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

Levi Waldron lwaldron.research at gmail.com
Sun Feb 19 16:58:40 CET 2017

On Sun, Feb 19, 2017 at 2:54 AM, Martin Morgan <
martin.morgan at roswellpark.org> wrote:
> 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
> should have been 'not easy'

Thanks, Martin. I reinstalled both the "installme" and "mydep" packages
below using biocLite(installme), then when that didn't work, I also tried
biocLite(mydep$phyloseq). I guess a full Bioconductor reinstall would be a
heavy-handed but effective fix?

> db = available.packages(repos=BiocInstaller::biocinstallRepos()[1])
   revdeps = tools::package_dependencies("S4Vectors", db, recursive=TRUE,
> mydep = tools::package_dependencies("phyloseq", db, recursive=TRUE)
> installme = mydep$phyloseq[mydep$phyloseq %in% revdeps$S4Vectors]
> mydep
 [1] "BiocGenerics" "ade4"         "ape"          "biomformat"
 [6] "cluster"      "data.table"   "foreach"      "ggplot2"      "igraph"

[11] "methods"      "multtest"     "plyr"         "reshape2"     "scales"

[16] "vegan"        "Biobase"      "utils"        "graphics"     "stats"

[21] "parallel"     "jsonlite"     "Matrix"       "rhdf5"
[26] "IRanges"      "XVector"      "survival"     "MASS"         "stats4"

[31] "zlibbioc"
> installme
[1] "Biostrings" "IRanges"    "XVector"

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