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

[Martin Morgan]

On 02/18/2017 08:05 PM, Levi Waldron wrote:
>  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

It is a variant of

https://stat.ethz.ch/pipermail/bioc-devel/2017-February/010463.html

and requires re-installation of one or more of your Bioconductor 
packages that depend directly or indirectly on S4Vectors; it's easy to 
figure out which.

Martin

>> 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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>
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