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

Hervé Pagès hpages at fredhutch.org
Wed Feb 22 22:33:55 CET 2017

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.


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.
> 	[[alternative HTML version deleted]]
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=nZTeI-UIuD5hMTuROA6wkN5-wZTBYoKcKKKGr905TS8&s=F3gPX_Ud6Ah60K-UvTEUA1DibZSnKDoeswqryjQlt0c&e=

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

More information about the Bioc-devel mailing list