[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
Wed Feb 22 19:25:28 CET 2017

Thank you, Martin. I did that and went through the long tree re-installing
from source the re-starting R and trying my example again. It wasn't
successful until I tried re-installing phyloseq itself from source, and
that worked! I still don't understand why, since neither grep
vectorORfactor or vector_OR_factor matches anything in the R/ directory of
phyloseq. But, my phyloseq installation is working again.

On Tue, Feb 21, 2017 at 5:33 PM, Martin Morgan <
martin.morgan at roswellpark.org> wrote:

> On 02/21/2017 03:24 PM, Levi Waldron wrote:
>> On Tue, Feb 21, 2017 at 2:02 PM, Hervé Pagès <hpages at fredhutch.org
>> <mailto:hpages at fredhutch.org>> wrote:
>>     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.
>> Thank you, Hervé. I hadn't re-installed from source, and haven't gotten
>> around to doing a complete re-install, so I tried again with
>> `biocLite(..., type="source")`. But it still didn't fix the problem
>> re-installing `mydep$phyloseq` above with type="source". It isn't a
>> great rush, so perhaps I'll just wait until you've updated the binaries.
> Here's an attempt to fail when the vectorORfactor class is contained in
> 'list', which I think is where the problem comes from
> trace(
>     loadNamespace,
>     quote(print(package)),
>     exit=quote({
>         contains <- names(getClass("list")@contains)
>         if (any(grepl("vectorORfactor", contains)))
>             stop("found after: ", package)
>     })
> )
> library(phyloseq)
>>     Sorry for the inconvenience,
>> No worries!
>> -Levi
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Levi Waldron
Assistant Professor of Biostatistics     CUNY School of Public Health
US: +1 646-364-9616                                           Skype:

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