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

[Hervé Pagès]

Hi Levi,

Were you able to sort this out? I think we should emphasize the
importance of re-installing packages *from source* (i.e. with
biocLite(..., type="source")). This is because some of the package
binaries we distribute seem to be affected by this problem too.
We're planning to fix these binaries over the next couple of days.

Sorry for the inconvenience,

H.

On 02/19/2017 07:58 AM, Levi Waldron wrote:
> On Sun, Feb 19, 2017 at 2:54 AM, Martin Morgan <
> martin.morgan at roswellpark.org> wrote:
>>
>> It is a variant of
>>>
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_2017-2DFebruary_010463.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=k6jN8WWwQDF4CDePzuCCjMH2qw1xQUbfc9cy6-FO48g&s=wuuIMKp7aAeTktf4VoEuYw4D22AFWWGGov1aDCNPloQ&e=
>>>
>>> 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$phyloseq). I guess a full Bioconductor reinstall would be a
> heavy-handed but effective fix?
>
>> db = available.packages(repos=BiocInstaller::biocinstallRepos()[1])
>    revdeps = tools::package_dependencies("S4Vectors", db, recursive=TRUE,
>        reverse=TRUE)
>> mydep = tools::package_dependencies("phyloseq", db, recursive=TRUE)
>> installme = mydep$phyloseq[mydep$phyloseq %in% revdeps$S4Vectors]
>> mydep
> $phyloseq
>  [1] "BiocGenerics" "ade4"         "ape"          "biomformat"
> "Biostrings"
>  [6] "cluster"      "data.table"   "foreach"      "ggplot2"      "igraph"
>
> [11] "methods"      "multtest"     "plyr"         "reshape2"     "scales"
>
> [16] "vegan"        "Biobase"      "utils"        "graphics"     "stats"
>
> [21] "parallel"     "jsonlite"     "Matrix"       "rhdf5"
>  "S4Vectors"
> [26] "IRanges"      "XVector"      "survival"     "MASS"         "stats4"
>
> [31] "zlibbioc"
>> installme
> [1] "Biostrings" "IRanges"    "XVector"
>>
>
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>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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