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

[Vincent Carey]

might there have been an object that references the obsolete class around?

On Wed, Feb 22, 2017 at 1:25 PM, Levi Waldron <lwaldron.research at gmail.com>
wrote:

> 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
> >>
> >>
> >
> > This email message may contain legally privileged and/or confidential
> > information.  If you are not the intended recipient(s), or the employee
> or
> > agent responsible for the delivery of this message to the intended
> > recipient(s), you are hereby notified that any disclosure, copying,
> > distribution, or use of this email message is prohibited.  If you have
> > received this message in error, please notify the sender immediately by
> > e-mail and delete this email message from your computer. Thank you.
> >
>
>
>
> --
> Levi Waldron
> http://www.waldronlab.org
> Assistant Professor of Biostatistics     CUNY School of Public Health
> US: +1 646-364-9616                                           Skype:
> levi.waldron
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

	[[alternative HTML version deleted]]