?
Thanks!

[vinksn]

I have the same problem. The distance function works for "wunifrac" but not "bray".

It seems there is a mismatch between the compiled library and phyloseq copies of vegan functions (see the following for a more complete discussion: [https://stackoverflow.com/questions/49882886/make-network-error-in-r-error-veg-distance-not-available-for-c-for-packag]

I installed the developer phyloseq package 1.23.1 and an older vegan package 2.4-6, but neither solved the problem.

[cjfields]

My guess is the upcoming Bioconductor release will address this, installing the Github development version works for me. Using devtools:

library("devtools")
install_github("joey711/phyloseq")

[sfeds]

Indeed, this seems to be solved by reinstalling Phyloseq from source..

I had posted this on a closed issue but still got this response from Jarioska:
"Your phyloseq is still based on vegan 2.4. You must either downgrade vegan to 2.4-6 or install phyloseq from the source file. It seems that Bioconductor binary of phyloseq is still today (Apr 23, 2018) based on vegan 2.4. You can see this by looking at Imports entry of Details in https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html
When writing this, it still had vegan (>= 2.4)."

I'm still having some issues with previously-working-code... Hoping the new release of Phyloseq will patch things up somehow.