[Bioc-devel] phloseq error: invalid class “sample_data” object: superclass "vectorORfactor" not defined in the environment of the object's class

[Levi Waldron]

 I am getting this error from a basic phyloseq function, which doesn't
appear in the build system's check.  Is this some strange thing wrong with
my installation? From a fresh R session:

> library(phyloseq)
> example("sample_data")

smpl_d> #
smpl_d> data(soilrep)

smpl_d> head(sample_data(soilrep))
Error in validObject(.Object) :
  invalid class “sample_data” object: superclass "vectorORfactor" not
defined in the environment of the object's class
> devtools::session_info()
Session info
------------------------------------------------------------------------------------------------------------
 setting  value
 version  R Under development (unstable) (2017-02-10 r72157)
 system   x86_64, darwin13.4.0
 ui       RStudio (1.0.136)
 language (EN)
 collate  en_US.UTF-8
 tz       America/New_York
 date     2017-02-18

Packages
----------------------------------------------------------------------------------------------------------------
 package      * version date       source
 ade4           1.7-5   2016-12-13 CRAN (R 3.4.0)
 ape            4.1     2017-02-14 CRAN (R 3.4.0)
 assertthat     0.1     2013-12-06 CRAN (R 3.4.0)
 Biobase        2.35.0  2016-10-23 Bioconductor
 BiocGenerics   0.21.3  2017-01-12 Bioconductor
 biomformat     1.3.0   2016-10-23 Bioconductor
 Biostrings     2.43.4  2017-02-02 Bioconductor
 cluster        2.0.5   2016-10-08 CRAN (R 3.4.0)
 codetools      0.2-15  2016-10-05 CRAN (R 3.4.0)
 colorspace     1.3-2   2016-12-14 CRAN (R 3.4.0)
 data.table     1.10.4  2017-02-01 CRAN (R 3.4.0)
 devtools       1.12.0  2016-06-24 CRAN (R 3.4.0)
 digest         0.6.12  2017-01-27 CRAN (R 3.4.0)
 foreach        1.4.3   2015-10-13 CRAN (R 3.4.0)
 ggplot2        2.2.1   2016-12-30 CRAN (R 3.4.0)
 gtable         0.2.0   2016-02-26 CRAN (R 3.4.0)
 igraph         1.0.1   2015-06-26 CRAN (R 3.4.0)
 IRanges        2.9.18  2017-02-02 Bioconductor
 iterators      1.0.8   2015-10-13 CRAN (R 3.4.0)
 jsonlite       1.2     2016-12-31 CRAN (R 3.4.0)
 lattice        0.20-34 2016-09-06 CRAN (R 3.4.0)
 lazyeval       0.2.0   2016-06-12 CRAN (R 3.4.0)
 magrittr       1.5     2014-11-22 CRAN (R 3.4.0)
 MASS           7.3-45  2016-04-21 CRAN (R 3.4.0)
 Matrix         1.2-8   2017-01-20 CRAN (R 3.4.0)
 memoise        1.0.0   2016-01-29 CRAN (R 3.4.0)
 mgcv           1.8-17  2017-02-08 CRAN (R 3.4.0)
 multtest       2.31.0  2016-10-23 Bioconductor
 munsell        0.4.3   2016-02-13 CRAN (R 3.4.0)
 nlme           3.1-131 2017-02-06 CRAN (R 3.4.0)
 permute        0.9-4   2016-09-09 CRAN (R 3.4.0)
 phyloseq     * 1.19.1  2016-11-21 Bioconductor
 plyr           1.8.4   2016-06-08 CRAN (R 3.4.0)
 Rcpp           0.12.9  2017-01-14 CRAN (R 3.4.0)
 reshape2       1.4.2   2016-10-22 CRAN (R 3.4.0)
 rhdf5          2.19.0  2016-10-23 Bioconductor
 S4Vectors      0.13.15 2017-02-14 Bioconductor
 scales         0.4.1   2016-11-09 CRAN (R 3.4.0)
 stringi        1.1.2   2016-10-01 CRAN (R 3.4.0)
 stringr        1.1.0   2016-08-19 CRAN (R 3.4.0)
 survival       2.40-1  2016-10-30 CRAN (R 3.4.0)
 tibble         1.2     2016-08-26 CRAN (R 3.4.0)
 vegan          2.4-2   2017-01-17 CRAN (R 3.4.0)
 withr          1.0.2   2016-06-20 CRAN (R 3.4.0)
 XVector        0.15.2  2017-02-02 Bioconductor
 zlibbioc       1.21.0  2016-10-23 Bioconductor
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