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

[Martin Morgan]

On 02/21/2017 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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