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

[Levi Waldron]

Thanks Hervé for both the fix and the explanation, I learned a few things
from this thread.
Sincerely,
Levi

On Wed, Feb 22, 2017 at 4:33 PM, Hervé Pagès <hpages at fredhutch.org> wrote:

> Hi Levi,
>
> At installation time, class definitions are cached somewhere in
> the package installation folder. So when you installed phyloseq
> the definition of the sample_data class got cached on your machine.
> Note that sample_data was extending vectorORfactor and it seems that
> this information gets cached somehow. When vectorORfactor got renamed
> vector_OR_factor, the information in the cache got out-of-sync which
> is why phyloseq needed to be re-installed.
>
> Re-installing the phyloseq binary doesn't help because binary packages
> contain their own cache of class definitions, Since the current binary
> (1.19.1) was made before the renaming of vectorORfactor (which happened
> in S4Vectors), the information contained in its cache of class
> definitions is also out-of-sync.
>
> I just bumped phyloseq version so new Windows and Mac binaries will
> be made and they'll have up-to-date class definitions in their cache.
>
> H.
>
>
> On 02/22/2017 11:20 AM, Levi Waldron wrote:
>
>> On Feb 22, 2017 1:42 PM, "Vincent Carey" <stvjc at channing.harvard.edu>
>> wrote:
>>
>> might there have been an object that references the obsolete class around?
>>
>>
>> There were no objects in the environment, ie being loaded from an .RData,
>> if that's what you mean.
>>
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> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>



-- 
Levi Waldron
http://www.waldronlab.org
Assistant Professor of Biostatistics     CUNY School of Public Health
US: +1 646-364-9616                                           Skype:
levi.waldron

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