[Bioc-devel] phloseq error: invalid class “sample_data” object: superclass "vectorORfactor" not defined in the environment of the object's class
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
> contains <- names(getClass("list")@contains)
> if (any(grepl("vectorORfactor", contains)))
> stop("found after: ", package)
>> Sorry for the inconvenience,
>> No worries!
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