# R package grur: missing_visualization() fails during redundancy analysis of .vcf

I am trying to use the R package grur to process GBS SNP data, which is installed from github as instructed. For starters, I am running the test code in this vignette. As suggested I am running it from console in RStudio (v. 1.1.383), and with a recent R installation (below). I do, and get:

 > ibm <- grur::missing_visualization(data = "example_vcf2dadi_ferchaud_2015.vcf", strata = "strata.stickleback.tsv")
#######################################################################
#################### grur::missing_visualization ######################
#######################################################################
Folder created:
missing_visualization_20181209@1523

Importing data

Generated a filters parameters file: filters_parameters_20181209@1523.tsv

Number of SNPs: 31802
Number of samples: 177

conversion timing: 1 sec

VCF: biallelic SNPs
Cleaning VCF sample names

Synchronizing sample IDs in VCF and strata...
Filters parameters file: updated

Number of chromosome/contig/scaffold: 196
Number of locus: 17095
Number of markers: 31802
Number of individuals: 177

Working time: 1 sec

Deprecated function, update your code to use: filter_monomorphic

Scanning for monomorphic markers...
Number of markers before/blacklisted/after: 31802/0/31802

Tidy genomic data:
Number of markers: 31802
Number of chromosome/contig/scaffold: 196
Number of individuals: 177
Number of populations: 8

Informations:
Number of populations: 8
Number of individuals: 177
Number of ind/pop:
HAL = 19
KIB = 17
KRO = 20
MOS = 20
MAR = 20
NOR = 20
ODD = 40

Number of duplicate id: 0
Number of chrom/scaffolds: 196
Number of locus: 17095
Number of SNPs: 31802

Proportion of missing genotypes (overall): 0.022169

Identity-by-missingness (IBM) analysis using
Principal Coordinate Analysis (PCoA)...
Generating Identity by missingness plot

Redundancy analysis...

Error in UseMethod("ungroup") :
no applicable method for 'ungroup' applied to an object of class "character"
In addition: Warning message:
Trying to compute distinct() for variables not found in the data:
- strata.select
This is an error, but only a warning is raised for compatibility reasons.
The operation will return the input unchanged.


The final object is not generated, however some plots of the PCoA analysis are. I get this result on two Macs, one with Sierra, the other with High Sierra, but both with the same RStudio and R versions. All R packages are up to date. I get the same error when I run my own .vcf

Does anyone else get these errors on this test dataset from the repo? Can anyone suggest how to deal with this?

> version
platform       x86_64-apple-darwin15.6.0
arch           x86_64
os             darwin15.6.0
system         x86_64, darwin15.6.0
status
major          3
minor          5.1
year           2018
month          07
day            02
svn rev        74947
language       R
version.string R version 3.5.1 (2018-07-02)
nickname       Feather Spray

• This seems to be an internal error (using dplyr::ungroup without doing dplyr::group) . If you provide a minimal reproducible example, the maintainer of the package might be able to solve it (The maintainer should be able to reproduce the error, so provide enough data to make it possible).
– llrs
Dec 10 '18 at 7:56